WorldWideScience

Sample records for bioinformatics links directory

  1. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

    2012-07-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

  2. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    , and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...

  3. Linked Data is People: Building a Knowledge Graph to Reshape the Library Staff Directory

    Directory of Open Access Journals (Sweden)

    Jason A. Clark

    2017-04-01

    Full Text Available One of our greatest library resources is people. Most libraries have staff directory information published on the web, yet most of this data is trapped in local silos, PDFs, or unstructured HTML markup. With this in mind, the library informatics team at Montana State University (MSU Library set a goal of remaking our people pages by connecting the local staff database to the Linked Open Data (LOD cloud. In pursuing linked data integration for library staff profiles, we have realized two primary use cases: improving the search engine optimization (SEO for people pages and creating network graph visualizations. In this article, we will focus on the code to build this library graph model as well as the linked data workflows and ontology expressions developed to support it. Existing linked data work has largely centered around machine-actionable data and improvements for bots or intelligent software agents. Our work demonstrates that connecting your staff directory to the LOD cloud can reveal relationships among people in dynamic ways, thereby raising staff visibility and bringing an increased level of understanding and collaboration potential for one of our primary assets: the people that make the library happen.

  4. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  5. New Link in Bioinformatics Services Value Chain: Position, Organization and Business Model

    Directory of Open Access Journals (Sweden)

    Mladen Čudanov

    2012-11-01

    Full Text Available This paper presents development in the bioinformatics services industry value chain, based on cloud computing paradigm. As genome sequencing costs per Megabase exponentially drop, industry needs to adopt. Paper has two parts: theoretical analysis and practical example of Seven Bridges Genomics Company. We are focused on explaining organizational, business and financial aspects of new business model in bioinformatics services, rather than technical side of the problem. In the light of that we present twofold business model fit for core bioinformatics research and Information and Communication Technologie (ICT support in the new environment, with higher level of capital utilization and better resistance to business risks.

  6. REPERTOIRE (DIRECTORY).

    Science.gov (United States)

    JOUBERT, MADELEINE

    THIS DIRECTORY DESCRIBES, IN FRENCH, THE STRUCTURE, OBJECTIVES, ADMISSION REQUIREMENTS, AFFILIATIONS, EDUCATIONAL ACTIVITIES, AND PUBLICATIONS OF 62 ADULT EDUCATION ORGANIZATIONS AND INSTITUTIONS SERVING FRENCH-SPEAKING CANADA. IT INCLUDES DATA ON TYPE OF ORGANIZATION OR INSTITUTION, SCOPE OF ACTIVITY, REGION (WHERE SPECIFIED), FINANCIAL SUPPORT,…

  7. Deaf directory.

    Science.gov (United States)

    1994-11-23

    The third edition of the 199415 Directory from the Council for the Advancement of Communication with Deaf People (CACDP) is now available. Information on 192 sign language interpreters, lipspeakers, interpreters for deafblind people and speech to text reporters is provided. Details from CACDP on 0191 374 3607.

  8. 1999 Directory

    International Nuclear Information System (INIS)

    1999-01-01

    This publication constitutes the membership directory of the Canadian Electricity Association, the national forum and voice of the evolving electrical business in Canada. The Association provides its members with access to world class products, services and partnership opportunities in areas such as research and development, networking, learning, benchmarking and information exchange. At the core of CEA membership are the utility member companies which account for about 95 per cent of installed generating capacity in the country. Major electrical manufacturers, corporate consulting companies and several hundred other company and individual members are also part of CEA's broad structure. The directory is arranged alphabetically providing company name, postal, E-mail and Internet addresses, telephone and fax numbers, names of principal officers, and capsule data about the company's customer base, number of employees, generation capacity, and investment

  9. Cancer Genetics Services Directory

    Science.gov (United States)

    ... Services Directory Cancer Prevention Overview Research NCI Cancer Genetics Services Directory This directory lists professionals who provide services related to cancer genetics (cancer risk assessment, genetic counseling, genetic susceptibility testing, ...

  10. A Linked Series of Laboratory Exercises in Molecular Biology Utilizing Bioinformatics and GFP

    Science.gov (United States)

    Medin, Carey L.; Nolin, Katie L.

    2011-01-01

    Molecular biologists commonly use bioinformatics to map and analyze DNA and protein sequences and to align different DNA and protein sequences for comparison. Additionally, biologists can create and view 3D models of protein structures to further understand intramolecular interactions. The primary goal of this 10-week laboratory was to introduce…

  11. Library OPACs on the Web: Finding and Describing Directories.

    Science.gov (United States)

    Henry, Marcia

    1997-01-01

    Provides current descriptions of some of the major directories that link to library catalogs on the World Wide Web. Highlights include LibWeb; Hytelnet; WebCats; WWW Library Directory; and techniques for finding new library OPAC (online public access catalog) directories. (LRW)

  12. Telephone-Directory Program

    Science.gov (United States)

    Vlahos, William

    2005-01-01

    eDirectory is a computer program that makes it possible to view entries in the Jet Propulsion Laboratory (JPL) telephone directory by use of PalmPilot(TradeMark) (or equivalent) personal digital assistants. When one uses eDirectory, a single click causes the downloading of a current copy of the directory (which is updated nightly) from a server. The downloaded directory data can be sorted and searched. The program can append a "JPL" category and save directory information in a file that can be imported into the Palm Desktop(TradeMark) software.

  13. Active Directory cookbook

    CERN Document Server

    Hunter, Laura

    2008-01-01

    When you need practical hands-on support for Active Directory, the updated edition of this extremely popular Cookbook provides quick solutions to more than 300 common (and uncommon) problems you might encounter when deploying, administering, and automating Microsoft's network directory service. For the third edition, Active Directory expert Laura E. Hunter offers troubleshooting recipes based on valuable input from Windows administrators, in addition to her own experience. You'll find solutions for the Lightweight Directory Access Protocol (LDAP), ADAM (Active Directory Application Mode), m

  14. Information Services Directory

    International Nuclear Information System (INIS)

    1986-08-01

    The Information Services Directory is intended to facilitate participation by states, affected Indian tribes and the public in the Civilian Radioactive Waste Management Program. The Directory is produced by the Information Services Division of the OCRWM's Office of Policy and Outreach and will be updated periodically. It is a reference document that identifies the sources of available program information

  15. Information Services Directory

    International Nuclear Information System (INIS)

    1985-11-01

    The Information Services directory is intended to facilitate participation by states, affected Indian tribes and the public in the Civilian Radioactive Waste Management program. The Directory is produced by the Information Services Division of the OCRWM's Office of Policy and Outreach and will be updated periodically. It is a reference document that identifies the sources of available program information

  16. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1991-11-01

    The first edition of the Directory of IAEA Databases is intended to describe the computerized information sources available to IAEA staff members. It contains a listing of all databases produced at the IAEA, together with information on their availability

  17. Supplier Directory Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — These are the official datasets used on the Medicare.gov Supplier Directory provided by the Centers for Medicare and Medicaid Services. They provide names,...

  18. Computer Technology Directory.

    Science.gov (United States)

    Exceptional Parent, 1990

    1990-01-01

    This directory lists approximately 300 commercial vendors that offer computer hardware, software, and communication aids for children with disabilities. The company listings indicate computer compatibility and specific disabilities served by their products. (JDD)

  19. EIA publications directory, 1991

    International Nuclear Information System (INIS)

    1992-01-01

    Enacted in 1977, the Department of Energy (DOE) Organization Act established the Energy Information Administration (EIA) as the Department's independent statistical and analytical agency, with a mandate to collect and publish data and prepare analyses on energy production, consumption, prices, and resources, and projections of energy supply and demand. This edition of the EIA Publications Directory contains titles and abstracts of periodicals and one-time reports produced by the EIA from January through December 1991. This edition supplements EIA Publications Directory 1977--1989 and EIA Publications Directory 1990. The body of the Directory contains citations and abstracts arranged by broad subject categories, such as coal, petroleum, and natural gas and subcategories such as reserves, produces and byproducts, and marketing and economics. All reports are indexed alphabetically by subject and title and numerically by report number

  20. Coal terminal directory

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-06-15

    The directory gives a comprehensive listing of the world's coal terminals, in a total of 50 countries including information on throughput, facilities, storage capacity, and vessel size limitation.

  1. EIA publications directory 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-04-01

    This edition of the EIA Publications Directory contains 68 titles and abstracts of periodicals and one time reports produced by EIA from January through December 1997. The body of the Directory contains citations and abstracts arranged by broad subject categories; (1) MetaData, (2) Coal, (3) Oil (4) Natural gas, (5) Nuclear, (6) Electricity, (7) Renewable energy and Alternative fuels, (8) Multifuel, (9) End use consumption, (10) Models, and (11) Forecasts.

  2. EIA publications directory 1996

    International Nuclear Information System (INIS)

    1997-05-01

    This edition of the EIA Publications Directory contains titles and abstracts of periodicals and one-time reports produced by the Energy Information Administration (EIA) from January through December 1996. The body of the Directory contains citations and abstracts arranged by broad subject categories; metadata, coal, oil and gas, nuclear, electricity, renewable and energy/alternative fuels, multifuel, end-use consumption, models, and forecasts

  3. The XWHO directory retires

    CERN Multimedia

    CERN Bulletin

    2011-01-01

    On 11 May a new web-based phonebook will take over from the 16-year old XWHO directory. It will provide access to basic contact information for people and services at CERN. A user-friendly interface will allow you to look for people and services using criteria such as first or last name, organisational unit and phone number. All requests submitted to the retired XWHO directory will be redirected to the new phonebook.   The new CERN Phonebook's user interface. CERN’s first electronic phonebook was created in 1995. The XWHO directory was first presented in July that year in a CERN Computer Newsletter (CNL) article entitled “Migrating the access to central directory services” by Miguel Marquina and Bernd Pollermann. Since then, it has been used by thousands of people at CERN and around the world looking for contact details of other members of the Organization. The XWHO directory is now retiring and is to be replaced by the new web-based CERN Phonebook. For several month...

  4. A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

    Directory of Open Access Journals (Sweden)

    Teresa Milano

    2016-01-01

    Full Text Available The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average that is homologous to fold type-I pyridoxal 5′-phosphate (PLP dependent enzymes like aspartate aminotransferase (AAT. These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. This group occurs mainly in the Actinobacteria and Gammaproteobacteria phyla. An analysis of the multiple sequence alignments of their wHTH and AAT domains suggested the presence of specificity-determining positions (SDPs. Mapping of SDPs onto a homology model of the AAT domain hinted at possible structural/functional roles in effector recognition. Likewise, SDPs in wHTH domain suggested the basis of specificity of Transcription Factor Binding Site recognition. The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.

  5. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    Directory of Open Access Journals (Sweden)

    Deodutta Roy

    2015-10-01

    Full Text Available We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs, bisphenols (BPs, and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors.

  6. EIA publications directory, 1990

    International Nuclear Information System (INIS)

    1991-01-01

    Enacted in 1977, the Department of Energy (DOE) Organization Act established the Energy Information Administration (EIA) as the Department's independent statistical and analytical agency, with a mandate to collect and publish data and prepare analyses on energy production, consumption, prices, and resources, and projections of energy supply and demand. This edition of the EIA Publications Directory contains titles and abstracts of periodicals and one-time reports produced by the EIA from January through December 1990. This edition supplements EIA Publications Directory 1977--1989. The body of the Directory contains citations and abstracts arranged by broad subject categories, such as coal, petroleum, and natural gas and subcategories such as reserves, products and byproducts, and marketing and economics. All reports are indexed alphabetically by subject and title and numerically by report number

  7. EIA publications directory 1994

    Science.gov (United States)

    1995-07-01

    Enacted in 1977, the Department of Energy (DOE) Organization Act established the Energy Information Administration (EIA) as the Department's independent statistical and analytical agency, with a mandate to collect and publish data and prepare analyses on energy production, consumption, prices, resources, and projections of energy supply and demand. This edition of the EIA Publications Directory contains titles and abstracts of periodicals and one-time reports produced by EIA from January through December 1994. The body of the Directory contains citations and abstracts arranged by broad subject categories: metadata, coal, oil and gas, nuclear, electricity, renewable energy/alternative fuels, multifuel, end-use consumption, models, and forecasts.

  8. EIA publications directory, 1992

    International Nuclear Information System (INIS)

    1993-01-01

    This directory contains abstracts and ordering information for EIA publications. The abstracts are arranged by broad subject category such as coal, petroleum, natural gas, and electric power. A comprehensive subject index, a title index, and a report number index are included. Each entry gives the title, report number, publication frequency, date, number of pages, and ordering information. Publication began with the 1979 edition

  9. EIA Publications Directory 1993

    International Nuclear Information System (INIS)

    1994-01-01

    This directory contains abstracts and ordering information for EIA publications released in the above time period. The abstracts are arranged by broad subject category such as coal, petroleum, natural gas, and electric power. A comprehensive subject index, a title index, and a report number index are included. Each entry gives the title, report number, publication frequency, date, number of pages, and ordering information

  10. Canadian ethanol retailers' directory

    International Nuclear Information System (INIS)

    1998-06-01

    This listing is a directory of all ethanol-blended gasoline retailers in Quebec, Ontario, Manitoba, Saskatchewan, Alberta, British Columbia, and the Yukon. The listing includes the name and address of the retailer. Bulk purchase facilities of ethanol-blended fuels are also included, but in a separate listing

  11. Section 1: Company directory

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    This is a 1992 directory of those companies doing business in all areas of the independent power producers industry. The listing includes the company name, address, telephone and FAX numbers, and the name of a company contact. The listing is international in scope

  12. Canada's ethanol retail directory

    International Nuclear Information System (INIS)

    1996-11-01

    A directory was published listing all ethanol-blended gasoline retailers in Quebec, Ontario, Manitoba, Saskatchewan, Alberta, British Columbia, and the Yukon. The listings include the name and address of the retailer. A list of bulk purchase facilities of ethanol-blended fuels is also included

  13. Plasma technology directory

    International Nuclear Information System (INIS)

    Ward, P.P.; Dybwad, G.L.

    1995-01-01

    The Plasma Technology Directory has two main goals: (1) promote, coordinate, and share plasma technology experience and equipment within the Department of Energy; and (2) facilitate technology transfer to the commercial sector where appropriate. Personnel are averaged first by Laboratory and next by technology area. The technology areas are accelerators, cleaning and etching deposition, diagnostics, and modeling

  14. Energy information directory 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The National Energy Information Center provides energy information and referral assistance to Federal, State, and local governments, the academic community, business and industrial organizations, and the general public. This Energy Information Directory is used to assist the Center staff as well as other DOE staff in directing inquires to the proper offices.

  15. Bioinformatics Data Mining Approach Suggests Coexpression of AGTPBP1 with an ALS-linked Gene C9orf72

    Directory of Open Access Journals (Sweden)

    Shouta Kitano

    2015-01-01

    Full Text Available Background Expanded GGGGCC hexanucleotide repeats located in the noncoding region of the chromosome 9 open reading frame 72 ( C9orf72 gene represent the most common genetic abnormality for familial and sporadic amyotrophic lateral sclerosis (ALS and frontotemporal dementia (FTD. Formation of nuclear RNA foci, accumulation of repeat-associated non-ATG-translated dipeptide-repeat proteins, and haploinsufficiency of C9orf72 are proposed for pathological mechanisms of C9ALS/FTD. However, at present, the physiological function of C9orf72 remains largely unknown. Methods By searching on a bioinformatics database named COXPRESdb composed of the comprehensive gene coexpression data, we studied potential C9orf72 interactors. Results We identified the ATP/GTP binding protein 1 ( AGTPBP1 gene alternatively named NNA1 encoding a cytosolic carboxypeptidase whose mutation is causative of the degeneration of Purkinje cells and motor neurons as the most significant gene coexpressed with C9orf72. We verified coexpression and interaction of AGTPBP1 and C9orf72 in transfected cells by immunoprecipitation and in neurons of the human brain by double-labeling immunohistochemistry. Furthermore, we found a positive correlation between AGTPBP1 and C9orf72 mRNA expression levels in the set of 21 human brains examined. Conclusions These results suggest that AGTPBP1 serves as a C9orf72 interacting partner that plays a role in the regulation of neuronal function in a coordinated manner within the central nervous system.

  16. Energy Information Directory 1991

    International Nuclear Information System (INIS)

    1992-01-01

    The National Energy Information Center (NEIC), as part of its mission, provides energy information and referral assistance to Federal, State, and local governments, the academic community, business and industrial organizations, and the general public. The two principal functions related to this task are (1) operating a general access telephone line, and (2) responding to energy-related correspondence addressed to the Energy Information Administration (EIA). The Energy Information Directory was developed to assist the NEIC staff as well as other Department of Energy (DOE) staff, in directing inquires to the proper offices within DOE, other Federal agencies, or energy-related trade associations. The Directory is a list of most Government offices and trade associations that are involved in energy matters. It does not include those DOE offices which do not deal with the public or public information

  17. Information services directory

    International Nuclear Information System (INIS)

    1987-05-01

    This Directory will facilitate dissemination of information. It is a reference document that lists the sources of program information available to the states, Indian Tribes, and the public. Chapter 1 describes current program information sources produced by OCRWM and by DOE's Office of Scientific and Technical Information (OSTI). Chapter 2 provides a directory of OCRWM and DOE technical information, and includes descriptions of computerized data bases and other resources. Chapter 3 is an index of OCRWM Headquarters and Project Office contacts, as well as state and Indian Tribe contacts. Chapter 4 enumerates Congressional Committees and Subcommittees that have jurisdiction over various components of the Civilian Radioactive Waste Management Program, and Chapter 5 lists DOE reading rooms, as well as information offices and the public libraries in affected states that are on one or more of OCRWM's mailing lists

  18. Energy information directory 1998

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-11-01

    The National Energy Information Center (NEIC), as part of its mission, provides energy information and referral assistance to Federal, State, and local governments, the academic community, business and industrial organizations, and the general public. The two principal functions related to this task are: (1) operating a general access telephone line, and (2) responding to energy-related correspondence addressed to the Energy Information Administration (EIA). The Energy Information Directory was developed to assist the NEIC staff, as well as other Department of Energy (DOE) staff, in directing inquiries to the proper offices within DOE, other Federal agencies, or energy-related trade associations. The Directory lists most Government offices and trade associations that are involved in energy matters.

  19. Energy information directory 1994

    Energy Technology Data Exchange (ETDEWEB)

    1994-03-28

    The National Energy Information Center (NEIC), as part of its mission, provides energy information and referral assistance to Federal, State, and local governments, the academic community, business and industrial organizations, and the general public. The two principal functions related to this task are (1) operating a general access telephone line, and (2) responding to energy-related correspondence addressed to the Energy Information Administration (EIA). The Energy Information Directory was developed to assist the NEIC staff, as well as other Department of Energy (DOE) staff, in directing inquiries to the proper offices within DOE, other Federal agencies, or energy-related trade associations. The Directory is a list of most Government offices and trade associations that are involved in energy matters. It does not include those DOE offices which do not deal with the public or public information.

  20. Directory of Design Support Methods

    National Research Council Canada - National Science Library

    Dean, T

    1998-01-01

    This Directory contains records of human factors databases, handbooks, data guides, texts, journals, standardization documents, prototype and interface design tools, analytic techniques, and computer simulation software...

  1. Directory of Design Support Methods

    National Research Council Canada - National Science Library

    Dean, T

    1997-01-01

    This Directory contains records of human factors databases, handbooks, data guides, texts, journals, standardization documents, prototype and interface design tools, analytic techniques, and computer simulation software...

  2. Active Directory Designing, Deploying, and Running Active Directory

    CERN Document Server

    Desmond, Brian

    2008-01-01

    By giving you a thorough grounding in Active Directory, this bestselling book teaches you how to design, manage, and maintain an AD infrastructure, whether it's for a small business network or a multinational enterprise with thousands of resources, services, and users. The fourth edition covers Active Directory from Windows 2000 through Windows Server 2008 in an easy-to-understand narrative style.

  3. Canadian Power directory 2000

    International Nuclear Information System (INIS)

    1999-06-01

    The directory supplies information on power project developers (small hydro, gas cogeneration, small cogeneration, combined cycle, wood waste/biomass, municipal solid waste and other); consultants (lawyers, accountants, financial, building energy systems, other); service suppliers (engineering, project management, construction, environmental, insurance, surveyors, training, water treatment, other); financiers (equity, venture capital, institutional lenders, other institutions, joint venture, other); equipment suppliers (generators, turbines, boilers, piping, etc., pumps, engines, gensets, electrical, control systems, other); provincial utilities, regulators and agencies; independent energy associations; gas suppliers; power suppliers; resource groups and trade organizations; biomass fuels; district heating and cooling; energy service companies; wind energy; solar energy; and European and international listings

  4. Canadian photovoltaic industry directory

    International Nuclear Information System (INIS)

    1998-01-01

    This directory has been prepared to help potential photovoltaic (PV) customers identify Canadian-based companies who can meet their needs, and to help product manufacturers and distributors identify potential new clients and/or partners within the PV industry for new and improved technologies. To assist the reader, an information matrix is provided that identifies the product and service types offered by each firm and its primary clients served. A list of companies by province or territory is also included. The main section lists companies in alphabetical order. Information presented for each includes address, contact person, prime activity, geographic area served, languages in which services are offered, and a brief company profile

  5. Early Adolescence: A Resource Directory.

    Science.gov (United States)

    Sheaves, David, Comp.

    This is a resource directory for professionals who work with young adolescents (10- to 15-year-olds). It is a multidisciplinary list of organizations, publications, and readings to help professionals in their research and practice. Although the directory is not meant to be all-inclusive, an attempt has been made to include the major networks,…

  6. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1992-12-01

    This second edition of the Directory of IAEA Databases has been prepared within the Division of Scientific and Technical Information (NESI). Its main objective is to describe the computerized information sources available to staff members. This directory contains all databases produced at the IAEA, including databases stored on the mainframe, LAN's and PC's. All IAEA Division Directors have been requested to register the existence of their databases with NESI. For the second edition database owners were requested to review the existing entries for their databases and answer four additional questions. The four additional questions concerned the type of database (e.g. Bibliographic, Text, Statistical etc.), the category of database (e.g. Administrative, Nuclear Data etc.), the available documentation and the type of media used for distribution. In the individual entries on the following pages the answers to the first two questions (type and category) is always listed, but the answers to the second two questions (documentation and media) is only listed when information has been made available

  7. Directory of awardee names

    Energy Technology Data Exchange (ETDEWEB)

    1999-07-01

    Standardization of grant and contract awardee names has been an area of concern since the development of the Department`s Procurement and Assistance Data System (PADS). A joint effort was begun in 1983 by the Office of Scientific and Technical Information (OSTI) and the Office of Procurement and Assistance Management/Information Systems and Analysis Division to develop a means for providing uniformity of awardee names. As a result of this effort, a method of assigning vendor identification codes to each unique awardee name, division, city, and state combination was developed and is maintained by OSTI. Changes to vendor identification codes or awardee names contained in PADS can be made only by OSTI. Awardee names in the Directory indicate that the awardee has had a prime contract (excluding purchase orders of $10,000 or less) with, or a financial assistance award from, the Department. Award status--active, inactive, or retired--is not shown. The Directory is in alphabetic sequence based on awardee name and reflects the OSTI-assigned vendor identification code to the right of the name. A vendor identification code is assigned to each unique awardee name, division, city, and state (for place of performance). The same vendor identification code is used for awards throughout the Department.

  8. Energy information directory 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    The National Energy Information Center (NEIC), as part of its mission, provides energy information and referral assistance to Federal, state, and local governments, the academic community, business and industrial organizations, and the general public. The two principal functions related to this task are: (1) operating a general access telephone line, and (2) responding to energy-related correspondence addressed to the Energy Information Administration (EIA). The Energy Information Directory was developed to assist the NEIC staff, as well as other Department of Energy (DOE) staff, in directing inquiries to the proper offices within DOE, other Federal agencies, or energy-related trade associations. The Directory lists some of the Government offices and trade associations that are involved in energy matters. It includes those DOE offices which deal with the public or public information. For the purposes of this publication, each entry has been given a numeric identification symbol. The index found in the back of this publication uses these identification numbers to refer the reader to relevant entries.

  9. Information services directory

    International Nuclear Information System (INIS)

    1991-01-01

    Congress passed the Nuclear Waste Policy Act of 1982 (NWPA) and its amendments establishing the National policy for safely storing, transporting and disposing of spent nuclear fuel and high-level radioactive waste in a geologic repository. This legislation created the Office of Civilian Radioactive Waste Management (OCRWM) within the US Department of Energy (DOE) to develop an integrated system for the safe and efficient disposal of high-level radioactive waste. The NWPA, as amended, directs DOE to study in detail the Yucca Mountain site in Nevada as the only candidate site for the Nation's geologic repository. In Nevada, the DOE/OCRWM Yucca Mountain Site Characterization Project Office (YMPO) manages scientific investigations to determine the suitability of Yucca Mountain for effectively isolating radioactive waste from the public and the environment. This Information Services Directory is intended to facilitate dissemination of information. The Directory is produced by the Education and Information Division of OCRWM's Office of External Relations and will be updated periodically. This is the third such update since its issuance in August 1986. It is a reference document that lists the sources of program information available to States, Indian Tribes and the public

  10. Harwell directory of technology

    International Nuclear Information System (INIS)

    1988-02-01

    The Directory of Technology series of leaflets (10 in this folder) provides comprehensive information on the research and development facilities and expertise available at the Harwell laboratory of the United Kingdom Atomic Energy Authority. Each leaflet covers a field of technology and lists the Business Centres and related customer services offered. The leaflets are Process and Chemical Engineering Technology, Materials Technology, Evaluation and Monitoring Techniques and Instrumentation, Computing Science and Applications, Environmental, Medical and Analytical Sciences, Nuclear Engineering, Reactor Materials Behaviour and Safety Research, Radioactive Waste Management and Disposal, Nuclear Fuels Processing and Isotopes, Major Nuclear research and development facilities. There is a cross-referenced index which provides information to enable contact to be made with the appropriate business centre manager. (U.K.)

  11. Directory of fire research specialists

    Science.gov (United States)

    Junod, T. L.; Mandel, G.; Jason, N. H.

    1979-01-01

    Directory indexes, 1,475 researchers and various organizations in the United States or Canada who have recently participated in or made contributions to fire science research or related areas of concern.

  12. GSA Bureau IT Leadership Directory

    Data.gov (United States)

    General Services Administration — Each agency is expected to post a JSON file for their Bureau IT Leadership Directory. Each dataset should include one record for each agency employee with the title...

  13. Canadian wind energy industry directory

    International Nuclear Information System (INIS)

    1996-01-01

    The companies and organizations involved, either directly or indirectly, in the wind energy industry in Canada, are listed in this directory. Some U.S. and international companies which are active or interested in Canadian industry activities are also listed. The first section of the directory is an alphabetical listing which includes corporate descriptions, company logos, addresses, phone and fax numbers, e-mail addresses and contact names. The second section contains 54 categories of products and services associated with the industry

  14. NSF-RANN Trace Contaminants Program directory. [Personnel directory

    Energy Technology Data Exchange (ETDEWEB)

    Purnell, P.A.; Smith, S.K.; Wilkes, C.F.

    1976-10-01

    This directory is designed to aid effective communication throughout the National Science Foundation's Trace Contaminants Program, Research Applied to National Needs. The majority of the participants in the Program are represented by name, address, telephone number, and a very brief description of research interest. The directory has five major divisions to facilitate its use. Section I contains a listing of the program managers associated with the NSF-RANN Trace Contaminants Program. Section II lists the principal investigators, co-principal investigators, and coordinators of each of the research grants in the Program. Section III lists the personnel by individual projects. Section IV contains a total alphabetic listing complete with project titles and Section V contains a keyword index. This directory is maintained by the Toxic Materials Information Center as part of the Environmental Resource Center of the Information Center Complex, Information Division, Oak Ridge National Laboratory.

  15. Electronic Animal Drug Product Listing Directory

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Electronic Animal Drug Product Listing Directory is a directory of all animal drug products that have been listed electronically since June 1, 2009, to comply...

  16. Resources guide and directory 2000

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-05-01

    The Resource Guide and Directory contains a review of the Chamber's activities during 1999, a series of special reviews on the Foothills Forest Grizzly Bear Study, the future of oil and natural gas production in Alberta, progress towards zero emission coal technology, natural gas-coal power generation, Shell Canada's Athabasca Oil Sands project, Suncor's Millenium Project, Klinger's Oilfield and Industrial Services, Wajax Industries' oil sands projects in northern Alberta, and the Chamber's Directory of Members. The Directory is alphabetical by company name. Each entry contains the address, telephone and fax numbers and the name of a senior officer of the company as the contact for further information.

  17. World nuclear directory. 6. ed.

    International Nuclear Information System (INIS)

    Wilson, C.W.J.

    1981-01-01

    The purpose of the directory is to provide a comprehensive, worldwide guide to organizations which conduct, promote, or encourage research into atomic energy. The term research is interpreted fairly generously. The directory is intended to be a reference source useful to scientists and administrators in the nuclear field, to information workers, librarians, journalists, market researchers, and others. It therefore includes nuclear research institutes; government departments; public corporations; industrial firms; electricity generating boards; learned and professional societies; and universities, polytechnics, and other institutes of higher education with nuclear departments. (author)

  18. Cancer immunology, bioinformatics and chemokine evidence link vaccines contaminated with animal proteins to autoimmune disease: a detailed look at Crohn's disease and Vitiligo

    OpenAIRE

    Arumugham, Vinu

    2017-01-01

    Cancer research has demonstrated that immunization with homologous xenogeneic proteins (such as vaccines contaminated with animal proteins that resemble human proteins) results in autoimmunity. Bioinformatics analysis demonstrates that animal proteins have occasional amino acids differences compared to equivalent human proteins. So mutated human protein epitopes can be identical to animal protein derived epitopes. Low affinity self reactive T cells suited for detection of mutated human epitop...

  19. Web directories as topical context

    NARCIS (Netherlands)

    Kaptein, R.; Kamps, J.; Aly, R.; Hauff, C.; den Hamer, I.; Hiemstra, D.; Huibers, T.; de Jong, F.

    2009-01-01

    In this paper we explore whether the Open Directory (or DMOZ) can be used to classify queries into topical categories on different levels and whether we can use this topical context to improve retrieval performance. We have set up a user study to let test persons explicitly classify queries into

  20. National directory of nuclear services

    International Nuclear Information System (INIS)

    1974-09-01

    This directory contains information on nuclear services which can be provided in South Africa. These services have to do with the application of nuclear materials and techniques in medicine, industry, agriculture, research, etc. A list of locally manufactured radioisotopes is given

  1. Cooley's Anemia: A Psychosocial Directory.

    Science.gov (United States)

    National Center for Education in Maternal and Child Health, Washington, DC.

    The directory is intended to aid patients and their families who are coping with the genetic disorder of Cooley's anemia. A brief review of the disease covers background, genetics, symptoms, effect on the patient, treatment, and current research. The next section looks at psychosocial needs at various times (time of diagnosis, infancy and toddler…

  2. Canada's directory of ethanol retailers

    International Nuclear Information System (INIS)

    1997-07-01

    This document is a directory listing all ethanol-blended gasoline retailers in Quebec, Ontario, Manitoba, Saskatchewan, Alberta, British Columbia, and the Yukon. The listings include the name and address of the retailer by province from west to east. Appendices providing a list of bulk purchase facilities of ethanol-blended fuels was also included, as well as a list of ethanol-blended gasoline retailers

  3. Canadian photovoltaic industry directory --1998

    International Nuclear Information System (INIS)

    1998-01-01

    The directory is intended to help potential PV customers identify Canadian-based companies who can meet their needs, and to help product manufacturers and distributors identify potential new clients and/or partners within the PV industry for new and improved technologies leading to greater end-use customer satisfaction. The principal feature of the directory is an information matrix that identifies the product and service types offered by each firm and the primary clients served. There is also a list of companies by province and territory, followed by an alphabetical listing of all companies, with detailed information including, mailing address, contact person, prime activity, geographic area served, languages in which services are provided, and a brief company profile. Additional information provided by the companies themselves, dealing with items such as number of systems sold, the total installed capacity, etc., is included in an 'experience matrix' for each firm. Sources of additional information on photovoltaic systems are included in a list at the end of the directory

  4. Directory of Energy Information Administration Models 1994

    International Nuclear Information System (INIS)

    1994-07-01

    This directory revises and updates the 1993 directory and includes 15 models of the National Energy Modeling System (NEMS). Three other new models in use by the Energy Information Administration (EIA) have also been included: the Motor Gasoline Market Model (MGMM), Distillate Market Model (DMM), and the Propane Market Model (PPMM). This directory contains descriptions about each model, including title, acronym, purpose, followed by more detailed information on characteristics, uses and requirements. Sources for additional information are identified. Included in this directory are 37 EIA models active as of February 1, 1994

  5. Unique Physician Identification Number (UPIN) Directory

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Unique Physician Identification Number (UPIN) Directory contains selected information on physicians, doctors of Osteopathy, limited licensed practitioners and...

  6. Directory of Energy Information Administration Models 1994

    Energy Technology Data Exchange (ETDEWEB)

    1994-07-01

    This directory revises and updates the 1993 directory and includes 15 models of the National Energy Modeling System (NEMS). Three other new models in use by the Energy Information Administration (EIA) have also been included: the Motor Gasoline Market Model (MGMM), Distillate Market Model (DMM), and the Propane Market Model (PPMM). This directory contains descriptions about each model, including title, acronym, purpose, followed by more detailed information on characteristics, uses and requirements. Sources for additional information are identified. Included in this directory are 37 EIA models active as of February 1, 1994.

  7. Directory of energy data collection forms. Forms in use as of October 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-01-01

    This is an authoritative listing of selected public use forms currently used as basic energy information gathering tools by the Department of Energy (DOE). This directory provides an overview of DOE`s energy information collection programs for decisionmakers in Government and industry. Forms designed to collect energy information and used by the Energy Information Administration (EIA) as of October 1995 are included in this directory. For each form listed in this directory, an abstract is included that describes the form`s uses, its respondents, and the data collected. For the reader`s convenience in finding specific types of collections, several indices have been provided in this directory. A listing of the forms grouped by energy source and function begins on page 26. Beginning on page 38 are the publications derived from the collections, and on page 50, are the forms linked to general respondent categories.

  8. Biggest challenges in bioinformatics.

    Science.gov (United States)

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-04-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

  9. Biggest challenges in bioinformatics

    OpenAIRE

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-01-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held in October at Heidelberg University in Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics' in a ‘World Café' style event.

  10. A bioinformatics potpourri.

    Science.gov (United States)

    Schönbach, Christian; Li, Jinyan; Ma, Lan; Horton, Paul; Sjaugi, Muhammad Farhan; Ranganathan, Shoba

    2018-01-19

    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

  11. North Sea oil directory 1976

    Energy Technology Data Exchange (ETDEWEB)

    1976-01-01

    This edition of the North Sea Oil Directory has been revised to keep pace with the ever-changing North Sea industry. The information is grouped under the following topics: exploration and production; group licensees; Dutch and Norwegian licensees; UK Offshore Operators Association Committees; drilling contractors; offshore exploration and surveys; cement, drilling fluids, and related equipment; drilling equipment; prime mover, transmission equipment; production and process equipment; rig and platform equipment suppliers; rig builders, ship builders; rig and platform logistics; ports, supply bases; marine civil engineering; specialized equipment and services; classified index; and an alphabetical index. (MCW)

  12. Structural adhesives directory and databook

    CERN Document Server

    Wilson, Jo

    1996-01-01

    A worldwide directory of commercially available adhesive products for use in a wide range of engineering disciplines. Along with product names and suppliers, basic property data are tabulated and cross-referenced. The book is subdivided according to class of adhesive, with introductions to each class followed by comparison tables and datasheets for each adhesive. The datasheets contain detailed information, from product codes to environmental properties and are therefore of interest across a broad readership. Standardized data will aid the user in cross-comparison between different manufacturers and in easily identifying the required information.

  13. Product and Service Directory 2004 Issue

    International Nuclear Information System (INIS)

    Agnihotri, N.K.

    2003-01-01

    This annual November-December issue of the Nuclear Plant Journal serves as directory of information resources on products and services related to the nuclear power industry. The directory consists of over 3,000 products and services submitted by over 300 suppliers worldwide during October and November 2003. The issue is divided into 4 main areas: Products and Services, Corporate Capabilities, and Suppliers

  14. 1986 Index/Directory of Women's Media.

    Science.gov (United States)

    Allen, Martha Leslie, Ed.

    This is a directory of women's media, i.e., media primarily owned and operated by and for women. The mission of this annual publication is to aid networking among women, women's organizations, and women's media, both nationally and internationally. The directory includes two sections: women's media groups, and individual media women and…

  15. 25 CFR 43.20 - Directory information.

    Science.gov (United States)

    2010-04-01

    ... OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR EDUCATION MAINTENANCE AND CONTROL OF STUDENT RECORDS IN BUREAU SCHOOLS § 43.20 Directory information. (a) Any educational institution making public directory..., address, telephone listing, date and place of birth, major field of study, participation in officially...

  16. Building a Disciplinary Metadata Standards Directory

    Directory of Open Access Journals (Sweden)

    Alexander Ball

    2014-07-01

    Full Text Available The Research Data Alliance (RDA Metadata Standards Directory Working Group (MSDWG is building a directory of descriptive, discipline-specific metadata standards. The purpose of the directory is to promote the discovery, access and use of such standards, thereby improving the state of research data interoperability and reducing duplicative standards development work.This work builds upon the UK Digital Curation Centre's Disciplinary Metadata Catalogue, a resource created with much the same aim in mind. The first stage of the MSDWG's work was to update and extend the information contained in the catalogue. In the current, second stage, a new platform is being developed in order to extend the functionality of the directory beyond that of the catalogue, and to make it easier to maintain and sustain. Future work will include making the directory more amenable to use by automated tools.

  17. Bioinformatics and Cancer

    Science.gov (United States)

    Researchers take on challenges and opportunities to mine "Big Data" for answers to complex biological questions. Learn how bioinformatics uses advanced computing, mathematics, and technological platforms to store, manage, analyze, and understand data.

  18. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. 1997 Eleventh annual downstream suppliers directory

    International Nuclear Information System (INIS)

    Anon.

    1996-01-01

    An indexed directory of equipment and service suppliers to the oil and gas industry was provided. The index, preceding the directory, provides an alphabetic listing of companies grouped by major products or services, such as blowers, compressors, control systems, hauling, maintenance, pipes, pumps, valves, welding supplies, and many others. The directory itself is arranged in a single alphabet. Each entry provides brief, but adequate information about the products or services offered, distributed or manufactured, plant location, telephone, fax, E-mail/Internet addresses, and names of key personnel

  20. Directory of Energy Information Administration models 1996

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-07-01

    This directory revises and updates the Directory of Energy Information Administration Models 1995, DOE/EIA-0293(95), Energy Information Administration (EIA), U.S. Department of Energy, July 1995. Four models have been deleted in this directory as they are no longer being used: (1) Market Penetration Model for Ground-Water Heat Pump Systems (MPGWHP); (2) Market Penetration Model for Residential Rooftop PV Systems (MPRESPV-PC); (3) Market Penetration Model for Active and Passive Solar Technologies (MPSOLARPC); and (4) Revenue Requirements Modeling System (RRMS).

  1. FAA Certificated Maintenance Agencies Directory (1997)

    Science.gov (United States)

    1997-05-06

    This advisory circular (AC) transmits a consolidated directory of all : certificated Federal Aviation Administration (FAA) repair stations and : manufacturer's maintenance facilities. The repair stations and manufacturer's : maintenance facilities we...

  2. Directory of History of Medicine Collections (DHMC)

    Data.gov (United States)

    Federal Geographic Data Committee — The collections described in this Directory database provide research and reference services to scholars interested in the history of the health sciences. Some of...

  3. Global Social Media Directory: A Resource Guide

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, Christine F.; Piatt, Andrew W.

    2014-10-23

    The Global Social Media Directory is a resource guide providing information on social networking services around the globe. This information changes rapidly, therefore, this document will be updated on a regular basis and as funding permits.

  4. Directory Enabled Policy Based Networking; TOPICAL

    International Nuclear Information System (INIS)

    KELIIAA, CURTIS M.

    2001-01-01

    This report presents a discussion of directory-enabled policy-based networking with an emphasis on its role as the foundation for securely scalable enterprise networks. A directory service provides the object-oriented logical environment for interactive cyber-policy implementation. Cyber-policy implementation includes security, network management, operational process and quality of service policies. The leading network-technology vendors have invested in these technologies for secure universal connectivity that transverses Internet, extranet and intranet boundaries. Industry standards are established that provide the fundamental guidelines for directory deployment scalable to global networks. The integration of policy-based networking with directory-service technologies provides for intelligent management of the enterprise network environment as an end-to-end system of related clients, services and resources. This architecture allows logical policies to protect data, manage security and provision critical network services permitting a proactive defense-in-depth cyber-security posture. Enterprise networking imposes the consideration of supporting multiple computing platforms, sites and business-operation models. An industry-standards based approach combined with principled systems engineering in the deployment of these technologies allows these issues to be successfully addressed. This discussion is focused on a directory-based policy architecture for the heterogeneous enterprise network-computing environment and does not propose specific vendor solutions. This document is written to present practical design methodology and provide an understanding of the risks, complexities and most important, the benefits of directory-enabled policy-based networking

  5. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

    Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

  6. Active mines in Arizona - 1993. Directory 40

    International Nuclear Information System (INIS)

    Phillips, K.A.; Niemuth, N.J.; Bain, D.R.

    1992-01-01

    A directory of the active mines in Arizona is presented. The directory was compiled in November, 1992 from field visits and information received by the Department's technical staff. For the purpose of this directory, an active mine is defined as a mine in continuous operation, either in production or under full-time development for production. Custom milling operations that are active or available on a full-time basis are also included in the directory. It is acknowledged that there are additional mines not listed that are in an exploration, evaluation, or part-time development phase. There are others where production is on an intermittent basis that are not listed. The report is dependent on the cooperation of government agencies, private industry, and individuals who voluntarily provide information on their projects and activities. The directory is arranged alphabetically by company name. Each listing includes corporate addresses, mine name and location, operation description, and key personnel. The listing for the sand and gravel operations include name, address, and phone number

  7. Bioinformatics for Exploration

    Science.gov (United States)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  8. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conform

  9. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

    Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

  10. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  11. NSF-RANN Trace Contaminants Program directory

    International Nuclear Information System (INIS)

    Purnell, P.A.; Smith, S.K.; Wilkes, C.F.

    1976-10-01

    This directory is designed to aid effective communication throughout the National Science Foundation's Trace Contaminants Program, Research Applied to National Needs. The majority of the participants in the Program are represented by name, address, telephone number, and a very brief description of research interest. The directory has five major divisions to facilitate its use. Section I contains a listing of the program managers associated with the NSF-RANN Trace Contaminants Program. Section II lists the principal investigators, co-principal investigators, and coordinators of each of the research grants in the Program. Section III lists the personnel by individual projects. Section IV contains a total alphabetic listing complete with project titles and Section V contains a keyword index. This directory is maintained by the Toxic Materials Information Center as part of the Environmental Resource Center of the Information Center Complex, Information Division, Oak Ridge National Laboratory

  12. Toxicology research projects directory, 1978. Monthly repts

    International Nuclear Information System (INIS)

    1978-01-01

    The Toxicology Research Projects Directory is a monthly publication of ongoing research projects in toxicology and related fields selected from the files of the Smithsonian Science Information Exchange (SSIE). Each issue lists toxicology-related research projects reported to SSIE during the one-month period preceding that issue. Each of the summaries is categorized by scientific discipline and assigned a unique identification number for cross-referencing from the Directory Indexes--Subject, Investigator, Performing Organization, Supporting Agency, and Master Grant Number. The thirteenth issue consists of Cumulative Indexes for the entire volume with referencing to projects in all of the previous twelve issues. The emphasis of the Directory is on the manifestations of the exposure of man and animals to toxic substances. Projects are classified by toxic agents, research orientation, and areas of environmental concern

  13. United Kingdom Ireland coal ports directory

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    The directory gives details of ports at 65 locations in the UK and Ireland. For each port, the directory lists the name of the terminal; the name, address, contact name and numbers of the terminal owner and of the terminal operator; and the name and telephone/fax numbers of ship's agents. It also give details, for each terminal, where available, of tidal rise, access routes, vessel maxima, working hours, coal traders and handlers, discharge facilities, daily discharge rate, coal loading facilities, daily loading rate, stocking area dimensions and capacity, stocking area facilities and inland transport infrastructure. Research for the directory was undertaken by S. Fazal and C. Measham of Sheffield Hallam University, Business School.

  14. National solar energy education directory. Second edition

    Energy Technology Data Exchange (ETDEWEB)

    Corcoleotes, G; Cronin, S; Kramer, K; O& #x27; Connor, K

    1980-01-01

    The information contained in this directory is derived from responses to a national survey of educational institutions and organizations involved in solar energy educational activities beyond the secondary school level. Phone calls and follow-up mail requests were used to gather additional information when necessary. Every survey instrument was read, coded, and edited before entry into the data base from which this directory was produced. The Directory is organized alphabetically by state. Institutions and organizations within each state are categorized according to type (Colleges and Universities, Junior/Community Colleges, Vocational/Technical Schools, and Other Educational Institutions and Organizations) and listed alphabetically within these categories. Within each institutional listing the amount of information provided will vary according to the completeness of the survey response received from that institution. (MHR)

  15. Directory of IAEA databases. 4. ed.

    International Nuclear Information System (INIS)

    1997-06-01

    This fourth edition of the Directory of IAEA Databases has been prepared within the Division of NESI. ITs main objective is to describe the computerized information sources available to the public. This directory contains all publicly available databases which are produced at the IAEA. This includes databases stored on the mainframe, LAN servers and user PCs. All IAEA Division Directors have been requested to register the existence of their databases with NESI. At the data of printing, some of the information in the directory will be already obsolete. For the most up-to-date information please see the IAEA's World Wide Web site at URL: http:/www.iaea.or.at/databases/dbdir/. Refs, figs, tabs

  16. National Solar Energy Education Directory. First edition

    Energy Technology Data Exchange (ETDEWEB)

    O& #x27; Connor, K; Corcoleotes, G; Silversmith, J A; Kramer, K A

    1979-01-01

    The directory lists institutions alphabetically by institution type within a state. A complete alphabetical index of institutions is found in the back of the Directory along with a cross reference to program and curriculum titles. Within each institution, programs and curricula offered, if any, are listed following the institution name, ID number (found in parentheses to the right of the institution name), address and phone number. All solar-related courses are then listed alphabetically by course title. If a course is offered within a program or curriculum, the program or curriculum name with which it is associated is printed. The Directory contains entries for nearly 700 post-secondary education institutions in the 50 states, the District of Columbia, Guam, and Puerto Rico.

  17. WGISS-45 International Directory Network (IDN) Report

    Science.gov (United States)

    Morahan, Michael

    2018-01-01

    The objective of this presentation is to provide IDN (International Directory Network) updates on features and activities to the Committee on Earth Observation Satellites (CEOS) Working Group on Information Systems and Services (WGISS) and provider community. The following topics will be will be discussed during the presentation: Transition of Providers DIF-9 (Directory Interchange Format-9) to DIF-10 Metadata Records in the Common Metadata Repository (CMR); GCMD (Global Change Master Directory) Keyword Update; DIF-10 and UMM-C (Unified Metadata Model-Collections) Schema Changes; Metadata Validation of Provider Metadata; docBUILDER for Submitting IDN Metadata to the CMR (i.e. Registration); and Mapping WGClimate Essential Climate Variable (ECV) Inventory to IDN Records.

  18. Directory of Energy Information Administration Models 1993

    Energy Technology Data Exchange (ETDEWEB)

    1993-07-06

    This directory contains descriptions about each model, including the title, acronym, purpose, followed by more detailed information on characteristics, uses, and requirements. Sources for additional information are identified. Included in this directory are 35 EIA models active as of May 1, 1993. Models that run on personal computers are identified by ``PC`` as part of the acronym. EIA is developing new models, a National Energy Modeling System (NEMS), and is making changes to existing models to include new technologies, environmental issues, conservation, and renewables, as well as extend forecast horizon. Other parts of the Department are involved in this modeling effort. A fully operational model is planned which will integrate completed segments of NEMS for its first official application--preparation of EIA`s Annual Energy Outlook 1994. Abstracts for the new models will be included in next year`s version of this directory.

  19. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

    Data Mining for Bioinformatics Applications provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems, including problem definition, data collection, data preprocessing, modeling, and validation. The text uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems, containing 45 bioinformatics problems that have been investigated in recent research. For each example, the entire data mining process is described, ranging from data preprocessing to modeling and result validation. Provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems Uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems Contains 45 bioinformatics problems that have been investigated in recent research.

  20. Energy Information Directory (Formerly: Energy Information Referral Directory). First quarter 1981

    International Nuclear Information System (INIS)

    1981-01-01

    The National Energy Information Center (NEIC) provides energy information and referral assistance to federal, state, and local governments, the academic community, business and industrial organizations, and the general public. The two principal; functions related to this task are (1) operating a general access telephone line and (2) responding to energy-related correspondence addressed to the Energy Information Administration (EIA). To assist the NEIC staff, as well as other Department of Energy (DOE) staff, in directing inquiries to the proper office within DOE or other federal agencies, the Energy Information Referral Directory was developed. With this issue, the directory has a new title: the Energy Information Directory

  1. 1991 worldwide natural gas industry directory

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    This book provides information for the natural gas industry, just as other PennWell directories have for the petroleum industry. Comprehensive in scope, each company listing includes address, phone, fax telex and cable numbers, key personnel, subsidiaries, branches and brief descriptions. The directory is organized in major areas of operation and includes sections on: Distribution, Drilling/Exploration/Production, Gas Utilities, Gathering/Transmission, Industry Associations/Organizations, LNG, LPG, Marketing, Processing, Regulatory Agencies, and Service, Supply and Manufacturers. An invaluable reference source for the natural gas professional

  2. PNRA. South-pole directory listing

    OpenAIRE

    Biagioni, Stefania; Carlesi, Carlo; Carpen?, Andrea; Ramorino, Chiara; Rossi, Lucio

    1992-01-01

    In the following all DATA-SET descriptors (DSD) contained in the "South-Pole Directory" (vers. 1992) are listed. The "South-Pole Directory" was a joint project between ENEA and CNR. The IEI/CNR took care of the data digitalization and check and of the english translation (where necessary). The ARF/CNR and the Progetto Antartide/ENEA joined the IEI/CNR in defining the acronyms of the Sensor_Names and of the Source_Names, together with the short and long names for the Data_Centers. Finally, the...

  3. 2016 Fee Wind energy directory

    International Nuclear Information System (INIS)

    2015-12-01

    . This sector proves, once again, its significance and impact by responding the requirements of the society in terms of environmental protection, job creation, regional development, urbanisation etc. This wind energy directory is more than a practical tool displaying the wind energy in sector France: it details companies active in the sector as well as the major stakeholders in France and in the world

  4. Directory interchange format manual, version 3.0

    Science.gov (United States)

    1990-01-01

    The Directory Interchange Format (DIF) is a data structure used to exchange directory level information about data sets among information systems. The format consists of a number of fields that describe the attributes of a directory entry and text blocks that contain a descriptive summary of and references for the directory entry. All fields and the summary are preceded by labels identifying their contents. All values are ASCII character strings. The structure is intended to be flexible, allowing for future changes in the contents of directory entries.

  5. A Directory of English Language Teaching Videos.

    Science.gov (United States)

    Falsetti, Julie, Comp.

    This third edition of the video directory updates previous editions and alphabetically lists videos, by title. It is designed to assist in the teaching of English or the training of teachers of English. Information included are format, standard, variety, use, target, level, price, duration, quality, support materials included, distributor, year…

  6. Small Business Management Training Tools Directory.

    Science.gov (United States)

    American Association of Community and Junior Colleges, Washington, DC. National Small Business Training Network.

    This directory is designed to assist in the identification of supplementary materials to support program development for small businesses. Following introductory comments and an overview of small business management training, section I lists training tools available from the Small Business Administration (SBA). Section II provides descriptions and…

  7. International Directory of Mental Retardation Resources.

    Science.gov (United States)

    Dybwad, Rosemary F., Ed.

    The directory lists and describes governmental and voluntary agencies, research, and other resources in the field of mental retardation in foreign countries. The first section, on international organizations, gives names, addresses, names of directors, and one or more paragraphs of description for the United Nations and its specialized agencies,…

  8. International photovoltaic products and manufacturers directory, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Shepperd, L.W. [ed.] [Florida Solar Energy Center, Cocoa, FL (United States)

    1995-11-01

    This international directory of more than 500 photovoltaic-related manufacturers is intended to guide potential users of photovoltaics to sources for systems and their components. Two indexes help the user to locate firms and materials. A glossary describes equipment and terminology commonly used in the photovoltaic industry.

  9. Gas industry directory 1998. 101. ed.

    International Nuclear Information System (INIS)

    Anon.

    1997-01-01

    In the Gas Industry Directory 1988, the following information is available: key information contacts, a buyer's guide, brand and trade names, company data, country index to overseas suppliers, who's who in the gas industry, UK gas suppliers, associations and organisations. (UK)

  10. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

    Abdulganiyu Abdu Yusuf; Zahraddeen Sufyanu; Kabir Yusuf Mamman; Abubakar Umar Suleiman

    2016-01-01

    Bioinformatics is the application of computational tools to capture and interpret biological data. It has wide applications in drug development, crop improvement, agricultural biotechnology and forensic DNA analysis. There are various databases available to researchers in bioinformatics. These databases are customized for a specific need and are ranged in size, scope, and purpose. The main drawbacks of bioinformatics databases include redundant information, constant change, data spread over m...

  11. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

    Full Text Available Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

  12. Emergent Computation Emphasizing Bioinformatics

    CERN Document Server

    Simon, Matthew

    2005-01-01

    Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...

  13. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  14. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

    Kortsarts, Yana; Morris, Robert W.; Utell, Janine M.

    2010-01-01

    Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. We present our experience in teaching an interdisciplinary course, Introduction to Bioinformatics, which was developed…

  15. Virtual Bioinformatics Distance Learning Suite

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  16. Directory of computer users in nuclear medicine

    Energy Technology Data Exchange (ETDEWEB)

    Henne, R.L.; Erickson, J.J.; McClain, W.J.; Kirch, D.L.

    1977-01-01

    The directory is composed of two major divisions, a Users' section and a Vendors' section. The Users' section consists of detailed installation descriptions and indexes to these descriptions. A typical description contains the name, address, type, and size of the institution as well as names of persons to contact. Following the hardware descriptions are listed the type of studies for which the computers are utilized, including the languages used, the method of output and an estimate of how often the study is performed. The Vendors' section contains short descriptions of current commercially available nuclear medicine systems as supplied by the vendors themselves. In order to reduce the amount of obsolete data and to include new institutions in future updates of the directory, a user questionnaire is included. (HLW)

  17. Directory of computer users in nuclear medicine

    International Nuclear Information System (INIS)

    Henne, R.L.; Erickson, J.J.; McClain, W.J.; Kirch, D.L.

    1977-01-01

    The directory is composed of two major divisions, a Users' section and a Vendors' section. The Users' section consists of detailed installation descriptions and indexes to these descriptions. A typical description contains the name, address, type, and size of the institution as well as names of persons to contact. Following the hardware descriptions are listed the type of studies for which the computers are utilized, including the languages used, the method of output and an estimate of how often the study is performed. The Vendors' section contains short descriptions of current commercially available nuclear medicine systems as supplied by the vendors themselves. In order to reduce the amount of obsolete data and to include new institutions in future updates of the directory, a user questionnaire is included

  18. Directory of the French nuclear industry

    International Nuclear Information System (INIS)

    2002-10-01

    This directory includes data sheets on the French companies operating in the nuclear industry. It begins with an introduction containing information on the French nuclear industry: 1 - nuclear power development in France (national energy plan, history, organization, economic advantages, reactors); 2 - French operator: Electricite de France (EdF); 3 - the industry (Areva, Cogema, mining activities, uranium chemistry and enrichment, processing, recycling, engineering, services, Framatome ANP); 4 - R and D and knowledge dissemination: French atomic energy commission (CEA); 5 - nuclear safety, security, control and regulation: nuclear safety authority (ASN), general direction of nuclear safety and radioprotection (DGSNR), institute of radioprotection and nuclear safety (IRSN), radioactive wastes, ANDRA's role; 6 - associations: French atomic forum (FAF), French nuclear industry trade association (GIIN), French nuclear energy society (SFEN), French radiation protection society (SFRP). Then, the data sheets of the directory follows. (J.S.)

  19. Directory of Nuclear Research Reactors 1994

    International Nuclear Information System (INIS)

    1995-08-01

    The Directory of Nuclear Research Reactors is an output of the Agency's computerized Research Reactor Data Base (RRDB). It contains administrative, technical and utilization information on research reactors known to the Agency at the end of December 1994. The data base converted from mainframe to PC is written in Clipper 5.0 and the publication generation system uses Excel 4. The information was collected by the Agency through questionnaires sent to research reactor owners. All data on research reactors, training reactors, test reactors, prototype reactors and critical assemblies are stored in the RRDB. This system contains all the information and data previously published in the Agency's publication, Directory of Nuclear Research Reactor, as well as updated information

  20. Directory of energy information administration models 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-13

    This updated directory has been published annually; after this issue, it will be published only biennially. The Disruption Impact Simulator Model in use by EIA is included. Model descriptions have been updated according to revised documentation approved during the past year. This directory contains descriptions about each model, including title, acronym, purpose, followed by more detailed information on characteristics, uses, and requirements. Sources for additional information are identified. Included are 37 EIA models active as of February 1, 1995. The first group is the National Energy Modeling System (NEMS) models. The second group is all other EIA models that are not part of NEMS. Appendix A identifies major EIA modeling systems and the models within these systems. Appendix B is a summary of the `Annual Energy Outlook` Forecasting System.

  1. Elastic pointer directory organization for scalable shared memory multiprocessors

    Institute of Scientific and Technical Information of China (English)

    Yuhang Liu; Mingfa Zhu; Limin Xiao

    2014-01-01

    In the field of supercomputing, one key issue for scal-able shared-memory multiprocessors is the design of the directory which denotes the sharing state for a cache block. A good direc-tory design intends to achieve three key attributes: reasonable memory overhead, sharer position precision and implementation complexity. However, researchers often face the problem that gain-ing one attribute may result in losing another. The paper proposes an elastic pointer directory (EPD) structure based on the analysis of shared-memory applications, taking the fact that the number of sharers for each directory entry is typical y smal . Analysis re-sults show that for 4 096 nodes, the ratio of memory overhead to the ful-map directory is 2.7%. Theoretical analysis and cycle-accurate execution-driven simulations on a 16 and 64-node cache coherence non uniform memory access (CC-NUMA) multiproces-sor show that the corresponding pointer overflow probability is reduced significantly. The performance is observed to be better than that of a limited pointers directory and almost identical to the ful-map directory, except for the slight implementation complex-ity. Using the directory cache to explore directory access locality is also studied. The experimental result shows that this is a promis-ing approach to be used in the state-of-the-art high performance computing domain.

  2. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  3. Utilizing the Antarctic Master Directory to find orphan datasets

    Science.gov (United States)

    Bonczkowski, J.; Carbotte, S. M.; Arko, R. A.; Grebas, S. K.

    2011-12-01

    While most Antarctic data are housed at an established disciplinary-specific data repository, there are data types for which no suitable repository exists. In some cases, these "orphan" data, without an appropriate national archive, are served from local servers by the principal investigators who produced the data. There are many pitfalls with data served privately, including the frequent lack of adequate documentation to ensure the data can be understood by others for re-use and the impermanence of personal web sites. For example, if an investigator leaves an institution and the data moves, the link published is no longer accessible. To ensure continued availability of data, submission to long-term national data repositories is needed. As stated in the National Science Foundation Office of Polar Programs (NSF/OPP) Guidelines and Award Conditions for Scientific Data, investigators are obligated to submit their data for curation and long-term preservation; this includes the registration of a dataset description into the Antarctic Master Directory (AMD), http://gcmd.nasa.gov/Data/portals/amd/. The AMD is a Web-based, searchable directory of thousands of dataset descriptions, known as DIF records, submitted by scientists from over 20 countries. It serves as a node of the International Directory Network/Global Change Master Directory (IDN/GCMD). The US Antarctic Program Data Coordination Center (USAP-DCC), http://www.usap-data.org/, funded through NSF/OPP, was established in 2007 to help streamline the process of data submission and DIF record creation. When data does not quite fit within any existing disciplinary repository, it can be registered within the USAP-DCC as the fallback data repository. Within the scope of the USAP-DCC we undertook the challenge of discovering and "rescuing" orphan datasets currently registered within the AMD. In order to find which DIF records led to data served privately, all records relating to US data within the AMD were parsed. After

  4. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

  5. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians. PMID:25996054

  6. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

    Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

  7. When process mining meets bioinformatics

    NARCIS (Netherlands)

    Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Nurcan, S.

    2011-01-01

    Process mining techniques can be used to extract non-trivial process related knowledge and thus generate interesting insights from event logs. Similarly, bioinformatics aims at increasing the understanding of biological processes through the analysis of information associated with biological

  8. International directory of certified radioactive sources

    International Nuclear Information System (INIS)

    Grosse, G.; Bambynek, W.

    1983-01-01

    This directory lists the products of 16 suppliers of certified reference materials (CRM) of radioactivity as given in their catalogues. Included are only products for which certificates are delivered and whose uncertainties are given according to the rules defined in ICRU Report No. 12, ''Certification of Standardized Radioactive Sources'' (International Commission on Radiation and Measurements, Washington, 1968). Only those products are included of which the standard uncertainties according to the above rules are less than 10%. Prices of the products are not mentioned since they frequently change. The products are divided into four groups: Radioactive Solutions, Radioactive Gases, Solid Sources and Sources for Liquid Scintillation Counting). (orig./WL)

  9. Hanford Site radioactive hazardous materials packaging directory

    International Nuclear Information System (INIS)

    McCarthy, T.L.

    1995-12-01

    The Hanford Site Radioactive Hazardous Materials Packaging Directory (RHMPD) provides information concerning packagings owned or routinely leased by Westinghouse Hanford Company (WHC) for offsite shipments or onsite transfers of hazardous materials. Specific information is provided for selected packagings including the following: general description; approval documents/specifications (Certificates of Compliance and Safety Analysis Reports for Packaging); technical information (drawing numbers and dimensions); approved contents; areas of operation; and general information. Packaging Operations ampersand Development (PO ampersand D) maintains the RHMPD and may be contacted for additional information or assistance in obtaining referenced documentation or assistance concerning packaging selection, availability, and usage

  10. Photovoltaic Product Directory and Buyers Guide

    Energy Technology Data Exchange (ETDEWEB)

    Watts, R.L.; Smith, S.A.; Dirks, J.A.; Mazzucchi, R.P.; Lee, V.E.

    1984-04-01

    The directory guide explains photovoltaic systems briefly and shows what products are available off-the-shelf. Information is given to assist in designing a photovoltaic system and on financial incentives. Help is given for determining if photovoltaic products can meet a particular buyer's needs, and information is provided on actual photovoltaic user's experiences. Detailed information is appended on various financial incentives available from state and federal governments, sources of additional information on photovoltaics, sources of various photovoltaic products, and a listing of addresses of photovoltaic products suppliers. (LEW)

  11. Directory of the French thermal solar sector

    International Nuclear Information System (INIS)

    Demangeon, Elsa; Simmonet, Raphael; Canals, Jonathan

    2011-01-01

    After an overview of what is at stake for the thermal solar sector in terms of employment and industrial development, a discussion of the huge energy and industrial potential of this sector, and the proposition of a road map for the development of this sector in France, this publication proposes a directory of actors of the different activity sectors: research and development, engineering, electric and electronic hardware manufacturing, thermal equipment manufacturing, fluid manufacturing, reflector manufacturing, thermodynamic machine manufacturer, structure component manufacturer, control-command system, energy storage, developers, and so on

  12. Directory of transport packaging test facilities

    International Nuclear Information System (INIS)

    1983-08-01

    Radioactive materials are transported in packagings or containers which have to withstand certain tests depending on whether they are Type A or Type B packagings. In answer to a request by the International Atomic Energy Agency, 13 Member States have provided information on the test facilities and services existing in their country which can be made available for use by other states by arrangement for testing different kinds of packagings. The directory gives the technical information on the facilities, the services, the tests that can be done and in some cases even the financial arrangement is included

  13. International directory of certified radioactive sources

    Energy Technology Data Exchange (ETDEWEB)

    Grosse, G; Bambynek, W

    1983-01-01

    This directory lists the products of 16 suppliers of certified reference materials (CRM) of radioactivity as given in their catalogues. Included are only products for which certificates are delivered and whose uncertainties are given according to the rules defined in ICRU Report No. 12, ''Certification of Standardized Radioactive Sources'' (International Commission on Radiation and Measurements, Washington, 1968). Only those products are included of which the standard uncertainties according to the above rules are less than 10%. Prices of the products are not mentioned since they frequently change. The products are divided into four groups: Radioactive Solutions, Radioactive Gases, Solid Sources and Sources for Liquid Scintillation Counting).

  14. Energy Information Referral Directory. Fourth quarter 1980

    International Nuclear Information System (INIS)

    1980-01-01

    This directory provides the name, address, and phone number of various energy information offices within the DOE and other Federal agencies. The arrangement is topical. Each entry presents the name of the office, the address, the main contact person, and a summary of the office's primary activities. There is a comprehensive subject index to the entries as well as a name index. In addition, the publication contains several appendices in which DOE Regional Energy Information Centers, state energy offices, DOE commercialization-resource managers, and DOE research and development and field facilities are listed. Charts illustrate the DOE and the EIA organizational structure

  15. Alberta petroleum equipment and services directory, 1992

    International Nuclear Information System (INIS)

    1992-01-01

    A directory is presented of Alberta companies that provide equipment and services to the oil industry. In the main section, companies are listed alphabetically by name, along with their addresses, phone/fax numbers, contact personnel, and lists of products and/or services. A separate alphabetical name index and a product/service index are included. A section covering provincial and territorial government agencies and non-governmental associations and institutes is appended, giving name, address, phone/fax number, leading personnel, and a summary of activities

  16. Hanford Site radioactive hazardous materials packaging directory

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, T.L.

    1995-12-01

    The Hanford Site Radioactive Hazardous Materials Packaging Directory (RHMPD) provides information concerning packagings owned or routinely leased by Westinghouse Hanford Company (WHC) for offsite shipments or onsite transfers of hazardous materials. Specific information is provided for selected packagings including the following: general description; approval documents/specifications (Certificates of Compliance and Safety Analysis Reports for Packaging); technical information (drawing numbers and dimensions); approved contents; areas of operation; and general information. Packaging Operations & Development (PO&D) maintains the RHMPD and may be contacted for additional information or assistance in obtaining referenced documentation or assistance concerning packaging selection, availability, and usage.

  17. 76 FR 22681 - Defense Logistics Agency (DLA) Address Directory

    Science.gov (United States)

    2011-04-22

    ... DEPARTMENT OF DEFENSE Office of the Secretary Defense Logistics Agency (DLA) Address Directory AGENCY: Department of Defense. ACTION: Notice. SUMMARY: The Defense Logistics Agency (DLA) is updating... Directory: Defense Logistics Agency Headquarters, Andrew T. McNamara Building, 8725 John J. Kingman Road...

  18. AIDS Resource Directory and Repertoire de ressources sur le SIDA.

    Science.gov (United States)

    Department of National Health and Welfare, Ottawa (Ontario).

    This set of documents presents directories of resources on the topic of Acquired Immune Deficiency Syndrome (AIDS) available in Canada in English and in French. The first section in each directory contains a list of names, addresses, and telephone numbers of organizations from which readers may obtain the listed resources. Resources are then…

  19. Economic Education Programs and Resources Directory. Second Edition.

    Science.gov (United States)

    National Association of Manufacturers, Washington, DC.

    This directory provides a selective listing of information about economic education programs and resource activities of 299 corporations, organizations, universities, and colleges in the United States. This second edition of the directory is intended to stimulate interaction between business firms and schools and to help educators, members of the…

  20. Directorial style and stylization:'The photographic synthesis' in Felix ...

    African Journals Online (AJOL)

    This study examines the styles of directing on the Nigerian stage through the works of Felix Okolo with a view to documenting the various directorial codes, directorial signals and prospects of directing in Nigeria and the director's artistic choices. This research adopts analytical, participant observation and interview methods.

  1. CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter

      We have developed "GLYCANthrope " - CROSSWORKS for glycans:  a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...

  2. Directory of IAEA databases. 3. ed.

    International Nuclear Information System (INIS)

    1993-12-01

    This second edition of the Directory of IAEA Databases has been prepared within the Division of Scientific and Technical Information. Its main objective is to describe the computerized information sources available to staff members. This directory contains all databases produced at the IAEA, including databases stored on the mainframe, LAN's and PC's. All IAEA Division Directors have been requested to register the existence of their databases with NESI. For the second edition database owners were requested to review the existing entries for their databases and answer four additional questions. The four additional questions concerned the type of database (e.g. Bibliographic, Text, Statistical etc.), the category of database (e.g. Administrative, Nuclear Data etc.), the available documentation and the type of media used for distribution. In the individual entries on the following pages the answers to the first two questions (type and category) is always listed, but the answer to the second two questions (documentation and media) is only listed when information has been made available

  3. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.

  4. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Iwasaki, Wataru; Asai, Kiyoshi

    2011-01-01

    In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics. PMID:21365017

  5. Bioinformatics in translational drug discovery.

    Science.gov (United States)

    Wooller, Sarah K; Benstead-Hume, Graeme; Chen, Xiangrong; Ali, Yusuf; Pearl, Frances M G

    2017-08-31

    Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse 'big data' that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications. © 2017 The Author(s).

  6. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

    DEFF Research Database (Denmark)

    Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude

    2012-01-01

    and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review...

  7. Environment, Environmental Restoration, and Waste Management Field Organization Directory

    International Nuclear Information System (INIS)

    1993-07-01

    This directory was developed by the Office of Environmental Guidance, RCRA/CERCLA Division (EH-231) from an outgrowth of the Departments efforts to identify and establish the regulatory response lead persons in the Field Organizations. The directory was developed for intemal EH-231 use to identify both the DOE and DOE contractor Field Organizations in the Environment, Environmental Restoration and Waste Management areas. The Field Organization directory is divided into three substantive sections: (1) Environment; (2) Environmental Restoration; and (3) Waste Management which are organized to correspond to the management hierarchy at each Field Organization. The information provided includes the facility name and address, individual managers name, and telephone/fax numbers

  8. Environmental impact directory system: preliminary implementation for geothermal energy

    Energy Technology Data Exchange (ETDEWEB)

    Hess, F.D.; Hall, R.T.; Fullenwider, E.D.

    1976-07-01

    An Environmental Impact Directory System (EIDS) was proposed as a method for a computerized search of the widely distributed data files and models pertaining to energy-related environmental effects. To define the scope and content of the system, an example was prepared for the case of geothermal energy. The resulting sub-directory is known as GEIDs (Geothermal Environmental Impact Directory System). In preparing or reviewing an Environmental Impact Statement (EIS), the user may employ GEIDS as an extensive checklist to make sure he has taken into account all predictable impacts at any level of severity.

  9. Directory of Analytical Methods, Department 1820

    International Nuclear Information System (INIS)

    Whan, R.E.

    1986-01-01

    The Materials Characterization Department performs chemical, physical, and thermophysical analyses in support of programs throughout the Laboratories. The department has a wide variety of techniques and instruments staffed by experienced personnel available for these analyses, and we strive to maintain near state-of-the-art technology by continued updates. We have prepared this Directory of Analytical Methods in order to acquaint you with our capabilities and to help you identify personnel who can assist with your analytical needs. The descriptions of the various capabilities are requester-oriented and have been limited in length and detail. Emphasis has been placed on applications and limitations with notations of estimated analysis time and alternative or related techniques. A short, simplified discussion of underlying principles is also presented along with references if more detail is desired. The contents of this document have been organized in the order: bulky analysis, microanalysis, surface analysis, optical and thermal property measurements

  10. Local public document room directory. Revision 7

    International Nuclear Information System (INIS)

    1998-04-01

    This directory (NUREG/BR-0088, Revision 7) lists local public document rooms (LPDRs) for commercial nuclear power plants with operating or possession-only licenses or under construction, plus the LPDRs for potential high-level radioactive waste repository sites, gaseous diffusion plants, certain fuel cycle facilities, certain low-level waste disposal facilities, and any temporary LPDRs established for the duration of licensing proceedings. In some instances, the LPDR libraries maintain document collections for more than one licensed facility. The library staff members listed are the persons most familiar with the LPDR collections. Reference librarians in the NRC Headquarters Public Document Room (PDR) are also available to assist the public in locating NRC documents

  11. Transducer handbook user's directory of electrical transducers

    CERN Document Server

    Boyle, H B

    2013-01-01

    When selecting or using a particular type of transducer or sensor, there are a number of factors which must be considered. The question is not only for what kind of measurement, but under what physical conditions, constraints of accuracy, and to meet which service requirements, is a transducer needed? This handbook is designed to meet the selection needs of anyone specifying or using transducers with an electrical output. Each transducer is described in an easy-to-use tabular format, giving all of the necessary data including operating principles, applications, range limits, errors, over-range protection, supply voltage requirements, sensitivities, cross sensitivities, temperature ranges and sensitivities and signal conditioning needs. The author has added notes that reflect his broad practical experience. Added to this is an extensive worldwide suppliers directory.

  12. Directory of computer users in nuclear medicine

    International Nuclear Information System (INIS)

    Erickson, J.J.; Gurney, J.; McClain, W.J.

    1979-09-01

    The Directory of Computer Users in Nuclear Medicine consists primarily of detailed descriptions and indexes to these descriptions. A typical Installation Description contains the name, address, type, and size of the institution and the names of persons within the institution who can be contacted for further information. If the department has access to a central computer facility for data analysis or timesharing, the type of equipment available and the method of access to that central computer is included. The dedicated data processing equipment used by the department in its nuclear medicine studies is described, including the peripherals, languages used, modes of data collection, and other pertinent information. Following the hardware descriptions are listed the types of studies for which the data processing equipment is used, including the language(s) used, the method of output, and an estimate of the frequency of the particular study. An Installation Index and an Organ Studies Index are also included

  13. Directory of computer users in nuclear medicine

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, J.J.; Gurney, J.; McClain, W.J. (eds.)

    1979-09-01

    The Directory of Computer Users in Nuclear Medicine consists primarily of detailed descriptions and indexes to these descriptions. A typical Installation Description contains the name, address, type, and size of the institution and the names of persons within the institution who can be contacted for further information. If the department has access to a central computer facility for data analysis or timesharing, the type of equipment available and the method of access to that central computer is included. The dedicated data processing equipment used by the department in its nuclear medicine studies is described, including the peripherals, languages used, modes of data collection, and other pertinent information. Following the hardware descriptions are listed the types of studies for which the data processing equipment is used, including the language(s) used, the method of output, and an estimate of the frequency of the particular study. An Installation Index and an Organ Studies Index are also included. (PCS)

  14. 1991 worldwide refining and gas processing directory

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    This book ia an authority for immediate information on the industry. You can use it to find new business, analyze market trends, and to stay in touch with existing contacts while making new ones. The possibilities for business applications are numerous. Arranged by country, all listings in the directory include address, phone, fax and telex numbers, a description of the company's activities, names of key personnel and their titles, corporate headquarters, branch offices and plant sites. This newly revised edition lists more than 2000 companies and nearly 3000 branch offices and plant locations. This east-to-use reference also includes several of the most vital and informative surveys of the industry, including the U.S. Refining Survey, the Worldwide Construction Survey in Refining, Sulfur, Gas Processing and Related Fuels, the Worldwide Refining and Gas Processing Survey, the Worldwide Catalyst Report, and the U.S. and Canadian Lube and Wax Capacities Report from the National Petroleum Refiner's Association

  15. Energy laboratory data and model directory

    Science.gov (United States)

    Lahiri, S.; Carson, J.

    1981-07-01

    Over the past several years M.I.T. faculty, staff, and students have produced a substantial body of research and analysis relating to the production, conversion,, and use of energy in domestic and international markets. Much of this research takes the form of models and associated data bases that have enduring value in policy studies (models) and in supporting related research and modeling efforts (date). For such models and data it is important to ensure that the useful life cycle does not end with the conclusion of the research project. This directory is an important step in extending the usefulness of models and data bases available at the M.I.T. Energy Laboratory. It will be updated from time to time to include new models and data bases that have been developed, or significant changes that have occurred.

  16. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

    A handout used in a HUB (Heidelberg Unseminars in Bioinformatics) meeting focused on career development for bioinformaticians. It describes an activity for use to help introduce the idea of peer mentoring, potnetially acting as an opportunity to create peer-mentoring groups.

  17. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  18. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

    van Kampen, Antoine H. C.; Moerland, Perry D.

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically

  19. Bioinformatics and the Undergraduate Curriculum

    Science.gov (United States)

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  20. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  1. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Campos, Benito; Barnkob, Mike Stein

    2014-01-01

    therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...

  2. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  3. Application Form for NCI Cancer Genetics Services Directory

    Science.gov (United States)

    Professionals who provide services related to cancer genetics (cancer risk assessment, genetic counseling, genetic susceptibility testing, and others) may fill out this application form to be listed in the National Cancer Institute's Cancer Genetics Services Directory.

  4. Directory of Technology Support Services to Brownfields Localities

    Science.gov (United States)

    This directory provides information about EPA offices, nongovernment organizations funded by EPA, and other federal agencies, that may be able to provide expertise to assist in the selection of technologies to characterize and clean up brownfields.

  5. FDIC Institution Directory (ID) -- Insured Insitution Download File

    Data.gov (United States)

    Federal Deposit Insurance Corporation — The FDIC's Institution Directory (ID) download file provides a list of all FDIC-insured institutions. The file includes demographic information related to the...

  6. Inclusion Criteria for NCI Cancer Genetics Services Directory

    Science.gov (United States)

    Professionals who provide services related to cancer genetics (cancer risk assessment, genetic counseling, genetic susceptibility testing, and others) must meet these criteria before applying to be listed in the National Cancer Institute's Cancer Genetics Services Directory.

  7. Energy - 1986/87 photographic film and video tape directory

    International Nuclear Information System (INIS)

    1988-01-01

    The directory is addressed to power supply companies wishing to convey audiovisual information to the power consumer. With emphasis on electric power supplies the films and videos complied are also touching upon other topical subjects. The directory aims at informing about the films and videos available on different subjects as well as about the best sources of supply. The audiovisual media selected are classified by: General aspects, energy sources, energy conversion, electric power distribution, electric power uses, engineering, miscellaneous. (orig./HP) [de

  8. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

    While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which

  9. AN EFFICIENT WEB PERSONALIZATION APPROACH TO DISCOVER USER INTERESTED DIRECTORIES

    Directory of Open Access Journals (Sweden)

    M. Robinson Joel

    2014-04-01

    Full Text Available Web Usage Mining is the application of data mining technique used to retrieve the web usage from web proxy log file. Web Usage Mining consists of three major stages: preprocessing, clustering and pattern analysis. This paper explains each of these stages in detail. In this proposed approach, the web directories are discovered based on the user’s interestingness. The web proxy log file undergoes a preprocessing phase to improve the quality of data. Fuzzy Clustering Algorithm is used to cluster the user and session into disjoint clusters. In this paper, an effective approach is presented for Web personalization based on an Advanced Apriori algorithm. It is used to select the user interested web directories. The proposed method is compared with the existing web personalization methods like Objective Probabilistic Directory Miner (OPDM, Objective Community Directory Miner (OCDM and Objective Clustering and Probabilistic Directory Miner (OCPDM. The result shows that the proposed approach provides better results than the aforementioned existing approaches. At last, an application is developed with the user interested directories and web usage details.

  10. A Bioinformatics Facility for NASA

    Science.gov (United States)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  11. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; Gribskov, Michael; Tan, Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  12. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

    Science.gov (United States)

    Palma, Jonathan P.; Benitz, William E.; Tarczy-Hornoch, Peter; Butte, Atul J.; Longhurst, Christopher A.

    2012-01-01

    The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory health. As a result of advances in translational informatics, the care of neonates will become more data driven, evidence based, and personalized. PMID:22924023

  13. The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

    Science.gov (United States)

    Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E.

    2018-01-01

    The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe. PMID:29630066

  14. The Microbe Directory: An annotated, searchable inventory of microbes' characteristics.

    Science.gov (United States)

    Shaaban, Heba; Westfall, David A; Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E

    2018-01-05

    The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes' characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY-Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism's taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

  15. Directory of certificates of compliance for radioactive materials packages

    International Nuclear Information System (INIS)

    1992-10-01

    This directory contains a Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3), for Radioactive Materials Packages effective October 1, 1992. The purpose of this directory is to make available a convenient source of information on packaging which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volumes 1 and 2. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The reports include a listing of all users of each package-design and approved QA programs prior to the publication date of the directory

  16. Directory of Certificates of Compliance for Radioactive Materials Packages

    International Nuclear Information System (INIS)

    1992-10-01

    This directory contains a Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3), for Radioactive Materials Packages effective October 1, 1992. The purpose of this directory is to make available a convenient source of information on packaging which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volumes 1 and 2. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The reports include a listing of all users of each package-design and approved QA programs prior to the publication date of the directory

  17. Directory of certificates of compliance for radioactive materials packages

    International Nuclear Information System (INIS)

    1997-10-01

    The purpose of this directory is to make available a convenient source of information on packagings approved by the U.S. Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volumes 1 and 2. An alphabetical listing by user name is included in the back of Volume 3 for approved Quality Assurance programs. The reports include a listing of all users of each package design and approved Quality Assurance programs prior to the publication date of the directory. Comments to make future revisions of this directory more useful are invited and should be directed to the Spent Fuel Project Office, U.S. Nuclear Regulatory Commission

  18. Directory of certificates of compliance for radioactive materials packages

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-10-01

    The purpose of this directory is to make available a convenient source of information on packagings approved by the U.S. Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volumes 1 and 2. An alphabetical listing by user name is included in the back of Volume 3 for approved Quality Assurance programs. The reports include a listing of all users of each package design and approved Quality Assurance programs prior to the publication date of the directory. Comments to make future revisions of this directory more useful are invited and should be directed to the Spent Fuel Project Office, U.S. Nuclear Regulatory Commission.

  19. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  20. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-12-12

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

  1. 47 CFR 69.405 - Published directory expenses in Account 6620.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Published directory expenses in Account 6620... SERVICES (CONTINUED) ACCESS CHARGES Apportionment of Expenses § 69.405 Published directory expenses in Account 6620. Published Directory expenses shall be assigned to the Information element. ...

  2. Directory of Certificates of Compliance for Radioactive Materials Packages

    International Nuclear Information System (INIS)

    1993-10-01

    This directory contains Certificates of Compliance (Volume 2), for NRC Approved Packages. The purpose of this directory is to make available a convenient source of information on Quality Assurance Programs and Packagings which have been approved by the US Nuclear Regulatory Commission. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, is applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  3. Directory of certificates of compliance for radioactive materials packages

    International Nuclear Information System (INIS)

    1991-10-01

    This directory contains Certificates of Compliance (Volume 2) for Radioactive Materials Packages. The purpose of this directory is to make available a convenient source of information on Quality Assurance Programs and Packagings which have been approved by the US Nuclear Regulatory Commission. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  4. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  5. Biology in 'silico': The Bioinformatics Revolution.

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  6. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  7. A Mathematical Optimization Problem in Bioinformatics

    Science.gov (United States)

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  8. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Science.gov (United States)

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  9. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

    Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

  10. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-01-01

    “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  11. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

    Chakraborty, Chiranjib; George Priya Doss, C; Zhu, Hailong; Agoramoorthy, Govindasamy

    2017-06-01

    Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

  12. Bioinformatics clouds for big data manipulation

    Directory of Open Access Journals (Sweden)

    Dai Lin

    2012-11-01

    Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  13. The 2016 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

  14. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.

  15. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

    Dai, Lin; Gao, Xin; Guo, Yan; Xiao, Jingfa; Zhang, Zhang

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  16. National Institute on Disability and Rehabilitation Research Program Directory, 1999.

    Science.gov (United States)

    National Inst. on Disability and Rehabilitation Research (ED/OSERS), Washington, DC.

    This directory lists all projects funded by the National Institute of Disability and Rehabilitation Research (NIDRR) during the 1999 fiscal year. It includes summaries, funding data, and contact information for a broad range of programs. Programs are grouped into the following research priorities: (1) employment outcomes; (2) health and function;…

  17. Propane Canada's first ever auto propane conversion directory

    International Nuclear Information System (INIS)

    Anon.

    1999-01-01

    A directory of auto propane dealers in Alberta, British Columbia and Manitoba was presented. Dealers in Calgary, Edmonton, Burnaby, Dawson Creek and Winnipeg were listed along with their addresses, phone numbers, fax, and E-mail addresses. Some of the other information provided included accreditation, equipment used and manufacturer brands used by the dealers

  18. Directory of Research in Social Studies/Social Sciences.

    Science.gov (United States)

    Barret, Anna R.; Carnett, George S.

    Described are current trends in the social and behavioral sciences intended to meet the needs of the educational community. The projects listed include studies in anthropology, sociology, political science, history, geography, foreign area studies, economics, international relations, and environmental education. Part I of the directory lists…

  19. Invasive Species Working Group: Research Summary and Expertise Directory

    Science.gov (United States)

    Jack Butler; Dean Pearson; Mee-Sook Kim

    2009-01-01

    Rocky Mountain Research Station (RMRS) personnel have scientific expertise in widely ranging disciplines and conduct multidisciplinary research on invasive species issues with emphasis in terrestrial and aquatic habitats throughout the Interior West, Great Plains, and related areas (fig. 1; Expertise Directory; appendix). RMRS invasive species research covers an array...

  20. Directory of cyclotrons used for radionuclide production in Member States

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-03-01

    The directory of cyclotrons used for radionuclide production is an update of the data base on cyclotrons that was compiled in 1983 by the International Atomic Energy Agency. The directory contains technical, utilization and administrative information supplied to the IAEA as of October 1997. The directory was prepared through information collected by questionnaires sent to institutions that either have a cyclotron, or that were identified to be in the process of installation of a cyclotron. The directory contains 206 entries for cyclotrons operating in 34 Member States. The largest concentration of cyclotrons for radionuclide production are located in the United States of America (66), Japan (33) and Germany (22). The largest number of cyclotrons for a single country is the United States of America. The expansion in number of cyclotrons during the last decade has been driven by the advent of advances in medical imaging instrumentation (PET, SPET and more recently 511 KeV emission tomography); introduction of user friendly compact medical cyclotrons from several companies that manufacture cyclotrons; and recent decisions that {sup 15}O-oxygen PET studies in Japan, and {sup 18}F-FDG PET studies in Germany are eligible for reimbursement by government or insurance companies.

  1. International biotechnology directory 1986. Products, companies, research and organizations

    Energy Technology Data Exchange (ETDEWEB)

    Coombs, J. (comp.)

    1986-01-01

    This Directory covers biotechnology in Western Europe, North America, Brazil, Australasia and Japan. It provides both an overview of the extent of present interest with a summary of activities in the various geographical areas and a catalogue whereby suppliers of materials and services can be identified.

  2. Virtual Schools Report 2016: Directory and Performance Review

    Science.gov (United States)

    Miron, Gary; Gulosino, Charisse

    2016-01-01

    This 2016 report is the fourth in an annual series of National Education Policy Center (NEPC) reports on the fast-growing U.S virtual school sector. This year's report provides a comprehensive directory of the nation's full-time virtual and blended learning school providers. It also pulls together and assesses the available evidence on the…

  3. 1978-79 Directory of Physics & Astronomy Staff Members.

    Science.gov (United States)

    American Inst. of Physics, New York, NY.

    This directory gives names, addresses, and telephone numbers of staff members of astronomy and physics departments. The listings are made under the following headings: (1) American Institute of Physics and its member societies; (2) geographic listing of academic institutions and faculty - U.S., Canada, Mexico, and Central America; (3) U.S.…

  4. The 1988 Directory of Educational Software Publishing Companies.

    Science.gov (United States)

    Electronic Learning, 1988

    1988-01-01

    Based on questionnaires sent to educational software companies in January 1988, this directory lists 78 companies. Information given includes company address, curriculum subject areas for which the company publishes software, types of machines and operating systems on which the software operates, and grade level for which it is targeted. (LRW)

  5. Directory of cyclotrons used for radionuclide production in Member States

    International Nuclear Information System (INIS)

    1998-03-01

    The directory of cyclotrons used for radionuclide production is an update of the data base on cyclotrons that was compiled in 1983 by the International Atomic Energy Agency. The directory contains technical, utilization and administrative information supplied to the IAEA as of October 1997. The directory was prepared through information collected by questionnaires sent to institutions that either have a cyclotron, or that were identified to be in the process of installation of a cyclotron. The directory contains 206 entries for cyclotrons operating in 34 Member States. The largest concentration of cyclotrons for radionuclide production are located in the United States of America (66), Japan (33) and Germany (22). The largest number of cyclotrons for a single country is the United States of America. The expansion in number of cyclotrons during the last decade has been driven by the advent of advances in medical imaging instrumentation (PET, SPET and more recently 511 KeV emission tomography); introduction of user friendly compact medical cyclotrons from several companies that manufacture cyclotrons; and recent decisions that 15 O-oxygen PET studies in Japan, and 18 F-FDG PET studies in Germany are eligible for reimbursement by government or insurance companies

  6. Resource Directory of Hispanic Educational Materials on Child Abuse Prevention.

    Science.gov (United States)

    Hill, Nancy; And Others

    This annotated resource directory lists brochures, booklets, audiovisual materials, charts, and other educational materials, most of which are available in both English and Spanish, that address the following issues: (1) child abuse; (2) child development; (3) parenting skills; (4) mental health; (5) self-esteem; (6) stress management; (7) family…

  7. Directory of Post-Secondary Retailing and Marketing Vocational Programs.

    Science.gov (United States)

    American Vocational Association, Inc., Washington, DC.

    This directory lists 357 general and 135 special retailing and marketing vocational programs at the post secondary level. Institutions vary somewhat in the identification of general programs; for example, they may be called retailing, merchandising, marketing, mid-management, or distributive education programs. Specialized programs offered by…

  8. Information services directory: An Update of 5/87

    International Nuclear Information System (INIS)

    1989-03-01

    The Information Services Directory is intended to facilitate dissemination of information. The Directory is produced by the Information Services Division of OCRWM's Office of External Relations and Policy and will be updated periodically. This is the second such update since its issuance in August 1986. It is a reference document that lists the sources of program information available to States, Indian Tribes and the public. Chapter I of this Directory describes current program information sources, including the OCRWM Bulletin, the Electronic Bulletin Board (INFOLINK) and other periodic publications produced by OCRWM and DOE's Office of Scientific and Technical Information (OSTI). Chapter II is an index of DOE, State and Federal Agency contacts. Chapter III provides a directory of DOE technical information and includes descriptions of computerized data bases and other resources. Chapter IV enumerates Congressional Committees and Subcommittees that have jurisdiction over various components of the Civilian Radioactive Waste Management Program, and Chapter V lists DOE Reading Rooms and Information Offices, NRC Local Public Document Rooms, and public libraries in the State of Nevada that are on one or more of OCRWM's mailing lists. Chapter VI is an index of systems and Chapter VII offers listings of selected publications

  9. Directory of Instructional Programs in Supervision and Management Training.

    Science.gov (United States)

    Civil Service Commission, Washington, DC. Training Assistance Div.

    This directory, which is designed for the use of training officers in the Washington, D.C. area in prescribing learning programs to meet employee training needs, describes available group and self instructional programs used for the training of supervisors and managers. Each of the 21 courses listed contains the pertinent information necessary to…

  10. Directory of Library Automation Software, Systems, and Services. 1998 Edition.

    Science.gov (United States)

    Cibbarelli, Pamela R., Ed.; Cibbarelli, Shawn E., Ed.

    This book includes basic information to locate and compare available options for library automation based on various criteria such as hardware requirements, operating systems, components and applications, and price, and provides the necessary contact information to allow further investigation. The major part of the directory lists 211 software…

  11. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    Horbach, D.Y.; Usanov, S.A.

    2005-01-01

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  12. Bioinformatics in cancer therapy and drug design

    Energy Technology Data Exchange (ETDEWEB)

    Horbach, D Y [International A. Sakharov environmental univ., Minsk (Belarus); Usanov, S A [Inst. of bioorganic chemistry, National academy of sciences of Belarus, Minsk (Belarus)

    2005-05-15

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  13. Directory of financing sources for foreign energy projects

    Energy Technology Data Exchange (ETDEWEB)

    La Ferla, L. [La Ferla Associates, Washington, DC (United States)

    1995-09-01

    The Office of National Security Policy has produced this Directory of Financing Sources for Foreign Energy Projects. The Directory reviews programs that offer financing from US government agencies, multilateral organizations, public, private, and quasi-private investment funds, and local commercial and state development banks. The main US government agencies covered are the US Agency for International Development (USAID), the Export-Import Bank of the US (EXIM Bank), Overseas Private Investment Corporation (OPIC), US Department of Energy, US Department of Defense, and the US Trade and Development Agency (TDA). Other US Government Sources includes market funds that have been in part capitalized using US government agency funds. Multilateral organizations include the World Bank, International Finance Corporation (IFC), Asian Development Bank (ADB), European Bank for Reconstruction and Development (EBRD), and various organizations of the United Nations. The Directory lists available public, private, and quasi-private sources of financing in key emerging markets in the Newly Independent States and other developing countries of strategic interest to the US Department of Energy. The sources of financing listed in this directory should be considered indicative rather than inclusive of all potential sources of financing. Initial focus is on the Russian Federation, Ukraine, india, China, and Pakistan. Separate self-contained sections have been developed for each of the countries to enable the user to readily access market-specific information and to support country-specific Departmental initiatives. For each country, the directory is organized to follow the project life cycle--from prefeasibility, feasibility, project finance, cofinancing, and trade finance, through to technical assistance and training. Programs on investment and export insurance are excluded.

  14. BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

    Science.gov (United States)

    Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

    2015-01-01

    Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

  15. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  16. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

    Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  17. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

    In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

  18. Application of machine learning methods in bioinformatics

    Science.gov (United States)

    Yang, Haoyu; An, Zheng; Zhou, Haotian; Hou, Yawen

    2018-05-01

    Faced with the development of bioinformatics, high-throughput genomic technology have enabled biology to enter the era of big data. [1] Bioinformatics is an interdisciplinary, including the acquisition, management, analysis, interpretation and application of biological information, etc. It derives from the Human Genome Project. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets.[2]. This paper analyzes and compares various algorithms of machine learning and their applications in bioinformatics.

  19. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    Bioinformatics is an emerging scientific discipline that uses information ... complex biological questions. ... and computer programs for various purposes of primer ..... polymerase chain reaction: Human Immunodeficiency Virus 1 model studies.

  20. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

    Full Text Available Bioinformatics is a new field that is poorly served by any of the traditional science programs in Biology, Computer science or Biochemistry. Known to be a rapidly evolving discipline, Bioinformatics has emerged from experimental molecular biology and biochemistry as well as from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science. While institutions are responding to this increased demand by establishing graduate programs in bioinformatics, entrance barriers for these programs are high, largely due to the significant prerequisite knowledge which is required, both in the fields of biochemistry and computer science. Although many schools currently have or are proposing graduate programs in bioinformatics, few are actually developing new undergraduate programs. In this paper I explore the blend of a multidisciplinary approach, discuss the response of academia and highlight challenges faced by this emerging field.

  1. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  2. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.

    2014-01-01

    RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  3. Directory of certificates of compliance for radioactive materials packages

    International Nuclear Information System (INIS)

    1991-10-01

    This directory contains a Report of NRC Approved Packages (Volume 1) for Radioactive Materials Packages. The purpose of this directory is to make available a convenient source of information on Quality Assurance Programs and Packagings which have been approved by the US Nuclear Regulatory Commission. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  4. Directory of certificates of compliance for radioactive materials packages

    International Nuclear Information System (INIS)

    1991-10-01

    This directory contains a Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and Report of NRC Approved Quality Assurance Programs for Radioactive Materials Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on Quality Assurance Programs and Packagings which have been approved by the US Nuclear Regulatory Commission. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12., it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  5. Directory of French photovoltaic research and industry 2011

    International Nuclear Information System (INIS)

    Poubeau, Romain; Simmonet, Raphael; Canals, Jonathan

    2011-05-01

    After an overview of what is at stake in terms of industrial employment in the photovoltaic sector, a presentation of competitiveness clusters, a description of the value chain (cell manufacturers, arrays manufacturers, power inverter manufacturers, electric equipment manufacturers, structure component manufacturers, fabrication steps, etc.) in the photovoltaic sector, this document proposes a directory (addresses, activity descriptions) of research and industrial actors of the photovoltaic sector in France: research centres, manufacturers, industrial projects

  6. Propane Canada: Propane Canada's Second Annual Auto Propane Conversion Directory

    International Nuclear Information System (INIS)

    Anon.

    2000-01-01

    A directory of companies engaged in automotive propane conversion in Alberta and British Columbia is provided. There are a total of eight entries : three in Calgary, one in Edmonton in Alberta and two in Burnaby, one in Dawson Creek and one in Fort St. John in British Columbia. Each entry provides information about the company, including name, address, phone and fax numbers, owner's or manager's name, conversion equipment brands used, number of bays, type of retail sales and accreditation

  7. Nuclear directory 1987, part 2 - Nuclear buyers' guide

    International Nuclear Information System (INIS)

    1987-01-01

    This paper consists of a directory of suppliers' names and addresses, the name and address of the Canadian representative of non-domestic companies, and the name and phone number of the person to contact. In cases where non-domestic companies have no Canadian representative listed, contact should be made directly with the company. These companies have indicated a commitment to marketing in Canada

  8. Directory of Colon and Rectal Cancer Specialist Teams

    OpenAIRE

    Department of Health; Social Services and Public Safety

    2004-01-01

    The Directory of Colon and Rectal Cancer Specialist Teams has been produced under the auspices of the Northern Ireland Regional Advisory Committee on Cancer. It contains details of the full membership of the clinical teams providing care for colon and rectal cancer in each of Health and Social Services Board Area. Lead Clinicians For Colon and Rectal Cancer Services (PDF 74 KB) EHSSB (PDF 198 KB) NHSSB (PDF 107 KB) SHSSB (PDF 130 KB) WHSSB (PDF 131 KB)

  9. Directory of certificates of compliance for radioactive materials packages

    International Nuclear Information System (INIS)

    1989-10-01

    The purpose of this directory is to make available a convenient source of information on packaging which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory. Shipments of radioactive material utilizing these packages must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with a Nuclear Regulatory Commission approved quality assurance program

  10. Directory of personnel responsible for radiological health programs

    International Nuclear Information System (INIS)

    1977-01-01

    This is a directory of professional personnel who administer the radiological health program activities in state and local governmental agencies. Included in the directory is a listing of each state health officer or the head of the agency responsible for the radiological health program. The name, address, and telephone number of the radiological health personnel are listed, followed by the alternate contact who, in many instances, may be chief of a larger administrative unit of which the radiological health program is a subunit. The address for the program is also included if it differs from the official health department or agency. Generally, the titles of the personnel listed will indicate the administrative status of the radiological health program. The directory also includes a list of key professional personnel in the Bureau of Radiological Health, Radiation Operations Staff, Regional Radiological Health Representatives, Winchester Engineering and Analytical Center, Food and Drug Administration; Office of Radiation Programs, Regional Radiation Representatives, National Environmental Research Center, and Eastern Environmental Radiation Laboratory, Environmental Protection Agency; selected personnel in the U.S. Nuclear Regulatory Commission; and selected personnel in the National Bureau of Standards

  11. Atlantic Environmental Resource Directory, 1989: A directory of non-profit environmental and development organizations in Atlantic Canada

    Energy Technology Data Exchange (ETDEWEB)

    Cuthbertson, L.L.

    1989-01-01

    This directory lists 161 non-profit groups in the Atlantic region, along with contacts for the environmental networks across the country and in New England and appropriate federal and provincial offices in Atlantic Canada. The directory was compiled from questionnaires sent out to a list of contacts that were on an original mailing list of groups known to have taken stands on environmental issues in the past. Follow-up mailouts and phone calls were also made. As well, some contacts were discovered through word-of-mouth. Groups are listed alphabetically by province and are classified by subjects. Information includes address and phone number, contact, date formed, number of members, scope, language and objectives. Groups and resources are indexed by subject area and groups are listed by resources available, environmental networks, Eastern states-United States citizen groups, labour unions, federal and provincial government.

  12. Locating Biodiversity Data Through The Global Change Master Directory

    Science.gov (United States)

    Olsen, Lola M.

    1998-01-01

    The Global Change Master Directory (GCMD) presently holds descriptions for almost 7000 data sets held worldwide. The directory's primary purpose is for data discovery. The information provided through the GCMD's Directory Interchange Format (DIF) is the set of information that a researcher would need to determine if a particular data set could be of value. By offering data set descriptions worldwide in many scientific disciplines - including meteorology, oceanography, ecology, geology, hydrology, geophysics, remote sensing, paleoclimate, solar-terrestrial physics, and human dimensions of climate change - the GCMD simplifies the discovery of data sources. Direct linkages to many of the data sets are also provided. In addition, several data set registration tools are offered for populating the directory. To search the directory, one may choose the Guided Search or Free-Text Search. Two experimental interfaces were also made available with the latest software release - one based on a keyword search and another based on a graphical interface. The graphical interface was designed in collaboration with the Human Computer Interaction Laboratory at the University of Maryland. The latest version of the software, Version 6, was released in April, 1998. It features the implementation of a scheme to handle hierarchical data set collections (parent-child relationships); a hierarchical geospatial location search scheme; a Java-based geographic map for conducting geospatial searches; a Related-URL field for project-related data set collections, metadata extensions (such as more detailed inventory information), etc.; a new implementation of the Isite software; a new dataset language field; hyperlinked email addresses, and more. The key to the continued evolution of the GCMD is in the flexibility of the GCMD database, allowing modifications and additions to made relatively easily to maintain currency, thus providing the ability to capitalize on current technology while importing

  13. Directory of certificates of compliance for radioactive materials packages. Summary report of NRC approved packages

    International Nuclear Information System (INIS)

    1979-10-01

    This directory contains a Summary Report of NRC Approved Packages for radioactive material packages effective September 14, 1979. Purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory

  14. A directory for neonatal intensive care: potential for facilitating network-based research in neonatology.

    Science.gov (United States)

    Ariagno, Ronald L; Lee, Henry C; Stevenson, David K; Benjamin, Daniel K; Smith, P Brian; Escobedo, Marilyn B; Bhatt, Dilip R

    2018-03-15

    Directories of contact information have evolved over time from thick paperback times such as the "Yellow Pages" to electronic forms that are searchable and have other functionalities. In our clinical specialty, the development of a professional directory helped to promote collaboration in clinical care, education, and quality improvement. However, there are opportunities for increasing the utility of the directory by taking advantage of modern web-based tools, and expanding the use of the directory to fill a gap in the area of collaborative research.

  15. Directory of certificates of compliance for radioactive materials packages. Summary report of NRC approved packages

    Energy Technology Data Exchange (ETDEWEB)

    None

    1979-10-01

    This directory contains a Summary Report of NRC Approved Packages for radioactive material packages effective September 14, 1979. Purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory.

  16. Navigating the changing learning landscape: perspective from bioinformatics.ca

    OpenAIRE

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2013-01-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable...

  17. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  18. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  20. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

    Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

  1. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

    Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

  2. Canada's directory of ethanol-blended fuel retailers (December 1998)

    International Nuclear Information System (INIS)

    1998-12-01

    This publication serves as a directory of ethanol-blended gasoline retailers in Quebec, Ontario, Manitoba, Saskatchewan, Alberta, British Columbia, and the Yukon. The listings include the name and address of the retailer. The listing is organized by province and cities, beginning with the Yukon in the west and proceeding east to Quebec. A list of bulk purchase facilities of ethanol-blended fuels is also included. As of December 1998, there were a total of 929 retail outlets for ethanol blended gasoline in Canada

  3. The directory of US coal and technology export resources

    Energy Technology Data Exchange (ETDEWEB)

    1990-10-01

    The purpose of The Directory remains focused on offering a consolidated resource to potential buyers of US coal, coal technology, and expertise. This is consistent with the US policy on coal and coal technology trade, which continues to emphasize export market strategy implementation. Within this context, DOE will continue to support the teaming'' approach to marketing; i.e., vertically integrated large project teams to include multiple industry sectors, such as coal producers, engineering and construction firms, equipment manufacturers, financing and service organizations.

  4. Using Group Communication to Implement a Fault-Tolerant Directory Service

    NARCIS (Netherlands)

    Kaashoek, M.F.; Tanenbaum, A.S.; Verstoep, C.

    1993-01-01

    Group communication is an important paradigm for building distributed applications. This paper discusses a fault-tolerant distributed directory service based on group communication, and compares it with the previous design and implementation based on remote procedure call. The group directory

  5. Information Sources on Scientific Research Related to the Preservation of Books, Paper, and Adhesives. Directory.

    Science.gov (United States)

    Commission on Preservation and Access, Washington, DC.

    Produced as part of an effort by the Commission on Preservation and Access to assist with the formation of a preservation research agenda, this report contains: (1) a directory of laboratories and organizations working in the four specific areas of concern in preservation--books, paper, adhesives, and mold; (2) directories of indexes, abstracts,…

  6. Directory of certificates of compliance for radioactive materials packages: Summary report of NRC approved packages

    International Nuclear Information System (INIS)

    1987-11-01

    This directory contains a Summary Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1). This directory makes available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the back of Volume 1

  7. 76 FR 14034 - Proposed Collection; Comment Request; NCI Cancer Genetics Services Directory Web-Based...

    Science.gov (United States)

    2011-03-15

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Proposed Collection; Comment Request; NCI Cancer Genetics Services Directory Web-Based Application Form and Update Mailer Summary: In... Cancer Genetics Services Directory Web-based Application Form and Update Mailer. [[Page 14035

  8. Directory of Indochinese Health Education Materials for Southeast Asian Refugees, Refugee Sponsors and Refugee Health Providers.

    Science.gov (United States)

    Minnesota State Dept. of Health, St. Paul. Refugee Education Resource Center.

    This is a directory of (print) health education materials for Indochinese refugees, refugee sponsors, and refugee health providers. Materials listed for refugees cover dental health, diseases, family planning, infant and child health, maternal care and pregnancy, legal systems, nutrition, patient instruction, and education. The directory also…

  9. Counseling Directory and Consumer's Guide: Implementing Professional Disclosure and Consumer Protection.

    Science.gov (United States)

    Swanson, John L.

    1979-01-01

    The publication of a "counseling directory" and "consumer's guide" is a new approach that can be used to respond to the current professional issues of professional disclosure and consumer protection. Reviews the purposes, format, and content of both the directory and guide. (Author)

  10. The Language of Literacy: A National Resource Directory of Aboriginal Literacy Programs.

    Science.gov (United States)

    Sabourin, Beverly; Globensky, Peter Andre

    This directory presents, in narrative form, core information about the operations of approximately 100 Aboriginal literacy programs throughout Canada. To qualify for inclusion in the directory, each program had to offer basic, functional, or advanced literacy training; offer literacy training in English, French, or an Aboriginal language; be…

  11. 76 FR 35462 - Proposed Renewal of Information Collection; Source Directory of American Indian and Alaska Native...

    Science.gov (United States)

    2011-06-17

    ... contact the business. Internet Web site address To identify whether the business advertises and/or sells...; Source Directory of American Indian and Alaska Native Owned and Operated Arts and Crafts Businesses... Alaska Native Owned and Operated Arts and Crafts Businesses (Source Directory) is a program of the Indian...

  12. 76 FR 28439 - Submission for OMB Review; Comment Request; NCI Cancer Genetics Services Directory Web-Based...

    Science.gov (United States)

    2011-05-17

    ...; Comment Request; NCI Cancer Genetics Services Directory Web-Based Application Form and Update Mailer... currently valid OMB control number. Proposed Collection: Title: NCI Cancer Genetics Services Directory Web... included in the NCI Cancer Genetics Services Directory on NCI's Cancer.gov Web site. The information...

  13. Historical Post Office Directory Parser (POD Parser Software From the AddressingHistory Project

    Directory of Open Access Journals (Sweden)

    Nicola Osborne

    2014-07-01

    Full Text Available The POD Parser is Python software for parsing the OCR’d (optical character recognised text of digitised historical Scottish Post Office Directories (PODs to produce a consistent structured format for the data and for geocoding each address. The software was developed as part of the AddressingHistory project which sought to combine digitised historic directories with digitised and georeferenced historic maps.  The software has potential for reuse in multiple research contexts where historical post office directory data is relevant, and is therefore particularly of use in historical research into social, economic or demographic trends. The POD Parser is currently designed for use with Scottish directories but is extensible, perhaps with some adaptation, to use with other similarly formatted materials such as the English Trade Directories.

  14. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  15. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

  16. Bioinformatics: A History of Evolution "In Silico"

    Science.gov (United States)

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  17. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

    )-based bioinformatics approach. The ANN was trained to recognize feature-based patterns in proteins that are considered to be associated with lipid rafts. The trained ANN was then used to predict protein raftophilicity. We found that, in the case of α-helical membrane proteins, their hydrophobic length does not affect...

  18. Bioinformatics in Undergraduate Education: Practical Examples

    Science.gov (United States)

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  19. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  20. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    Science.gov (United States)

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  1. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

    Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

    2015-01-01

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

  2. Development and implementation of a bioinformatics online ...

    African Journals Online (AJOL)

    Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of ...

  3. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  4. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

    Science.gov (United States)

    Bokulich, Nicholas A; Rideout, Jai Ram; Mercurio, William G; Shiffer, Arron; Wolfe, Benjamin; Maurice, Corinne F; Dutton, Rachel J; Turnbaugh, Peter J; Knight, Rob; Caporaso, J Gregory

    2016-01-01

    Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.

  5. Market development directory for solar industrial process heat systems

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-02-01

    The purpose of this directory is to provide a basis for market development activities through a location listing of key trade associations, trade periodicals, and key firms for three target groups. Potential industrial users and potential IPH system designers were identified as the prime targets for market development activities. The bulk of the directory is a listing of these two groups. The third group, solar IPH equipment manufacturers, was included to provide an information source for potential industrial users and potential IPH system designers. Trade associates and their publications are listed for selected four-digit Standard Industrial Code (SIC) industries. Since industries requiring relatively lower temperature process heat probably will comprise most of the near-term market for solar IPH systems, the 80 SIC's included in this chapter have process temperature requirements less than 350/sup 0/F. Some key statistics and a location list of the largest plants (according to number of employees) in each state are included for 15 of the 80 SIC's. Architectural/engineering and consulting firms are listed which are known to have solar experience. Professional associated and periodicals to which information on solar IPH sytstems may be directed also are included. Solar equipment manufacturers and their associations are listed. The listing is based on the SERI Solar Energy Information Data Base (SEIDB).

  6. Safeguards and Security Technology Development Directory. FY 1993

    Energy Technology Data Exchange (ETDEWEB)

    1993-06-01

    The Safeguards and Security Technology Development Directory is published annually by the Office of Safeguards and Security (OSS) of the US Department of Energy (DOE), and is Intended to inform recipients of the full scope of the OSS R&D program. It is distributed for use by DOE headquarters personnel, DOE program offices, DOE field offices, DOE operating contractors, national laboratories, other federal agencies, and foreign governments. Chapters 1 through 7 of the Directory provide general information regarding the Technology Development Program, including the mission, program description, organizational roles and responsibilities, technology development lifecycle, requirements analysis, program formulation, the task selection process, technology development infrastructure, technology transfer activities, and current research and development tasks. These chapters are followed by a series of appendices which contain more specific information on aspects of the Program. Appendix A is a summary of major technology development accomplishments made during FY 1992. Appendix B lists S&S technology development reports issued during FY 1992 which reflect work accomplished through the OSS Technology Development Program and other relevant activities outside the Program. Finally, Appendix C summarizes the individual task statements which comprise the FY 1993 Technology Development Program.

  7. Directory of the French Photovoltaic Industry 2017 - 2018

    International Nuclear Information System (INIS)

    2017-02-01

    More than 500 companies, of which 200 are industrial companies with a manufacturing unit located in France, and some fifty are research centres, this is the rich panorama prepared by the 2017-18 directory of the French photovoltaic industry, representing more than 8,200 jobs. These companies operate throughout the photovoltaic value chain: from chemistry and electronics, to electricity production, to the development, construction and maintenance of photovoltaic systems. They constitute an economic sector in full developmental swing and one that is providing new, high-added value jobs. Therefore, some of our research centres (National Institute of Solar Energy, Photovoltaic Institute of Ile de France) are among the most advanced in the world. Our network of industrial and service companies is filled with little gems that we have to make fruitful. Content of this directory: Presentation of the French renewable energies syndicate (SER); Presentation of SER-SOLER, French solar photovoltaic professionals group; 'Putting France on the map', foreword by Jean-Louis Bal, President of SER and Xavier Daval, President of SER-SOLER; Presentation of France solar industry; Presentation of photovoltaic quality Alliance Photovoltaique; Areas of activity; The members of SER-SOLER; Other members of SER-SOLER; Other Companies; Index (Alphabetical, By activity, By region); Advertisers

  8. Directory of gamma processing facilities in Member States

    International Nuclear Information System (INIS)

    2004-02-01

    Ionizing radiation can modify physical, chemical and biological properties of materials. This characteristic of radiation was recognised very soon after the discovery of radioactivity. At present, the principal applications concern sterilisation of health care products, food irradiation and materials modification for polymers. Besides naturally occurring radioactive isotopes, artificial ones were produced using cyclotrons. A significant impetus, however, was given to the radiation processing industry with the advent of nuclear reactors, which were used to produce radioisotopes. Gamma ray emitters like cobalt-60 became popular radiation sources for medical and industrial applications. Many gamma ray irradiators have been built and it is estimated that less than 200 are currently in operation all over the world. In recent times, the use of electron accelerators as a radiation source (sometimes equipped with X ray converter) is increasing. However, gamma irradiators are difficult to replace, especially in the case of non-uniform and high-density products. The International Atomic Energy Agency (IAEA) has several programmes related to industrial irradiation applications for processing of various products including those related to health care, pharmaceuticals, food and polymers, and applications associated with plant design, dosimetry and safety. Through the technical co-operation programme, the IAEA supports these activities in developing countries and helps them to build local capacity to implement various industrial applications of radiation processing. The IAEA also organises and conducts training courses and workshops, provides individual training to personnel, and sends experts to the radiation facilities in Member States where help is needed. All these activities can be carried out much more efficiently and effectively if there were a comprehensive directory of radiation facilities operating in Member States. Also, such a compilation would be a valuable tool for

  9. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

  10. Component-Based Approach for Educating Students in Bioinformatics

    Science.gov (United States)

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  11. BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    François Moreews

    2015-12-01

    Full Text Available Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

  12. Bioinformatics and the Politics of Innovation in the Life Sciences

    Science.gov (United States)

    Zhou, Yinhua; Datta, Saheli; Salter, Charlotte

    2016-01-01

    The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. PMID:27546935

  13. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

    Science.gov (United States)

    Schönbach, Christian; Verma, Chandra; Bond, Peter J; Ranganathan, Shoba

    2016-12-22

    The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.

  14. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

    Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.

  15. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

    Full Text Available Objective: Within the information technology (IT industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise′s overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework

  16. The growing need for microservices in bioinformatics.

    Science.gov (United States)

    Williams, Christopher L; Sica, Jeffrey C; Killen, Robert T; Balis, Ulysses G J

    2016-01-01

    Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Bioinformatics relies on nimble IT framework which can adapt to changing requirements. To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics. Use of the microservices framework is an effective methodology for the fabrication and

  17. The growing need for microservices in bioinformatics

    Science.gov (United States)

    Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G. J.

    2016-01-01

    Objective: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework is an effective

  18. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

    Full Text Available PURPOSE: Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. METHODS: This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. RESULTS: The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. CONCLUSIONS: The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets

  20. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

  1. Penalized feature selection and classification in bioinformatics

    OpenAIRE

    Ma, Shuangge; Huang, Jian

    2008-01-01

    In bioinformatics studies, supervised classification with high-dimensional input variables is frequently encountered. Examples routinely arise in genomic, epigenetic and proteomic studies. Feature selection can be employed along with classifier construction to avoid over-fitting, to generate more reliable classifier and to provide more insights into the underlying causal relationships. In this article, we provide a review of several recently developed penalized feature selection and classific...

  2. Bioinformatics Training: A Review of Challenges, Actions and Support Requirements

    DEFF Research Database (Denmark)

    Schneider, M.V.; Watson, J.; Attwood, T.

    2010-01-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...

  3. Directory of certificates of compliance for radioactive materials packages: Certificates of compliance

    International Nuclear Information System (INIS)

    1987-11-01

    This directory contains a Summary Report of the US Nuclear Regulatory Commission's Certificates of Compliance (Volume 2) for Radioactive Material Packages effective October 1, 1987. This directory makes available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the back of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2

  4. Directory of crystal growth and solid state materials production and research

    Energy Technology Data Exchange (ETDEWEB)

    Connolly, T.F.; Battle, G.C.; Keesee, A.M. (comps.)

    1979-03-01

    This directory lists only those who returned questionnaires distributed by the Research Materials Information Center during 1978. The directory includes, in addition to crystal growers, those preparing starting materials for crystal growth and ultrapure noncrystalline research specimens. It also includes responses from those characterizing, or otherwise studying, the properties of materials provided by others. The international coverage of the directory is limited to the United States, Argentina, Australia, Bulgaria, Canada, Czechoslovakia, Egypt, Finland, East Germany, Hungary, India, Israel, Japan, Mexico, Poland, Romania, South Africa, Taiwan, Yugoslavia, and Zaire.

  5. World directory of crystallographers and of other scientists employing crystallographic methods

    CERN Document Server

    Filippini, G; Hashizume, H; Torriani, I; Duax, W

    1995-01-01

    The 9th edition of the World Directory of Crystallographers and of Other Scientists Employing Crystallographic Methods, which contains 7907 entries embracing 72 countries, differs considerably from the 8th edition, published in 1990. The content has been updated, and the methods used to acquire the information presented and to produce this new edition of the Directory have involved the latest advances in technology. The Directory is now also available as a regularly updated electronic database, accessible via e-mail, Telnet, Gopher, World-Wide Web, and Mosaic. Full details are given in an Appendix to the printed edition.

  6. Directory of crystal growth and solid state materials production and research

    International Nuclear Information System (INIS)

    Connolly, T.F.; Battle, G.C.; Keesee, A.M.

    1979-03-01

    This directory lists only those who returned questionnaires distributed by the Research Materials Information Center during 1978. The directory includes, in addition to crystal growers, those preparing starting materials for crystal growth and ultrapure noncrystalline research specimens. It also includes responses from those characterizing, or otherwise studying, the properties of materials provided by others. The international coverage of the directory is limited to the United States, Argentina, Australia, Bulgaria, Canada, Czechoslovakia, Egypt, Finland, East Germany, Hungary, India, Israel, Japan, Mexico, Poland, Romania, South Africa, Taiwan, Yugoslavia, and Zaire

  7. Energy research and development projects in the Nordic countries. Directory 1987

    International Nuclear Information System (INIS)

    Anon.

    1988-01-01

    This is the fifth directory of research, development and demonstration projects in the Nordic countries within the field of energy. The directory includes projects running in 1987. 2378 projects are described, all of them financed through special public funds (i.e. external funding). The energy research organisation in each Nordic country is briefly reviewed in the appendixes, and a list of relevant newsletters are given. The directory is published at the request of the Nordic Council of Ministers and a special Energy Research Committee set up by the Nordic energy ministers in order to coordinate and promote Nordic information sharing in the energy field. (author)

  8. Energy research and development projects in the Nordic countries. Directory 1986. Energiforskningsprojekter i Norden. Katalog 1986

    International Nuclear Information System (INIS)

    1987-01-01

    This is the fourth directory of research, development and demonstration projects in the Nordic countries within the field of energy. The 1986 directory includes projects running in 1986. 2172 projects are described and all of them are financed through special public funds (i.e. external funding). The energy research organisation in each Nordic country is briefly reviewed in the appendixes, and a list of relevant newsletters are given. The directory is published at the request if the Nordic Council of Ministers and a special Energy Reseach Committee set up by the Nordic energy ministers in order to coordinate and promote Nordic information sharing in the energy field. (author)

  9. Energy research and development projects in the Nordic countries. Directory 1985. Energiforskningsprojekter i Norden. Katalog 1985

    International Nuclear Information System (INIS)

    1985-01-01

    This is the third directory of research, development and demonstration projects in the Nordic countries within the field of energy. The 1985 directory includes projects running in 1985. 1757 projects are described and all of them are financed through special public funds (i.e. external funding). The directory is published at the request of the Nordic Council of Ministers and a special Energy Research Committee set up by the Nordic energy ministers in order to coordinate and promote Nordic information sharing in the energy field. (author)

  10. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. © The Author 2015. Published by Oxford University Press.

  11. Bioinformatics on the Cloud Computing Platform Azure

    Science.gov (United States)

    Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

  12. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

    Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

  13. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

  14. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

    Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

    2009-01-01

    Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

  15. Adapting bioinformatics curricula for big data

    Science.gov (United States)

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  16. 1991 worldwide petroleum phone/fax/telex directory

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    This book puts more than 34,000 worldwide locations just a phone call or fax or telex message away. The directory lists companies and their subsidiaries in locations from Alaska to Zaire, whether their operations are in exploration, production, refining, transportation, petrochemicals, etc., offshore or on land. The listings are organized by country, with the companies listed in alphabetical order. So if you happen to know the country you wish to reach, you simply choose the company listed under it. And if you happen to know only the company name, two company indices will help you find the specific location you want. The Company Index Hierarchical lists all subsidiaries, branches, divisions, etc., under their corporate names. The Company Index - Alphabetical lists all entries alphabetically. Country codes for telephone, fax or telex are provided

  17. CDD CERN Drawings Directory User's manual Version 1.1

    CERN Document Server

    Delamare, Christophe; Jeannin, F; Petit, S

    1996-01-01

    CDD (CERN Drawings Directory) is a multi-platform utility which manages engineering drawings made in any division at CERN. The aim of CDD is not to store the graphical drawing itself, but to store a reference with some information related to the drawing. Access to this data is provided via a graphical user interface which is based upon ORACLE Forms and via WWW. Drawings following different numbering systems and different management rules can be handled by CDD. The only condition is that those particular functionalities are well defined. Several drawing systems have been identified in CERN and therefore considered when designing the application. The current version of CDD focuses on systems EST, LEP, ST-IE, SPS, ST-CE and the experiments ALICE, ATLAS, CMS and LHCb. Other CERN systems could be easily integrated upon demand.

  18. Open DOAR the Directory of Open Access Repositories

    CERN Multimedia

    CERN. Geneva

    2005-01-01

    The last year has seen wide-spread growth in the idea of using open access repositories as a part of a research institution's accepted infrastructure. Policy development from institutions and funding bodies has also supported the growth of the repository network. The next stage of expansion will be in the provision of services and cross-repository facilities and resources. Of course, it is hoped that these will then establish a feed-back loop to encourage repository population and further repository establishment, as the potential of open access to research materials is realised. The growth of repositories has been organic, with a variety of different repositories based in departments, institutions, funding agencies or subject communities, with a range of content, both in type and subject. Existing repositories are expanding their holdings, from eprints to associated research data-sets, or with learning objects and multimedia material. This presentation will look at the development of the Directory of Open Ac...

  19. 1991-92 Canadian directory of efficiency and alternative energy technologies

    International Nuclear Information System (INIS)

    1992-01-01

    The 1991-1992 Canadian Directory of efficiency and alternative energy technologies. The three main sections cover Alternative Energy Companies, Energy Efficiency Companies and Energy Service Companies. Contact and company information is provided

  20. Directory of certificates of compliance for radioactive materials packages, Certificates of compliance

    International Nuclear Information System (INIS)

    1990-10-01

    This directory contains a Report of the US Nuclear Regulatory Commissions's Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Materials Packages effective October 1, 1990. The purpose of this directory is to make available a convenient source of information on packaging which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of easy package design and approved QA programs prior to the publication date of the directory

  1. Directory of Certificates of Compliance for Radioactive Materials Packages: Certificates of Compliance

    International Nuclear Information System (INIS)

    1988-12-01

    This directory contains a Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), all Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Material Packages effective October 1, 1988. The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  2. Directory of Certificates of Compliance for Radioactive-Materials Packages. Certificates of Compliance

    International Nuclear Information System (INIS)

    1983-01-01

    This directory contains a Summary Report of the US Nuclear Regulatory Commission's Approved Packages (Volume I), all Certificates of Compliance (Volume 2), and Summary Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Material Packages effective December 31, 1982. The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the back of Volumes 1 and 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Summary Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  3. Directory of Certificates of Compliance for Radioactive Materials Packages: Report of NRC approved packages

    International Nuclear Information System (INIS)

    1988-12-01

    This directory contains a Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), all Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Material Packages effective October 1, 1988. The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  4. Directory of Certificates of Compliance for Radioactive-Materials Packages. Summary report of NRC approved packages

    International Nuclear Information System (INIS)

    1983-01-01

    This directory contains a Summary Report of the US Nuclear Regulatory Commission's Approved Packages (Volume I), all Certificates of Compliance (Volume 2), and Summary Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Material Packages effective December 31, 1982. The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the back of Volumes 1 and 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by company name is included in the back of Volume 3 for approved QA programs. The Summary Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  5. Report: Results of Technical Vulnerability Assessment: EPA’s Directory Service System Authentication and Authorization Servers

    Science.gov (United States)

    Report #11-P-0597, September 9, 2011. Vulnerability testing of EPA’s directory service system authentication and authorization servers conducted in March 2011 identified authentication and authorization servers with numerous vulnerabilities.

  6. 1991-92 Canadian directory of efficiency and alternative energy technologies

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1993-12-31

    The 1991-1992 Canadian Directory of efficiency and alternative energy technologies. The three main sections cover Alternative Energy Companies, Energy Efficiency Companies and Energy Service Companies. Contact and company information is provided.

  7. Directory of Energy Data Collection Forms: Forms in use as of October 1996

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-01

    This is the twentieth edition of the Directory of Energy Collection Data Forms, an authoritative listing of selected public use forms currently used as basic energy information gathering tools by the Department of Energy.

  8. Directory of certificates of compliance for radioactive materials packages, Report of NRC approved packages

    International Nuclear Information System (INIS)

    1990-10-01

    This directory contains a Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Materials Packages effective October 1, 1990. The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  9. Design criteria for a worldwide directory of radioactively contaminated sites (DRCS)

    International Nuclear Information System (INIS)

    2001-11-01

    The publication attempts to fulfil two main objectives: (a) to describe the activities and underlying considerations and concepts for the development by the IAEA of a worldwide Directory of Radioactively Contaminated Sites; (b) to give some recommendations for the development of such directories at the Member States level. In addition to a discussion of the conceptual considerations on the design of an IAEA-level directory, the results of previous efforts on data collation are presented. The DRCS also intends to collate technical information on remedial actions taken or proposed, thus giving examples for consultation in similar cases. Hence, the information available in such a Directory is intended to provide decision makers with a useful reference frame for their own actions. In this the IAEA attempts to assume the role of a clearing-house of information pertinent to characterization of radioactively contaminated sites and their remediation and restoration

  10. Design criteria for a worldwide directory of radioactively contaminated sites (DRCS)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-11-01

    The publication attempts to fulfil two main objectives: (a) to describe the activities and underlying considerations and concepts for the development by the IAEA of a worldwide Directory of Radioactively Contaminated Sites; (b) to give some recommendations for the development of such directories at the Member States level. In addition to a discussion of the conceptual considerations on the design of an IAEA-level directory, the results of previous efforts on data collation are presented. The DRCS also intends to collate technical information on remedial actions taken or proposed, thus giving examples for consultation in similar cases. Hence, the information available in such a Directory is intended to provide decision makers with a useful reference frame for their own actions. In this the IAEA attempts to assume the role of a clearing-house of information pertinent to characterization of radioactively contaminated sites and their remediation and restoration.

  11. Directory of certificates of compliance for radioactive materials packages. Certificates of compliance

    International Nuclear Information System (INIS)

    1979-10-01

    This volume contains all Certificates of Compliance for radioactive material packages effective September 14, 1979. Purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory

  12. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

    Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First

  13. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

    Traditional Chinese medicine (TCM) is gaining increasing attention with the emergence of integrative medicine and personalized medicine, characterized by pattern differentiation on individual variance and treatments based on natural herbal synergism. Investigating the effectiveness and safety of the potential mechanisms of TCM and the combination principles of drug therapies will bridge the cultural gap with Western medicine and improve the development of integrative medicine. Dealing with rapidly growing amounts of biomedical data and their heterogeneous nature are two important tasks among modern biomedical communities. Bioinformatics, as an emerging interdisciplinary field of computer science and biology, has become a useful tool for easing the data deluge pressure by automating the computation processes with informatics methods. Using these methods to retrieve, store and analyze the biomedical data can effectively reveal the associated knowledge hidden in the data, and thus promote the discovery of integrated information. Recently, these techniques of bioinformatics have been used for facilitating the interactional effects of both Western medicine and TCM. The analysis of TCM data using computational technologies provides biological evidence for the basic understanding of TCM mechanisms, safety and efficacy of TCM treatments. At the same time, the carrier and targets associated with TCM remedies can inspire the rethinking of modern drug development. This review summarizes the significant achievements of applying bioinformatics techniques to many aspects of the research in TCM, such as analysis of TCM-related '-omics' data and techniques for analyzing biological processes and pharmaceutical mechanisms of TCM, which have shown certain potential of bringing new thoughts to both sides. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  14. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  15. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    Science.gov (United States)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  16. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

    The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.

  17. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    Science.gov (United States)

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  18. OpenHelix: bioinformatics education outside of a different box.

    Science.gov (United States)

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.

  19. A method of searching LDAP directories using XQuery

    International Nuclear Information System (INIS)

    Hesselroth, Ted

    2011-01-01

    A method by which an LDAP directory can be searched using XQuery is described. The strategy behind the tool consists of four steps. First the XQuery script is examined and relevant XPath expressions are extracted, determined to be sufficient to define all information needed to perform the query. Then the XPath expressions are converted into their equivalent LDAP search filters by use of the published LDAP schema of the service, and search requests are made to the LDAP host. The search results are then merged and converted to an XML document that conforms to the hierarchy of the LDAP schema. Finally, the XQuery script is executed on the working XML document by conventional means. Examples are given of application of the tool in the Open Science Grid, which for discovery purposes operates an LDAP server that contains Glue schema-based information on site configuration and authorization policies. The XQuery scripts compactly replace hundreds of lines of custom python code that relied on the unix ldapsearch utility. Installation of the tool is available through the Virtual Data Toolkit.

  20. Personnel involved in nuclear standards development: 1980 directory

    International Nuclear Information System (INIS)

    Carr, S.J.

    1980-03-01

    The development of nuclear standards is an active and necessary endeavor that is concerned with the safe, orderly, and economic development of nuclear potential. There are almost 4100 people from the teachnical community who are presently involved either in writing nuclear standards, including codes, or in the management and processing roles necessary for their approval and promulgation. This document identifies the current participation of each individual as member, chairman, cochairman (vice-chairman), or secretary of about 700 standards development committees and groups. The standards committees and groups are identified with the organizations that are responsible for the preparation, review, and maintenance of the standards and that provide support through supervisory committees and headquarters staff. This directory includes four major sections: personnel, employers, committees, and a Key-Word-in-Context (KWIC) Index of committee titles. It can also be used to identify the participation of employers as well as to recognize the contributions of individuals to the often interdisciplinary activity of standards development

  1. Personnel involved in nuclear standards development: 1980 directory

    Energy Technology Data Exchange (ETDEWEB)

    Carr, S.J. (ed.)

    1980-03-01

    The development of nuclear standards is an active and necessary endeavor that is concerned with the safe, orderly, and economic development of nuclear potential. There are almost 4100 people from the teachnical community who are presently involved either in writing nuclear standards, including codes, or in the management and processing roles necessary for their approval and promulgation. This document identifies the current participation of each individual as member, chairman, cochairman (vice-chairman), or secretary of about 700 standards development committees and groups. The standards committees and groups are identified with the organizations that are responsible for the preparation, review, and maintenance of the standards and that provide support through supervisory committees and headquarters staff. This directory includes four major sections: personnel, employers, committees, and a Key-Word-in-Context (KWIC) Index of committee titles. It can also be used to identify the participation of employers as well as to recognize the contributions of individuals to the often interdisciplinary activity of standards development.

  2. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

    Directory of Open Access Journals (Sweden)

    Thoraval Samuel

    2005-04-01

    Full Text Available Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. Results We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results can be reproduced or shared among users. Availability: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive, ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download. Conclusion From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous

  3. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  4. Bioinformatics for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Alberto Magi

    2010-09-01

    Full Text Available The emergence of next-generation sequencing (NGS platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.

  5. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    Yukinawa, N; Ishii, S; Takenouchi, T; Oba, S

    2008-01-01

    Multi-class classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. This article reviews two recent approaches to multi-class classification by combining multiple binary classifiers, which are formulated based on a unified framework of error-correcting output coding (ECOC). The first approach is to construct a multi-class classifier in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. In the second approach, misclassification of each binary classifier is formulated as a bit inversion error with a probabilistic model by making an analogy to the context of information transmission theory. Experimental studies using various real-world datasets including cancer classification problems reveal that both of the new methods are superior or comparable to other multi-class classification methods

  6. Data mining in bioinformatics using Weka.

    Science.gov (United States)

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-10-12

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it. http://www.cs.waikato.ac.nz/ml/weka.

  7. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

    Full Text Available Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  8. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  9. A directory of computer programs for assessment of radioactive waste disposal in geological formations. Volume 2

    International Nuclear Information System (INIS)

    Ashton, J.; Broyd, T.W.; Jones, M.A.; Knowles, N.C.; Liew, S.K.; Mawbey, C.S.; Read, D.; Smith, S.L.

    1993-01-01

    This directory describes computer programs suitable for the assessment of radioactive waste disposal facilities in geological formations. The programs, which are mainly applicable to the post-closure analysis of the repository, address combinations of the following topics: nuclide inventory, corrosion, leaching, geochemistry, geomechanics, heat transfer, groundwater flow, radionuclide migration, biosphere modelling, safety assessment and site evolution. A total of 320 programs are identified, of which 84 are reviewed in detail, 192 in summary and 44 in tabular fashion. Originally published in 1983, the directory was updated in 1985 with the addition of new programs and the revision of some of the existing program reviews. This directory has been completely rewritten in 1991 with the addition of more new programs and a full revision of all the existing program reviews, some of which have been deleted as they are no longer in general use. Although the directory is specific to the post-closure assessment of a repository site, some of the programs described can also be used in other areas of repository (e.g. repository design). This directory is composed of two volumes, the present volume is the second

  10. A directory of computer programs for assessment of radioactive waste disposal in geological formations. Volume 1

    International Nuclear Information System (INIS)

    Ashton, J.; Broyd, T.W.; Jones, M.A.; Knowles, N.C.; Liew, S.K.; Mawbey, C.S.; Read, D.; Smith, S.L.

    1993-01-01

    This directory describes computer programs suitable for the assessment of radioactive waste disposal facilities in geological formations. The programs, which are mainly applicable to the post-closure analysis of the repository, address combinations of the following topics: nuclide inventory, corrosion, leaching, geochemistry, geomechanics, heat transfer, groundwater flow, radionuclide migration, biosphere modelling, safety assessment and site evolution. A total of 320 programs are identified of which 84 are reviewed in detail, 192 in summary and 44 in tabular fashion. Originally published in 1983, the directory was updated in 1985 with the addition of new programs and the revision of some of the existing program reviews. This directory has been completely rewritten in 1991 with the addition of more new programs and a full revision of all the existing program reviews, some of which have been deleted as they are no longer in general use. Although the directory is specific to the post-closure assessment of a repository site, some of the programs described can also be used in other areas of repository (e.g. repository design). This directory is composed of two volumes, the present volume is the first

  11. FHIR Healthcare Directories: Adopting Shared Interfaces to Achieve Interoperable Medical Device Data Integration.

    Science.gov (United States)

    Tyndall, Timothy; Tyndall, Ayami

    2018-01-01

    Healthcare directories are vital for interoperability among healthcare providers, researchers and patients. Past efforts at directory services have not provided the tools to allow integration of the diverse data sources. Many are overly strict, incompatible with legacy databases, and do not provide Data Provenance. A more architecture-independent system is needed to enable secure, GDPR-compatible (8) service discovery across organizational boundaries. We review our development of a portable Data Provenance Toolkit supporting provenance within Health Information Exchange (HIE) systems. The Toolkit has been integrated with client software and successfully leveraged in clinical data integration. The Toolkit validates provenance stored in a Blockchain or Directory record and creates provenance signatures, providing standardized provenance that moves with the data. This healthcare directory suite implements discovery of healthcare data by HIE and EHR systems via FHIR. Shortcomings of past directory efforts include the ability to map complex datasets and enabling interoperability via exchange endpoint discovery. By delivering data without dictating how it is stored we improve exchange and facilitate discovery on a multi-national level through open source, fully interoperable tools. With the development of Data Provenance resources we enhance exchange and improve security and usability throughout the health data continuum.

  12. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    Science.gov (United States)

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  13. Bioinformatics education dissemination with an evolutionary problem solving perspective.

    Science.gov (United States)

    Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

    2010-11-01

    Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

  14. Bioinformatics and its application in animal health: a review | Soetan ...

    African Journals Online (AJOL)

    Bioinformatics is an interdisciplinary subject, which uses computer application, statistics, mathematics and engineering for the analysis and management of biological information. It has become an important tool for basic and applied research in veterinary sciences. Bioinformatics has brought about advancements into ...

  15. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...

  16. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    Science.gov (United States)

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  17. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  18. Concepts Of Bioinformatics And Its Application In Veterinary ...

    African Journals Online (AJOL)

    Bioinformatics has advanced the course of research and future veterinary vaccines development because it has provided new tools for identification of vaccine targets from sequenced biological data of organisms. In Nigeria, there is lack of bioinformatics training in the universities, expect for short training courses in which ...

  19. Current status and future perspectives of bioinformatics in Tanzania ...

    African Journals Online (AJOL)

    The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and ...

  20. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  1. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

    When bioinformatics education is considered, several issues are addressed. At the undergraduate level, the main issue revolves around conveying information from two main and different fields: biology and computer science. At the graduate level, the main issue is bridging the gap between biology students and computer science students. However, there is an educational component that is rarely addressed within the context of bioinformatics education: the ethics component. Here, a different perspective is provided on bioinformatics education, and the current status of ethics is analyzed within the existing bioinformatics programs. Analysis of the existing undergraduate and graduate programs, in both Europe and the United States, reveals the minimal attention given to ethics within bioinformatics education. Given that bioinformaticians speedily and effectively shape the biomedical sciences and hence their implications for society, here redesigning of the bioinformatics curricula is suggested in order to integrate the necessary ethics education. Unique ethical problems awaiting bioinformaticians and bioinformatics ethics as a separate field of study are discussed. In addition, a template for an "Ethics in Bioinformatics" course is provided.

  2. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

    Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

    2013-08-12

    Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

  3. LXtoo: an integrated live Linux distribution for the bioinformatics community.

    Science.gov (United States)

    Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

    2012-07-19

    Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  4. The development and application of bioinformatics core competencies to improve bioinformatics training and education.

    Science.gov (United States)

    Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D; Brooksbank, Cath; Gaeta, Bruno; Morgan, Sarah L; Pauley, Mark A; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie

    2018-02-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

  5. The development and application of bioinformatics core competencies to improve bioinformatics training and education

    Science.gov (United States)

    Brooksbank, Cath; Morgan, Sarah L.; Rosenwald, Anne; Warnow, Tandy; Welch, Lonnie

    2018-01-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. PMID:29390004

  6. A fuzzy-match search engine for physician directories.

    Science.gov (United States)

    Rastegar-Mojarad, Majid; Kadolph, Christopher; Ye, Zhan; Wall, Daniel; Murali, Narayana; Lin, Simon

    2014-11-04

    A search engine to find physicians' information is a basic but crucial function of a health care provider's website. Inefficient search engines, which return no results or incorrect results, can lead to patient frustration and potential customer loss. A search engine that can handle misspellings and spelling variations of names is needed, as the United States (US) has culturally, racially, and ethnically diverse names. The Marshfield Clinic website provides a search engine for users to search for physicians' names. The current search engine provides an auto-completion function, but it requires an exact match. We observed that 26% of all searches yielded no results. The goal was to design a fuzzy-match algorithm to aid users in finding physicians easier and faster. Instead of an exact match search, we used a fuzzy algorithm to find similar matches for searched terms. In the algorithm, we solved three types of search engine failures: "Typographic", "Phonetic spelling variation", and "Nickname". To solve these mismatches, we used a customized Levenshtein distance calculation that incorporated Soundex coding and a lookup table of nicknames derived from US census data. Using the "Challenge Data Set of Marshfield Physician Names," we evaluated the accuracy of fuzzy-match engine-top ten (90%) and compared it with exact match (0%), Soundex (24%), Levenshtein distance (59%), and fuzzy-match engine-top one (71%). We designed, created a reference implementation, and evaluated a fuzzy-match search engine for physician directories. The open-source code is available at the codeplex website and a reference implementation is available for demonstration at the datamarsh website.

  7. Biennial Supplement to The Directory of US Coal ampersand Technology Export Resources

    International Nuclear Information System (INIS)

    1991-10-01

    The purpose of this directory is to provide a listing of available US coal and coal related resources to potential purchasers of those resources abroad. The directory lists business entities within the United States which offer coal related resources, products and services for sale on the international market. Each listing is intended to describe the particular business niche or range of product and/or services offered by a particular company. The listing provides addresses, telephones, and telex/fax for key staff in each company committed to the facilitation of international trade. The content of each listing has been formulated especially for this directory and reflects data current as of the date of this edition

  8. Supporting the diffusion of healthy public policy in Canada: the Prevention Policies Directory.

    Science.gov (United States)

    Politis, Christopher E; Halligan, Michelle H; Keen, Deb; Kerner, Jon F

    2014-01-01

    Healthy public policy plays an essential role in a comprehensive public health approach to preventing cancer and chronic disease. Public policies spread through the 'policy diffusion' process, enabling governments to learn from another's enacted policy solutions. The Prevention Policies Directory (the Directory), an online database of municipal, provincial/territorial, and federal cancer and chronic disease prevention policies from across Canada, was developed to facilitate the diffusion of healthy public policies and support the work of prevention researchers, practitioners, and policy specialists. This information technology solution was implemented, through a participatory engagement approach, as a communication channel or policy knowledge transfer tool. It also addressed the intrinsic shortcomings of environmental scanning for policy surveillance and monitoring. A combination of quantitative web metrics and qualitative anecdotal evidence have illustrated that the Directory is becoming an important tool for healthy public policy surveillance and policy diffusion in Canada.

  9. Bioinformatics analyses of Shigella CRISPR structure and spacer classification.

    Science.gov (United States)

    Wang, Pengfei; Zhang, Bing; Duan, Guangcai; Wang, Yingfang; Hong, Lijuan; Wang, Linlin; Guo, Xiangjiao; Xi, Yuanlin; Yang, Haiyan

    2016-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.

  10. Directory of Certificates of Compliance for Radioactive Materials Packages: Report of NRC Approved Packages

    International Nuclear Information System (INIS)

    1993-10-01

    This directory contains a Report of NRC Approved Packages (Volume 1). The purpose of this directory is to make available a convenient source of information on Quality Assurance Programs and Packagings which have been approved by the US Nuclear Regulatory Commission. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  11. Bioinformatics research in the Asia Pacific: a 2007 update.

    Science.gov (United States)

    Ranganathan, Shoba; Gribskov, Michael; Tan, Tin Wee

    2008-01-01

    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

  12. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.

  13. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  14. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  15. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  16. Bioinformatics Analysis Reveals Genes Involved in the Pathogenesis of Ameloblastoma and Keratocystic Odontogenic Tumor.

    Science.gov (United States)

    Santos, Eliane Macedo Sobrinho; Santos, Hércules Otacílio; Dos Santos Dias, Ivoneth; Santos, Sérgio Henrique; Batista de Paula, Alfredo Maurício; Feltenberger, John David; Sena Guimarães, André Luiz; Farias, Lucyana Conceição

    2016-01-01

    Pathogenesis of odontogenic tumors is not well known. It is important to identify genetic deregulations and molecular alterations. This study aimed to investigate, through bioinformatic analysis, the possible genes involved in the pathogenesis of ameloblastoma (AM) and keratocystic odontogenic tumor (KCOT). Genes involved in the pathogenesis of AM and KCOT were identified in GeneCards. Gene list was expanded, and the gene interactions network was mapped using the STRING software. "Weighted number of links" (WNL) was calculated to identify "leader genes" (highest WNL). Genes were ranked by K-means method and Kruskal-Wallis test was used (Preview data was used to corroborate the bioinformatics data. CDK1 was identified as leader gene for AM. In KCOT group, results show PCNA and TP53 . Both tumors exhibit a power law behavior. Our topological analysis suggested leader genes possibly important in the pathogenesis of AM and KCOT, by clustering coefficient calculated for both odontogenic tumors (0.028 for AM, zero for KCOT). The results obtained in the scatter diagram suggest an important relationship of these genes with the molecular processes involved in AM and KCOT. Ontological analysis for both AM and KCOT demonstrated different mechanisms. Bioinformatics analyzes were confirmed through literature review. These results may suggest the involvement of promising genes for a better understanding of the pathogenesis of AM and KCOT.

  17. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisci......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...... into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....

  18. An Overview of Bioinformatics Tools and Resources in Allergy.

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

    The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

  19. Development of a cloud-based Bioinformatics Training Platform.

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

    2017-05-01

    The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

  20. Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

    OpenAIRE

    Whyte, Barry James

    2008-01-01

    The National Science Foundation has awarded the Virginia Bioinformatics Institute at Virginia Tech $918,000 to expand its education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring, commonly known as the CI-TEAM.

  1. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal; Salama, Khaled N.; Zidan, Mohammed A.

    2012-01-01

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we

  2. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  3. Bioinformatics Education in Pathology Training: Current Scope and Future Direction

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

    Full Text Available Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate, institutional support, educational resources, and adequate faculty expertise.

  4. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to clone Fusarium ...

  5. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrö nen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-01-01

    concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource

  6. Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

    The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

  7. Bioinformatics tools for development of fast and cost effective simple ...

    African Journals Online (AJOL)

    Bioinformatics tools for development of fast and cost effective simple sequence repeat ... comparative mapping and exploration of functional genetic diversity in the ... Already, a number of computer programs have been implemented that aim at ...

  8. Directory of certificates of compliance for radioactive materials packages. Volume 2. Certificates of compliance

    International Nuclear Information System (INIS)

    1977-12-01

    Purpose of this directory is to make available a convenient source of information on packagings which have been approved by the U.S. Nuclear Regulatory Commission. This volume contains all certificates of compliance for radioactive material packages effective Nov. 30, 1977

  9. Directory of certificates of compliance for radioactive materials packages. Volume 2, Revision 6

    International Nuclear Information System (INIS)

    1983-09-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure them that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note that the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR Parts 30 to 36, 40, 50, or 70

  10. Directory of certificates of compliance for radioactive materials packages. Certificates of compliance. Volume 2. Revision 9

    International Nuclear Information System (INIS)

    1986-10-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1). Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volumes 3). The purpose of this directory is make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure them that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note that the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR 30 to 36, 40, 50, or 70

  11. Directory of Certificates of Compliance for Radioactive Materials Packages. Certificates of Compliance. Volume 2, Revision 8

    International Nuclear Information System (INIS)

    1985-10-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure them that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note that the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR Parts 30 to 36, 40, 50, or 70

  12. Windows Server 2003 Active Directory Design and Implementation Creating, Migrating, and Merging Networks

    CERN Document Server

    Savill, John

    2005-01-01

    This book is for Windows network administrators, analysts, or architects,  with a grasp of the basic operations of Active Directory, and are looking for a book that goes beyond rudimentary operations. However, all of the concepts are explained from the g

  13. Films--Too Good for Words. A Directory of Nonnarrated 16mm Films.

    Science.gov (United States)

    Parlato, Salvatore J., Jr.

    A nonnarrated film is one that communicates pictorially on the strength of its visual unity, continuity, and coherence without relying on narration or dialogue. This directory lists 1,000 such 16mm films, mostly curriculum-oriented educational films, in three main parts. The first part describes films under subject headings such as the arts, other…

  14. Index/Directory of Women's Media. To Increase Communication Nationally and Internationally among Women.

    Science.gov (United States)

    Women's Inst. for Freedom of the Press, Washington, DC.

    This directory includes two sections: women's media groups, and individual media women and media-concerned women. In the first section, there are listings of periodicals, presses/publishers, news services, columns, radio-TV groups, regular programs-radio, regular programs-TV, video and cable, film, multi-media, music, arts, writers groups, public…

  15. Technical Profile of Seven Data Element Dictionary/Directory Systems. Computer Science & Technology Series.

    Science.gov (United States)

    Leong-Hong, Belkis; Marron, Beatrice

    A Data Element Dictionary/Directory (DED/D) is a software tool that is used to control and manage data elements in a uniform manner. It can serve data base administrators, systems analysts, software designers, and programmers by providing a central repository for information about data resources across organization and application lines. This…

  16. Directory of Facilities for Mentally Ill Children in the United States.

    Science.gov (United States)

    National Association for Mental Health, New York, NY.

    Facilities for mentally ill children are listed by states in this directory for parents and professional people. Each entry includes information on diagnostic considerations, capacity, admission criteria, whether the facility is residential or day care, geographic eligibility, and fees. Separate indexes list residential and day care facilities and…

  17. A directory of computer programs for assessment of radioactive waste disposal in geological formations

    International Nuclear Information System (INIS)

    Broyd, T.W.; Dean, R.B.; Hobbs, G.D.; Knowles, N.C.; Putney, J.M.; Wrigley, J.

    1984-01-01

    This Directory describes computer programs suitable for the assessment of radioactive waste disposal facilities in geological formations. The programs, which are mainly applicable to the post closure analysis of the repository, address combinations of the following topics: nuclide inventory, corrosion, leaching, geochemistry, stress analysis, heat transfer, groundwater flow and radionuclide transport. Biosphere modelling, surface water flow and risk analysis are not covered. A total of 248 programs are identified, of which 50 are reviewed in detail, 134 in summary and 64 in tabular fashion. The directory has been compiled using a combination of literature searches, telephone and postal correspondence and meetings with recognised experts in the respective areas of work covered. It differs from previous reviews of computer programs for similar topics areas in two main respects. Firstly, the method of obtaining information has resulted in program descriptions of considerable breadth and detail. Secondly, the Directory has concentrated wherever possible on European codes, whereas most previous work of this nature has looked solely at programs developed in North America. The reviews are presented in good faith, but it has not been possible to run any of the programs on a computer, and so truly objective comparisons may not be made. Finally, although the Directory is specific to the post-closure assessment of a repository site, some of the programs described could also be used in other areas of repository analysis (eg repository design)

  18. Self-Advocacy Groups: 1994-95 Directory for North America.

    Science.gov (United States)

    Hayden, Mary F.; Senese, Dick

    This 1994-95 directory of disability self-advocacy groups contains listings of over 700 organizations in the United States, Mexico, and Canada. The associations are organized by country and state or province. Listings typically contain the following information: the name of a contact (the name of the member who is the chair, president, or…

  19. Microform Market Place 1974/1975. An International Directory of Micropublishing.

    Science.gov (United States)

    Veaner, Allen B., Ed.; Meckler, Alan M., Ed.

    The information for this international buyer's guide for the microform purchaser was gathered from questionnaires to the publishers themselves. The guide is divided into eight sections: directory of micropublishers, mergers and acquisitions, bibliography of first sources for the microform library, microform jobbers, organizations, a geographical…

  20. Directory of certificates of compliance for radioactive materials packages: certificates of compliance. Volume 2, Revision 7

    International Nuclear Information System (INIS)

    1984-11-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR Parts 30 to 36, 40, 50, or 70

  1. Directory of certificates of compliance for radioactive materials packages; Summary Report of NRC Approved Packages

    International Nuclear Information System (INIS)

    1980-12-01

    This directory contains a Summary Report of NRC approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the U.S. Nuclear Regulatory Commission. To assist in identifying packaging, and index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material using these packagings must be in accordance with the provisions of 49 CFR 173.393a and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure them--that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  2. Member and Affiliate Contact Directory. Triangle Coalition for Science and Technology Education. Second Edition.

    Science.gov (United States)

    Triangle Coalition for Science and Technology Education, College Park, MD.

    This directory is designed to assist local action groups (existing local alliances; science mathematics, and technology teachers; superintendents, principals, and supervisors; guidance counselors and resource specialists; and university and college professors) in making contact with the local structure of the Triangle Coalition for Science and…

  3. The Easter Seal Directory of Resident Camps for Persons with Special Health Needs.

    Science.gov (United States)

    National Easter Seal Society for Crippled Children and Adults, Chicago, IL.

    The directory of resident camps is designed for persons with special health needs (children and adults with physical, mental, social, or emotional handicaps). Published by the National Easter Seal Society for Crippled Children and Adults, the listing contains residential facilities only (day care camp program information is not included). Listed…

  4. Directory of Academic Institutions and Organizations Offering Drug, Alcohol, and Employee Assistance Program Educational Resources.

    Science.gov (United States)

    National Inst. on Drug Abuse (DHHS/PHS), Rockville, MD.

    This directory lists academic institutions, State offices of alcohol and drug abuse, and national organizations which offer drug, alcohol, and employee assistance program (EAP) educational resources. A matrix format is used. Entries include name, address, telephone number, and contact person. A dot appears directly under column headings which are…

  5. Use of World Wide Web-based directories for tracing subjects in epidemiologic studies.

    Science.gov (United States)

    Koo, M M; Rohan, T E

    2000-11-01

    The recent availability of World Wide Web-based directories has opened up a new approach for tracing subjects in epidemiologic studies. The completeness of two World Wide Web-based directories (Canada411 and InfoSpace Canada) for subject tracing was evaluated by using a randomized crossover design for 346 adults randomly selected from respondents in an ongoing cohort study. About half (56.4%) of the subjects were successfully located by using either Canada411 or InfoSpace. Of the 43.6% of the subjects who could not be located using either directory, the majority (73.5%) were female. Overall, there was no clear advantage of one directory over the other. Although Canada411 could find significantly more subjects than InfoSpace, the number of potential matches returned by Canada411 was also higher, which meant that a longer list of potential matches had to be examined before a true match could be found. One strategy to minimize the number of potential matches per true match is to first search by InfoSpace with the last name and first name, then by Canada411 with the last name and first name, and finally by InfoSpace with the last name and first initial. Internet-based searches represent a potentially useful approach to tracing subjects in epidemiologic studies.

  6. 76 FR 68775 - Renewal of Information Collection for Source Directory Publication

    Science.gov (United States)

    2011-11-07

    .... Internet Web site address To identify whether the business advertises and/or sells inventory online. Main... Businesses (Source Directory). In compliance with the Paperwork Reduction Act of 1995, the IACB has submitted... owned and operated arts and crafts businesses that may be accessed by the public on the Indian Arts and...

  7. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  8. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  9. An innovative approach for testing bioinformatics programs using metamorphic testing

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

    Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work

  10. BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

    Science.gov (United States)

    Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

    2015-06-02

    Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

  11. Comparing the Scale of Web Subject Directories Precision in Technical-Engineering Information Retrieval

    Directory of Open Access Journals (Sweden)

    Mehrdokht Wazirpour Keshmiri

    2012-07-01

    Full Text Available The main purpose of this research was to compare the scale of web subject directories precision in information retrieval of technical-engineering science. Information gathering was documentary and webometric. Keywords of technical-engineering science were chosen at twenty different subjects from IEEE (Institute of Electrical and Electronics Engineers and engineering magazines that situated in sciencedirect site. These keywords are used at five subject directories Yahoo, Google, Infomine, Intute, Dmoz, that were web directories high-utilization. Usually first results in searching tools are connected to searching keywords. Because, first ten results was evaluated in every search. These assessments to consist of scale of precision, scale of error, scale retrieval items in technical-engineering categories to retrieval items entirely. The used criteria for determining the scale of precision that was according to high-utilization standards in different documents, to consist of presence of the keywords in title, appearance of keywords at the part of web retrieved pages, keywords adjacency, URL of page, page description and subject categories. Information analysis was according to Kruskal-Wallis Test and L.S.D fisher. Results revealed that there was meaningful difference about precision of web subject directories in information retrieval of technical-engineering science, Therefore this theory was confirmed.web subject directories ranked from point of precision as follows. Google, Yahoo, Intute, Dmoz, and Infomine. The scale of observed error at the first results was another criterion that was used for comparing web subject directories. In this research, Yahoo had minimum scale of error and Infomine had most of error. This research also compared the scale of retrieval items in all of categories web subject directories entirely to retrieval items in technical-engineering categories, results revealed that there was meaningful difference between them. And

  12. Directory of cyclotrons used for radionuclide production in Member States [2006 update

    International Nuclear Information System (INIS)

    2006-10-01

    The present directory of cyclotron facilities used for the production of radionuclides in Member States is an update of the one compiled by the International Atomic Energy Agency (IAEA) in late 2001 and published in 2002. This directory was prepared through information collected by questionnaires that the IAEA sent to known institutions operating cyclotrons for radionuclide production. Technical as well as administrative data supplied to the IAEA as of November 2005 were taken into account. The directory is considered to include most of the cyclotrons of the world that are used at least partially for radionuclide production. There are 262 entries for cyclotrons operating in 39 Member States of the IAEA. This is an increase of 7% over the 246 reported in the 2002 cyclotron directory. This can be compared to the 350 or so cyclotrons believed to be presently operating in the world, which are involved in some aspects of radionuclide production. The increase has been in the number of cyclotrons in developed countries, but even more so in the developing countries. The increase in number during the last four years was driven by several factors, i.e. advent of advances in medical imaging, introduction of compact, user friendly medical cyclotron, and a recent decision that costs for 15 O-oxygen position emission tomography (PET) studies in Japan and 18 F-FDG PET studies in Germany and the United States of America are eligible for reimbursement by government or health insurance companies. There is no doubt that the fastest growing segment of the market is in the commercial distribution of FDG to local hospitals. The IAEA is promoting cyclotron technology as applied to nuclear medicine. Requests for cyclotron technology is steadily increasing; many developing Member States are interested in this technology. There is need to stimulate, build and maintain consulting capability in interested developing Member States. There are good reasons to believe that the number of cyclotron

  13. Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

    Full Text Available As a focal point of biotechnology, bioinformatics integrates knowledge from biology, mathematics, physics, chemistry, computer science and information science. It generally deals with genome informatics, protein structure and drug design. However, the data or information thus acquired from the main areas of bioinformatics may not be effective. Some researchers combined bioinformatics with wireless sensor network (WSN into biosensor and other tools, and applied them to such areas as fermentation, environmental monitoring, food engineering, clinical medicine and military. In the combination, the WSN is used to collect data and information. The reliability of the WSN in bioinformatics is the prerequisite to effective utilization of information. It is greatly influenced by factors like quality, benefits, service, timeliness and stability, some of them are qualitative and some are quantitative. Hence, it is necessary to develop a method that can handle both qualitative and quantitative assessment of information. A viable option is the fuzzy linguistic method, especially 2-tuple linguistic model, which has been extensively used to cope with such issues. As a result, this paper introduces 2-tuple linguistic representation to assist experts in giving their opinions on different WSNs in bioinformatics that involve multiple factors. Moreover, the author proposes a novel way to determine attribute weights and uses the method to weigh the relative importance of different influencing factors which can be considered as attributes in the assessment of the WSN in bioinformatics. Finally, an illustrative example is given to provide a reasonable solution for the assessment.

  14. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Directory of Open Access Journals (Sweden)

    Enis Afgan

    Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints

  15. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Science.gov (United States)

    Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

    2015-01-01

    Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the

  16. Directory of certificates of compliance for radioactive materials packages: Report of NRC approved quality assurance programs for radioactive materials packages

    International Nuclear Information System (INIS)

    1990-10-01

    The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  17. Directory of certificates of compliance for radioactive materials packages: Report of NRC approved quality assurance programs for radioactive materials packages

    International Nuclear Information System (INIS)

    1989-10-01

    The purpose of this directory is to make available a convenient source of information on packaging which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  18. Evolution of web services in bioinformatics

    NARCIS (Netherlands)

    Neerincx, P.B.T.; Leunissen, J.A.M.

    2005-01-01

    Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore,

  19. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

    Science.gov (United States)

    Ibrahim, Bashar; Arkhipova, Ksenia; Andeweg, Arno C; Posada-Céspedes, Susana; Enault, François; Gruber, Arthur; Koonin, Eugene V; Kupczok, Anne; Lemey, Philippe; McHardy, Alice C; McMahon, Dino P; Pickett, Brett E; Robertson, David L; Scheuermann, Richard H; Zhernakova, Alexandra; Zwart, Mark P; Schönhuth, Alexander; Dutilh, Bas E; Marz, Manja

    2018-05-14

    The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

  20. Biometry, biometrics, biostatistics, bioinformatics, . . . , bio-X

    OpenAIRE

    Molenberghs, Geert

    2005-01-01

    Recent scientific evolutions force us to rethink our profession's position on the scientific map, in relation to our neighboring professions, the ones with which we traditionally have strong collaborative links as well as the newly emerging fields, but also within our own, diverse professional group. We will show that great inspiration can be drawn from our own history, in fact from the early days of the Society. A recent inspiring example has been set by the late Rob Kempton, who died sudden...

  1. User Management with LDAP(Light weight Directory Access Protocolfor access to technology and Information Services in Companies

    Directory of Open Access Journals (Sweden)

    José Teodoro Mejía Viteri

    2016-08-01

    Full Text Available This research aims to conduct an analysis of management services information and users with LDAP (Lightweight / Simplified Directory Access Protocol, their interaction with other technology services company, allowing it to be accessed through a single user and password. This study allowed us to collect information through a literature review on the LDAP service and its ability to interact with your user directory Open source technology services; also with Windows Server and Active Directory service is used by companies for their ease of management and access resources on Windows clients; is intended to provide an alternative for the implementation of each of the services required by public and private companies with tools free use and access to services for management and administration can be done by integrating or synchronizing with the directory LDAP.

  2. Directory of certificates of compliance for radioactive materials packages: Report of NRC approved quality assurance programs for radioactive material packages

    International Nuclear Information System (INIS)

    1988-12-01

    This directory contains a Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), all Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Material Packages effective October 1, 1988. The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volume 2 of the directory. A listing by packaging types is included in the back of Volume 2. An alphabetical listing by Company name is included in the back of Volume 3 for approved QA programs. The Reports include a listing of all users of each package design and approved QA programs prior to the publication date of the directory

  3. A directory of information resources on radioactive waste management, decontamination and decommissioning, and environmental restoration. Data as of June 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-11-01

    This directory is intended to aid scientists, engineers, policy makers and managers in finding other information sources in addition to the information they derive from their personal contacts. 14 refs, 11 tabs.

  4. A directory of information resources on radioactive waste management, decontamination and decommissioning, and environmental restoration. Data as of June 1995

    International Nuclear Information System (INIS)

    1995-11-01

    This directory is intended to aid scientists, engineers, policy makers and managers in finding other information sources in addition to the information they derive from their personal contacts. 14 refs, 11 tabs

  5. Biometry, biometrics, biostatistics, bioinformatics,..., bio-X.

    Science.gov (United States)

    Molenberghs, Geert

    2005-03-01

    Recent scientific evolutions force us to rethink our profession's position on the scientific map, in relation to our neighboring professions, the ones with which we traditionally have strong collaborative links as well as the newly emerging fields, but also within our own, diverse professional group. We will show that great inspiration can be drawn from our own history, in fact from the early days of the Society. A recent inspiring example has been set by the late Rob Kempton, who died suddenly just months before he was to become President of the International Biometric Society.

  6. Bioinformatics in the Netherlands: the value of a nationwide community.

    Science.gov (United States)

    van Gelder, Celia W G; Hooft, Rob W W; van Rijswijk, Merlijn N; van den Berg, Linda; Kok, Ruben G; Reinders, Marcel; Mons, Barend; Heringa, Jaap

    2017-09-15

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. © The Author 2017. Published by Oxford University Press.

  7. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Science.gov (United States)

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  8. Global Change Master Directory (GCMD) Keywords and Their Applications in Earth Science Data Discovery

    Science.gov (United States)

    Aleman, A.

    2017-12-01

    This presentation will provide an overview and discussion of the Global Change Master Directory (GCMD) Keywords and their applications in Earth science data discovery. The GCMD Keywords are a hierarchical set of controlled keywords covering the Earth science disciplines, including: science keywords, service keywords, data centers, projects, location, data resolution, instruments and platforms. Controlled vocabularies (keywords) help users accurately, consistently and comprehensively categorize their data and also allow for the precise search and subsequent retrieval of data. The GCMD Keywords are a community resource and are developed collaboratively with input from various stakeholders, including GCMD staff, keyword users and metadata providers. The GCMD Keyword Landing Page and GCMD Keyword Community Forum provide access to keyword resources and an area for discussion of topics related to the GCMD Keywords. See https://earthdata.nasa.gov/about/gcmd/global-change-master-directory-gcmd-keywords

  9. A Directory Service for the CERN PS/SL Java Programming Interface

    International Nuclear Information System (INIS)

    Cuperus, J.; Charrue, P.; DiMaio, F.; Kostro, K.; Watson, W.

    1999-01-01

    The CERN PS and SL accelerator control groups developed a common application programming interface (API) in Java [1]. Part of this API is a directory service that provide information about the underlying hardware and software. With this information, it is possible to write generic programs that do general actions on lists of devices without hard coding of device names. And, starting from a device name, full details about related devices, the device itself and its class and properties, can be obtained, including the meaning of bits and bit-patterns in status words. The interface definition is independent of any implementation but a reference implementation is provided using Java Database Connectivity (JDBC) against a set of tables in a relational database. Data from very different systems can be brought together and presented in a uniform way to the user. The full potential of the directory service is reached when it is used in software components (Java Beans)

  10. Environmental cleanup privatization, products and services directory, January 1997. Second edition

    International Nuclear Information System (INIS)

    1997-01-01

    The US Department of Energy has undertaken an ambitious ''Ten Year Plan'' for the Weapons Complex, an initiative to complete cleanup at most nuclear sites within a decade. This Second Edition of the Directory is designed to facilitate privatization which is key to the success of the Plan. The Directory is patterned after the telephone Yellow Pages. Like the Yellow Pages, it provides the user with points of contact for inquiring further into the capabilities of the listed companies. This edition retains the original format of three major sections under the broad headings: Treatment, Characterization, and Extraction/Deliver/Materials Handling. Within each section, companies are listed alphabetically. Also, ''company name'' and ''process type'' indices are provided at the beginning of each section to allow the user quick access to listings of particular interest

  11. Environmental cleanup privatization, products and services directory, January 1997. Second edition

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-01-01

    The US Department of Energy has undertaken an ambitious ``Ten Year Plan`` for the Weapons Complex, an initiative to complete cleanup at most nuclear sites within a decade. This Second Edition of the Directory is designed to facilitate privatization which is key to the success of the Plan. The Directory is patterned after the telephone Yellow Pages. Like the Yellow Pages, it provides the user with points of contact for inquiring further into the capabilities of the listed companies. This edition retains the original format of three major sections under the broad headings: Treatment, Characterization, and Extraction/Deliver/Materials Handling. Within each section, companies are listed alphabetically. Also, ``company name`` and ``process type`` indices are provided at the beginning of each section to allow the user quick access to listings of particular interest.

  12. Directory of certificates of compliance for radioactive materials packages. Volume 2, Revision 17: Certificates of compliance

    International Nuclear Information System (INIS)

    1994-10-01

    This directory contains a Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Report of NRC Approved Quality Assurance Programs for Radioactive Materials Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on Quality Assurance Programs and Packagings which have been approved by the US Nuclear Regulatory Commission. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR section 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure themselves that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program

  13. Annual report of the Brazilian Directory of R and D - 1995

    International Nuclear Information System (INIS)

    1996-03-01

    The Directory of Research and Development of the Brazilian CNEN (National Nuclear Energy Commission) presents the report for 1995. The publication describes and cover activities carried out in the following areas: nuclear reactors, nuclear fuel cycle, control and instrumentation, application of nuclear techniques, radioisotope production, materials of nuclear interest, radioactive wastes and irradiated materials. Three institutes accomplish Directory's Programme: Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/MG); Instituto de Engenharia Nuclear (IEN/RJ); and Instituto de Pesquisas Energeticas e Nucleares (IPEN/SP). It is important to mention that the Institutes carry out a numberless of activities in cooperation with others institutions such as: universities, industries, private and government organizations. This cooperation is administrated through research contracts and agreements. 28 figs., 11 tabs

  14. Linked Ocean Data

    Science.gov (United States)

    Leadbetter, Adam; Arko, Robert; Chandler, Cynthia; Shepherd, Adam

    2014-05-01

    "Linked Data" is a term used in Computer Science to encapsulate a methodology for publishing data and metadata in a structured format so that links may be created and exploited between objects. Berners-Lee (2006) outlines the following four design principles of a Linked Data system: Use Uniform Resource Identifiers (URIs) as names for things. Use HyperText Transfer Protocol (HTTP) URIs so that people can look up those names. When someone looks up a URI, provide useful information, using the standards (Resource Description Framework [RDF] and the RDF query language [SPARQL]). Include links to other URIs so that they can discover more things. In 2010, Berners-Lee revisited his original design plan for Linked Data to encourage data owners along a path to "good Linked Data". This revision involved the creation of a five star rating system for Linked Data outlined below. One star: Available on the web (in any format). Two stars: Available as machine-readable structured data (e.g. An Excel spreadsheet instead of an image scan of a table). Three stars: As two stars plus the use of a non-proprietary format (e.g. Comma Separated Values instead of Excel). Four stars: As three stars plus the use of open standards from the World Wide Web Commission (W3C) (i.e. RDF and SPARQL) to identify things, so that people can point to your data and metadata. Five stars: All the above plus link your data to other people's data to provide context Here we present work building on the SeaDataNet common vocabularies served by the NERC Vocabulary Server, connecting projects such as the Rolling Deck to Repository (R2R) and the Biological and Chemical Oceanography Data Management Office (BCO-DMO) and other vocabularies such as the Marine Metadata Interoperability Ontology Register and Repository and the NASA Global Change Master Directory to create a Linked Ocean Data cloud. Publishing the vocabularies and metadata in standard RDF XML and exposing SPARQL endpoints renders them five-star Linked

  15. Nuclear Regulatory Commission directory of high-technology 8(a) firms. Revision 1

    International Nuclear Information System (INIS)

    1986-05-01

    An overview is given for each of the high-technology small business firms qualifying under section 8(a) of the Small Business Act for consideration under Minority Business Development Plans. Each overview gives detailed profiles of relevant technical classification data, client contacts, and information on the professional personnel of each firm. In addition, the directory contains information about average gross receipts and facilities, including testing capabilities and computer availability

  16. Directory of national competent authorities' approval certificates for package design and shipment of radioactive material

    International Nuclear Information System (INIS)

    1990-04-01

    The authorization of packages and shipments of radioactive materials are issued in the form of certificates by the national competent authority of the IAEA Member State in which the package is designed or from which a shipment originates, and may be validated or endorsed by the corresponding authority of other Member States as the need arises. This directory summarizes in tabular form the key information on existing package approval certificates contained in PACKTRAM database. 5 tabs

  17. A directory of computer software applications: energy. Report for 1974--1976

    International Nuclear Information System (INIS)

    Grooms, D.W.

    1977-04-01

    The computer programs or the computer program documentation cited in this directory have been developed for a variety of applications in the field of energy. The cited computer software includes applications in solar energy, petroleum resources, batteries, electrohydrodynamic generators, magnetohydrodynamic generators, natural gas, nuclear fission, nuclear fusion, hydroelectric power production, and geothermal energy. The computer software cited has been used for simulation and modeling, calculations of future energy requirements, calculations of energy conservation measures, and computations of economic considerations of energy systems

  18. Genomics and bioinformatics resources for translational science in Rosaceae.

    Science.gov (United States)

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  19. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    Science.gov (United States)

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  20. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik

    2013-01-01

    their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes...... to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse...

  1. PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

    Science.gov (United States)

    Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

    2017-11-01

    High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.

  2. Construction of a bibliographic information database and a web directory for the nuclear science and engineering

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jeong Hoon; Kim, Tae Whan; Lee, Ji Ho; Chun, Young Chun; Yu, An Na

    2005-11-15

    The objective of this project is to construct the bibliographic information database and the web directory in the nuclear field. Its construction is very timely and important. Because nuclear science and technology has an considerable effect all over the other sciences and technologies due to its property of giant and complex engineering. We aimed to firmly build up a basis of efficient management of the bibliographic information database and the web directory in the nuclear field. The results of this project that we achieved in this year are as follows : first, construction of the bibliographic information database in the nuclear field(the target title: 1,500 titles ; research report: 1,000 titles, full-text report: 250 titles, full-text article: 250 titles). Second, completion of construction of the web directory in the nuclear field by using SWING (the total figure achieved : 2,613 titles). We plan that we will positively give more information to the general public interested in the nuclear field and to the experts of the field through this bibliographic information database on KAERI's home page, KAERI's electronic library and other related sites as well as participation at various seminars and meetings related to the nuclear field.

  3. A tale of two directories Implementing distributed shared objects in Java

    CERN Document Server

    Herlihy, M

    1999-01-01

    A directory service keep tracks of the location and status of mobile objects in a distributed system. This paper describes our experience implementing two distributed directory protocols as part of the Aleph toolkit, a distributed shared object system implemented in Java. One protocol is a conventional home-based protocol, in which a fixed node keeps track of the object's location and status. The other is a novel arrow protocol, based on a simple path-reversal algorithm. We were surprised to discover that the arrow protocol outperformed the home protocol, sometimes substantially, across a range of system sizes. This paper describes a series of experiments testing whether the discrepancy is due to an artifact of the Java run-time system (such as differences in thread management or object serialization costs), or whether it is something inherent in the protocols themselves. In the end, we use insights gained from these experimental results to design a new directory protocol that usually outperforms both. (29 re...

  4. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  5. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

    Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

    2005-09-01

    The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

  6. Directory of certificates of compliance for radioactive materials packages. Volume 3, revision 1. Summary report of NRC approved quality assurance programs for radioactive material packages

    International Nuclear Information System (INIS)

    1981-12-01

    The directory contains a Summary Report of NRC approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the U.S. Nuclear Regulatory Commission. To assist in identifying packaging, and index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory

  7. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  8. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  9. Bioinformatics in the Netherlands : The value of a nationwide community

    NARCIS (Netherlands)

    van Gelder, Celia W.G.; Hooft, Rob; van Rijswijk, Merlijn; van den Berg, Linda; Kok, Ruben; Reinders, M.J.T.; Mons, Barend; Heringa, Jaap

    2017-01-01

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures

  10. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no ...

  11. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  12. Hidden in the Middle: Culture, Value and Reward in Bioinformatics

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…

  13. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    Science.gov (United States)

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

  14. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  15. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  16. Rapid cloning and bioinformatic analysis of spinach Y chromosome ...

    Indian Academy of Sciences (India)

    Rapid cloning and bioinformatic analysis of spinach Y chromosome- specific EST sequences. Chuan-Liang Deng, Wei-Li Zhang, Ying Cao, Shao-Jing Wang, ... Arabidopsis thaliana mRNA for mitochondrial half-ABC transporter (STA1 gene). 389 2.31E-13. 98.96. SP3−12. Betula pendula histidine kinase 3 (HK3) mRNA, ...

  17. Staff Scientist - RNA Bioinformatics | Center for Cancer Research

    Science.gov (United States)

    The newly established RNA Biology Laboratory (RBL) at the Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) in Frederick, Maryland is recruiting a Staff Scientist with strong expertise in RNA bioinformatics to join the Intramural Research Program’s mission of high impact, high reward science. The RBL is the equivalent of an

  18. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  19. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

    Directory of Open Access Journals (Sweden)

    Tilmann Weber

    2016-06-01

    Full Text Available Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

  20. A P2P Framework for Developing Bioinformatics Applications in Dynamic Cloud Environments

    Directory of Open Access Journals (Sweden)

    Chun-Hung Richard Lin

    2013-01-01

    Full Text Available Bioinformatics is advanced from in-house computing infrastructure to cloud computing for tackling the vast quantity of biological data. This advance enables large number of collaborative researches to share their works around the world. In view of that, retrieving biological data over the internet becomes more and more difficult because of the explosive growth and frequent changes. Various efforts have been made to address the problems of data discovery and delivery in the cloud framework, but most of them suffer the hindrance by a MapReduce master server to track all available data. In this paper, we propose an alternative approach, called PRKad, which exploits a Peer-to-Peer (P2P model to achieve efficient data discovery and delivery. PRKad is a Kademlia-based implementation with Round-Trip-Time (RTT as the associated key, and it locates data according to Distributed Hash Table (DHT and XOR metric. The simulation results exhibit that our PRKad has the low link latency to retrieve data. As an interdisciplinary application of P2P computing for bioinformatics, PRKad also provides good scalability for servicing a greater number of users in dynamic cloud environments.

  1. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  2. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  3. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

    Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  4. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    Science.gov (United States)

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  5. Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of…

  6. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    Science.gov (United States)

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  7. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    Science.gov (United States)

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  8. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    Science.gov (United States)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    / H. Kamimura -- Massive collection of full-length complementary DNA clones and microarray analyses: keys to rice transcriptome analysis / S. Kikuchi -- Changes of influenza A(H5) viruses by means of entropic chaos degree / K. Sato and M. Ohya -- Basics of genome sequence analysis in bioinformatics - its fundamental ideas and problems / T. Suzuki and S. Miyazaki -- A basic introduction to gene expression studies using microarray expression data analysis / D. Wanke and J. Kilian -- Integrating biological perspectives: a quantum leap for microarray expression analysis / D. Wanke ... [et al.].

  9. The Antarctic Master Directory -- the Electronic Card Catalog of Antarctic Data

    Science.gov (United States)

    Scharfen, G.; Bauer, R.

    2003-12-01

    The Antarctic Master Directory (AMD) is a Web-based, searchable record of thousands of Antarctic data descriptions. These data descriptions contain information about what data were collected, where they were collected, when they were collected, who the scientists are, who the point of contact is, how to get the data, and information about the format of the data and what documentation and bibliographic information exists. With this basic descriptive information about content and access for thousands of Antarctic scientific data sets, the AMD is a resource for scientists to advertise the data they have collected and to search for data they need. The AMD has been created by more than twenty nations which conduct research in the Antarctic under the auspices of the Antarctic Treaty. It is a part of the International Directory Network/Global Change Master Directory (IDN/GCMD). Using the AMD is easy. Users can search on subject matter key words, data types, geographic place-names, temporal or spatial ranges, or conduct free-text searches. To search the AMD go to: http://gcmd.nasa.gov/Data/portals/amd/. Contributing your own data descriptions for Antarctic data that you have collected is also easy. Scientists can start by submitting a short data description first (as a placeholder in the AMD, and to satisfy National Science Foundation (NSF) reporting requirements), and then add to, modify or update their record whenever it is appropriate. An easy to use on-line tool and a simple tutorial are available at: http://nsidc.org/usadcc. With NSF Office of Polar Programs (OPP) funding, the National Snow and Ice Data Center (NSIDC) operates the U.S. Antarctic Data Coordination Center (USADCC), partly to assist scientists in using and contributing to the AMD. The USADCC website is at http://nsidc.org/usadcc.

  10. Directory of Certificates of Compliance for radioactive materials packages: Certificates of Compliance. Volume 2, Revision 18

    International Nuclear Information System (INIS)

    1995-10-01

    The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volumes 1 and 2. An alphabetical listing by user name is included in the back of Volume 3 of approved QA programs. The reports include a listing of all users of each package design and approved QA programs prior to the publication date

  11. Directory of Certificates of Compliance for radioactive materials packages: Certificates of Compliance. Volume 2, Revision 18

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance Number is included at the front of Volumes 1 and 2. An alphabetical listing by user name is included in the back of Volume 3 of approved QA programs. The reports include a listing of all users of each package design and approved QA programs prior to the publication date.

  12. Experimental Directory Structure (Exdir: An Alternative to HDF5 Without Introducing a New File Format

    Directory of Open Access Journals (Sweden)

    Svenn-Arne Dragly

    2018-04-01

    Full Text Available Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available specifications which facilitate data sharing and reproducible research. Hierarchical Data Format 5 (HDF5 is a popular open format widely used in neuroscience, often as a foundation for other, more specialized formats. However, drawbacks related to HDF5's complex specification have initiated a discussion for an improved replacement. We propose a novel alternative, the Experimental Directory Structure (Exdir, an open specification for data storage in experimental pipelines which amends drawbacks associated with HDF5 while retaining its advantages. HDF5 stores data and metadata in a hierarchy within a complex binary file which, among other things, is not human-readable, not optimal for version control systems, and lacks support for easy access to raw data from external applications. Exdir, on the other hand, uses file system directories to represent the hierarchy, with metadata stored in human-readable YAML files, datasets stored in binary NumPy files, and raw data stored directly in subdirectories. Furthermore, storing data in multiple files makes it easier to track for version control systems. Exdir is not a file format in itself, but a specification for organizing files in a directory structure. Exdir uses the same abstractions as HDF5 and is compatible with the HDF5 Abstract Data Model. Several research groups are already using data stored in a directory hierarchy as an alternative to HDF5, but no common standard exists. This complicates and limits the opportunity for data sharing and development of common tools for reading, writing, and analyzing data. Exdir facilitates improved data storage, data sharing, reproducible research, and novel

  13. Experimental Directory Structure (Exdir): An Alternative to HDF5 Without Introducing a New File Format.

    Science.gov (United States)

    Dragly, Svenn-Arne; Hobbi Mobarhan, Milad; Lepperød, Mikkel E; Tennøe, Simen; Fyhn, Marianne; Hafting, Torkel; Malthe-Sørenssen, Anders

    2018-01-01

    Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available specifications which facilitate data sharing and reproducible research. Hierarchical Data Format 5 (HDF5) is a popular open format widely used in neuroscience, often as a foundation for other, more specialized formats. However, drawbacks related to HDF5's complex specification have initiated a discussion for an improved replacement. We propose a novel alternative, the Experimental Directory Structure (Exdir), an open specification for data storage in experimental pipelines which amends drawbacks associated with HDF5 while retaining its advantages. HDF5 stores data and metadata in a hierarchy within a complex binary file which, among other things, is not human-readable, not optimal for version control systems, and lacks support for easy access to raw data from external applications. Exdir, on the other hand, uses file system directories to represent the hierarchy, with metadata stored in human-readable YAML files, datasets stored in binary NumPy files, and raw data stored directly in subdirectories. Furthermore, storing data in multiple files makes it easier to track for version control systems. Exdir is not a file format in itself, but a specification for organizing files in a directory structure. Exdir uses the same abstractions as HDF5 and is compatible with the HDF5 Abstract Data Model. Several research groups are already using data stored in a directory hierarchy as an alternative to HDF5, but no common standard exists. This complicates and limits the opportunity for data sharing and development of common tools for reading, writing, and analyzing data. Exdir facilitates improved data storage, data sharing, reproducible research, and novel insight from

  14. Directory of Solar Energy Research Activities in the United States: First Edition, May 1980. [1220 projects

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-05-01

    Information covering 1220, FY 1978 and FY 1979 solar energy research projects is included. In addition to the title and text of project summaries, the directory contains the following indexes: subject index, investigator index, performing organization index, and supporting organization index. This information was registered with the Smithsonian Science Information Exchange by Federal, State, and other supporting organizations. The project summaries are categorized in the following areas: biomass, ocean energy, wind energy,photovoltaics, photochemical energy conversion, photobiological energy conversion, solar heating and cooling, solar process heat, solar collectors and concentrators, solar thermal electric generation, and other solar energy conversion. (WHK)

  15. Nuclear Fuel Cycle Information System. A directory of nuclear fuel cycle facilities. 2009 ed

    International Nuclear Information System (INIS)

    2009-04-01

    The Nuclear Fuel Cycle Information System (NFCIS) is an international directory of civilian nuclear fuel cycle facilities, published online as part of the Integrated Nuclear Fuel Cycle Information System (iNFCIS: http://www-nfcis.iaea.org/). This is the fourth hardcopy publication in almost 30 years and it represents a snapshot of the NFCIS database as of the end of 2008. Together with the attached CD-ROM, it provides information on 650 civilian nuclear fuel cycle facilities in 53 countries, thus helping to improve the transparency of global nuclear fuel cycle activities

  16. A directory of computer software applications: astronomy and astrophysics, 1970-May, 1979

    International Nuclear Information System (INIS)

    1979-05-01

    Astronomy and astrophysics reports that list computer programs and/or their documentation are cited. These software applications pertain to topics such as solar activity, atmospheric radiative transfer, stellar and galactic structure, lunar and planetary studies, and astrophysical data reduction. The directory contains complete bibliographic data for each report as well as a subject and a corporate author index. The computer software offered by NTIS was created by a variety of Federal agencies to meet their diverse but quite specific objectives. It is provided without installation, support, or maintenance services and sometimes requires customer modifications to run effectively in customer environments

  17. Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.

  18. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  19. Rise and demise of bioinformatics? Promise and progress.

    Directory of Open Access Journals (Sweden)

    Christos A Ouzounis

    Full Text Available The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.

  20. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  1. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

  2. Architecture exploration of FPGA based accelerators for bioinformatics applications

    CERN Document Server

    Varma, B Sharat Chandra; Balakrishnan, M

    2016-01-01

    This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

  3. 2nd Colombian Congress on Computational Biology and Bioinformatics

    CERN Document Server

    Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

    2014-01-01

    This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

  4. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  5. Statistical modelling in biostatistics and bioinformatics selected papers

    CERN Document Server

    Peng, Defen

    2014-01-01

    This book presents selected papers on statistical model development related mainly to the fields of Biostatistics and Bioinformatics. The coverage of the material falls squarely into the following categories: (a) Survival analysis and multivariate survival analysis, (b) Time series and longitudinal data analysis, (c) Statistical model development and (d) Applied statistical modelling. Innovations in statistical modelling are presented throughout each of the four areas, with some intriguing new ideas on hierarchical generalized non-linear models and on frailty models with structural dispersion, just to mention two examples. The contributors include distinguished international statisticians such as Philip Hougaard, John Hinde, Il Do Ha, Roger Payne and Alessandra Durio, among others, as well as promising newcomers. Some of the contributions have come from researchers working in the BIO-SI research programme on Biostatistics and Bioinformatics, centred on the Universities of Limerick and Galway in Ireland and fu...

  6. Annual report of the Brazilian Directory of R and D - 1995; Relatorio anual da Diretoria de P e D 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    The Directory of Research and Development of the Brazilian CNEN (National Nuclear Energy Commission) presents the report for 1995. The publication describes and cover activities carried out in the following areas: nuclear reactors, nuclear fuel cycle, control and instrumentation, application of nuclear techniques, radioisotope production, materials of nuclear interest, radioactive wastes and irradiated materials. Three institutes accomplish Directory`s Programme: Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/MG); Instituto de Engenharia Nuclear (IEN/RJ); and Instituto de Pesquisas Energeticas e Nucleares (IPEN/SP). It is important to mention that the Institutes carry out a numberless of activities in cooperation with others institutions such as: universities, industries, private and government organizations. This cooperation is administrated through research contracts and agreements. 28 figs., 11 tabs.

  7. Directory of Regional Centers and Educational Programs Providing Services to Deaf/Blind Children and Youth in the United States (Including Puerto Rico and the Virgin Islands).

    Science.gov (United States)

    Alonso, Lou, Comp.

    Listed in the directory are over 200 educational programs and services for deaf blind children in the United States and U. S. territories. It is noted that the 10 coordinators of regional centers for services to deaf blind children have aided in compilation of the directory. Listings are arranged by state within the New England, Mid-Atlantic…

  8. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Science.gov (United States)

    Fristensky, Brian

    2007-01-01

    Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere. PMID:17291351

  9. Bioinformatics meets user-centred design: a perspective.

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

    Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  10. Kubernetes as an approach for solving bioinformatic problems.

    OpenAIRE

    Markstedt, Olof

    2017-01-01

    The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how th...

  11. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Directory of Open Access Journals (Sweden)

    Fristensky Brian

    2007-02-01

    Full Text Available Abstract Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

  12. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

    High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  13. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  14. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

    Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

    2018-03-01

    Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

  15. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

    Science.gov (United States)

    Atwood, Teresa K.; Bongcam-Rudloff, Erik; Brazas, Michelle E.; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M.; Schneider, Maria Victoria; van Gelder, Celia W. G.

    2015-01-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  16. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  17. KBWS: an EMBOSS associated package for accessing bioinformatics web services.

    Science.gov (United States)

    Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

    2011-04-29

    The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

  18. Combining medical informatics and bioinformatics toward tools for personalized medicine.

    Science.gov (United States)

    Sarachan, B D; Simmons, M K; Subramanian, P; Temkin, J M

    2003-01-01

    Key bioinformatics and medical informatics research areas need to be identified to advance knowledge and understanding of disease risk factors and molecular disease pathology in the 21 st century toward new diagnoses, prognoses, and treatments. Three high-impact informatics areas are identified: predictive medicine (to identify significant correlations within clinical data using statistical and artificial intelligence methods), along with pathway informatics and cellular simulations (that combine biological knowledge with advanced informatics to elucidate molecular disease pathology). Initial predictive models have been developed for a pilot study in Huntington's disease. An initial bioinformatics platform has been developed for the reconstruction and analysis of pathways, and work has begun on pathway simulation. A bioinformatics research program has been established at GE Global Research Center as an important technology toward next generation medical diagnostics. We anticipate that 21 st century medical research will be a combination of informatics tools with traditional biology wet lab research, and that this will translate to increased use of informatics techniques in the clinic.

  19. KBWS: an EMBOSS associated package for accessing bioinformatics web services

    Directory of Open Access Journals (Sweden)

    Tomita Masaru

    2011-04-01

    Full Text Available Abstract The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS, adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded and http://soap.g-language.org/kbws_dl.wsdl (Document/literal.

  20. A comparison of common programming languages used in bioinformatics.

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

    The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

  1. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra

    2013-06-25

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

  2. Bioinformatics process management: information flow via a computational journal

    Directory of Open Access Journals (Sweden)

    Lushington Gerald

    2007-12-01

    Full Text Available Abstract This paper presents the Bioinformatics Computational Journal (BCJ, a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.

  3. National Identities and Cinema: a critical recension of the book Directory of World Cinema: Spain

    Directory of Open Access Journals (Sweden)

    Isabel Macedo

    2012-12-01

    Full Text Available This critical review concerns the book Directory of World Cinema: Spain. This book is part of a series of volumes published in the Directory of World Cinema, by Intellect Books. The first part consists of a critique of the film "Biutiful", an interview with the director Jaime Rosales, followed by a reflection on the Spanish film industry. This part is also composed of a chapter in which are discussed the aspects that the authors consider to define the Spanish culture, concluding with a reflection on the work of some Spanish filmmakers. In the second part are presented ten film genres that characterize the Spanish cinema, and analyzed ten films by each gender. This book would benefit from a final reflection on the Spanish cinema, by recognizing and discussing the national character of the films produced, very marked by the national spaces and by the political, cultural and social history lived. Many European cinematographies became known as belonging to a particular national culture, and some even developed a style or have become specialized in a particular genre. This seems to be the reality of Spanish cinema, were the genre classified in this book as author melodram is very present.

  4. Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program.

    Science.gov (United States)

    Rein, Diane C

    2006-07-01

    Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus. After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services. The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning. Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making.

  5. Promoting synergistic research and education in genomics and bioinformatics.

    Science.gov (United States)

    Yang, Jack Y; Yang, Mary Qu; Zhu, Mengxia Michelle; Arabnia, Hamid R; Deng, Youping

    2008-01-01

    Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and

  6. 45 CFR 303.108 - Quarterly wage and unemployment compensation claims reporting to the National Directory of New...

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Quarterly wage and unemployment compensation... OPERATIONS § 303.108 Quarterly wage and unemployment compensation claims reporting to the National Directory of New Hires. (a) What definitions apply to quarterly wage and unemployment compensation claims...

  7. Directory of Certificates of Compliance for Radioactive Materials Packages. Summary report of NRC approved packages. Volume 1, Revision 8

    International Nuclear Information System (INIS)

    1985-10-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure them that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note that the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR Parts 30 to 36, 40, 50, or 70

  8. Directory of certificates of compliance for radioactive materials packages. Summary report of NRC approved packages. Volume 1. Revision 9

    International Nuclear Information System (INIS)

    1986-10-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and Corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Sections 71.12, it is the responsibility of the licensees to insure them that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note that the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR Parts 30 to 36, 40, 50, or 70

  9. Directory of certificates of compliance for radioactive materials packages. Volume 1. Summary report of NRC approved packages. Revision 6

    International Nuclear Information System (INIS)

    1983-09-01

    This directory contains a Summary Report of the US Nuclear Regulatory Commission's Approved Packages (Volume 1), all Certificates of Compliance (Volume 2), and Summary Report of NRC Approved Quality Assurance Programs (Volume 3) for Radioactive Material Packages effective September 14, 1983

  10. Directory of certificates of compliance for radioactive materials packages. Summary report of NRC approved packages. Volume 1, Revision 7

    International Nuclear Information System (INIS)

    1984-11-01

    This directory contains a Summary Report of NRC Approved Packages (Volume 1), Certificates of Compliance (Volume 2), and a Summary Report of NRC Approved Quality Assurance Programs for Radioactive Material Packages (Volume 3). The purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory. Shipments of radioactive material utilizing these packagings must be in accordance with the provisions of 49 CFR 173.471 and 10 CFR Part 71, as applicable. In satisfying the requirements of Section 71.12, it is the responsibility of the licensees to insure that they have a copy of the current approval and conduct their transportation activities in accordance with an NRC approved quality assurance program. Copies of the current approval may be obtained from the US Nuclear Regulatory Commission Public Document Room files (see Docket No. listed on each certificate) at 1717 H Street, Washington, DC 20555. Note that the general license of 10 CFR 71.12 does not authorize the receipt, possession, use or transfer of byproduct source, or special nuclear material; such authorization must be obtained pursuant to 10 CFR Parts 30 to 36, 40, 50, or 70

  11. Directory of certificates of compliance for radioactive materials packages. Volume 1. Summary report of NRC approved packages

    International Nuclear Information System (INIS)

    1977-12-01

    Purpose of this directory is to make available a convenient source of information on packagings which have been approved by the U.S. Nuclear Regulatory Commission. This volume contains a summary report of NRC-approved packages for radioactive material packages effective Nov. 30, 1977

  12. Access: A Directory of Contacts, Environmental Data Bases, and Scientific Infrastructure on 175 Biosphere Reserves in 32 Countries.

    Science.gov (United States)

    Department of State, Washington, DC. Bureau of Oceans and International Environmental and Scientific Affairs.

    Following the EuroMAB meeting in Strasbourg, France (September 1991) and on an initiative of the Man and the Biosphere National Committee of the United States, a decision was made to create a research network from information available in biosphere reserves in 30 European countries, Canada and the United States. This Directory of EuroMAB Biosphere…

  13. Microcomputer Materials from MEP. An Annotated Directory of Packages of Interest to Further Education. An Occasional Paper.

    Science.gov (United States)

    Gilbert, Leslie

    Designed to disseminate information to the post-school sector of United Kingdom education, this directory provides information on 50 microcomputer software packages developed by the Microelectronics Education Program (MEP) and available through educational publishers. Subject areas represented include accountancy, biology, business education,…

  14. Easing the Discovery of NASA and International Near-Real-Time Data Using the Global Change Master Directory

    Science.gov (United States)

    Ritz, S.; Olsen, L. M.; Morahan, M.; Stevens, T.; Aleman, A.; Grebas, S. K.

    2011-12-01

    The Global Change Master Directory (GCMD) provides an extensive directory of descriptive and spatial information about data sets and data-related services, which are relevant to Earth science research. The directory's data discovery components include controlled keywords, free-text searches, and map/date searches. The GCMD portal for NASA's Land Atmosphere Near-real-time Capability for EOS (LANCE) data products leverages these discovery features by providing users a direct route to NASA's Near-Real-Time (NRT) collections. This portal offers direct access to collection entries by instrument name, informing users of the availability of data. After a relevant collection entry is found through the GCMD's search components, the "Get Data" URL within the entry directs the user to the desired data. Building on the importance of Near-Real-Time (NRT) data, the Committee on Earth Observation Satellites (CEOS) International Directory Network (IDN) is targeting an effort to identify NRT data set collections from the CEOS international members. The international collections will be advertised as the "CEOS IDN NRT" portal to assist users in rapidly discovering these products, which are potentially useful for their research or public response. [This portal is expected to be released in 2012.

  15. Navy Directory

    Science.gov (United States)

    Youtube US Navy Flickr US Navy Instagram US Navy Snapchat US Navy Pinterest US Navy Periscope NAVY GROUPS Facebook Twitter Instagram EDIT Chief of Naval Operations Facebook Twitter YouTube Instagram EDIT Chief of Facebook Twitter YouTube Instagram EDIT Chief of Supply Corps Facebook EDIT CNE MPP 413 Twitter EDIT CNIC

  16. DDN Directory,

    Science.gov (United States)

    1984-06-01

    2224 • (CRAIG.EVERHARTVCMU-CS-A-ARPA) (619) 225-2140 or 225-7282 ,T Carnegie-Mellon University FADUM, Torgeir Computer Science Department EZZELL , Jr...RADAR Development Section (OCDR) Washington, D.C. 20375 - , , Griffiss Air Force Base, NY 13441 (202) 767-3190 (AV) 297-3190 ",, ,, MILES , Cairn (315) 330... MILES , Monica L (315) 330-3406 (AV) 587-3406 MILLER, Arnold (DSDC-SDMRUGUNTER-ADAM.ARPA) (FTS) 952-3406 (arnodeMARYLAND.ARPA) Air Force Data Systems

  17. SeqHound: biological sequence and structure database as a platform for bioinformatics research

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2002-10-01

    Full Text Available Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

  18. GENEASE: Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization.

    Science.gov (United States)

    Ghandikota, Sudhir; Hershey, Gurjit K Khurana; Mersha, Tesfaye B

    2018-03-24

    Advances in high-throughput sequencing technologies have made it possible to generate multiple omics data at an unprecedented rate and scale. The accumulation of these omics data far outpaces the rate at which biologists can mine and generate new hypothesis to test experimentally. There is an urgent need to develop a myriad of powerful tools to efficiently and effectively search and filter these resources to address specific post-GWAS functional genomics questions. However, to date, these resources are scattered across several databases and often lack a unified portal for data annotation and analytics. In addition, existing tools to analyze and visualize these databases are highly fragmented, resulting researchers to access multiple applications and manual interventions for each gene or variant in an ad hoc fashion until all the questions are answered. In this study, we present GENEASE, a web-based one-stop bioinformatics tool designed to not only query and explore multi-omics and phenotype databases (e.g., GTEx, ClinVar, dbGaP, GWAS Catalog, ENCODE, Roadmap Epigenomics, KEGG, Reactome, Gene and Phenotype Ontology) in a single web interface but also to perform seamless post genome-wide association downstream functional and overlap analysis for non-coding regulatory variants. GENEASE accesses over 50 different databases in public domain including model organism-specific databases to facilitate gene/variant and disease exploration, enrichment and overlap analysis in real time. It is a user-friendly tool with point-and-click interface containing links for support information including user manual and examples. GENEASE can be accessed freely at http://research.cchmc.org/mershalab/genease_new/login.html. Tesfaye.Mersha@cchmc.org, Sudhir.Ghandikota@cchmc.org. Supplementary data are available at Bioinformatics online.

  19. Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

    Science.gov (United States)

    Lin, Sabrina; Fonteno, Shawn; Satish, Shruthi; Bhanu, Bir; Talbot, Prue

    2010-01-01

    Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion. PMID:20495527

  20. [Pharmacogenetics II. Research molecular methods, bioinformatics and ethical concerns].

    Science.gov (United States)

    Daudén, E

    2007-01-01

    Pharmacogenetics refers to the study of the individual pharmacological response based on the genotype. Its objective is to optimize treatment in an individual basis, thereby creating a more efficient and safe personalized therapy. In the second part of this review, the molecular methods of study in pharmacogenetics, including microarray technology or DNA chips, are discussed. Among them we highlight the microarrays used to determine the gene expression that detect specific RNA sequences, and the microarrays employed to determine the genotype that detect specific DNA sequences, including polymorphisms, particularly single nucleotide polymorphisms (SNPs). The relationship between pharmacogenetics, bioinformatics and ethical concerns is reviewed.