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Sample records for krner kaido kaust

  1. KAUST Supercomputing Laboratory

    KAUST Repository

    Bailey, April Renee; Kaushik, Dinesh; Winfer, Andrew

    2011-01-01

    KAUST has partnered with IBM to establish a Supercomputing Research Center. KAUST is hosting the Shaheen supercomputer, named after the Arabian falcon famed for its swiftness of flight. This 16-rack IBM Blue Gene/P system is equipped with 4 gigabyte memory per node and capable of 222 teraflops, making KAUST campus the site of one of the world’s fastest supercomputers in an academic environment. KAUST is targeting petaflop capability within 3 years.

  2. KAUST Supercomputing Laboratory

    KAUST Repository

    Bailey, April Renee

    2011-11-15

    KAUST has partnered with IBM to establish a Supercomputing Research Center. KAUST is hosting the Shaheen supercomputer, named after the Arabian falcon famed for its swiftness of flight. This 16-rack IBM Blue Gene/P system is equipped with 4 gigabyte memory per node and capable of 222 teraflops, making KAUST campus the site of one of the world’s fastest supercomputers in an academic environment. KAUST is targeting petaflop capability within 3 years.

  3. 2020 vision for KAUST

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    Felicitas Pauss, Head of International Relations at CERN, greets Members of the Board of Trustees of the King Abdullah University of Science and Technology, KAUST, who visited CERN on Friday 6 August.   Members of Board of Trustees of the King Abdullah University of Science and Technology upon their arrival at CERN. KAUST, which is situated on Saudi Arabia’s Red Sea coast, is a new, forward-looking co-educational and research university with a vision to become one of the world’s top ten science and technology Universities by 2020, stimulating the intellectual life of Saudi Arabia and making significant contributions to the country’s economy. CERN’s Director General, Rolf Heuer, is a member of the Board of Trustees. “I accepted the invitation to join the board because I believe that KAUST’s values can make a real difference to the region and to the world,” he said. The University’s mission statement emphasises achiev...

  4. Marine Metagenomics activities at KAUST

    KAUST Repository

    Kodzius, Rimantas

    2014-09-19

    Renaissance of Middle East countries King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Center (CBRC) The Red Sea as a source for our research Pipeline for the research platform Comparative Genomics and Genetics (CGG) laboratory

  5. KCC1: First Nanoparticle developed by KAUST Catalysis Center

    KAUST Repository

    Basset, Jean-Marie

    2010-08-01

    KCC1 is the first Nanoparticle developed by KAUST Catalysis Center. Director of KAUST Catalysis Center, Dr. Jean-Marie Basset, Senior Research Scientist at KCC, Dr. Vivek Polshettiwar, and Dr. Dongkyu Cha of the Advanced Nanofabrication Imaging & Characterization Core Laboratory discuss the details of this recent discovery. This video was produced by KAUST Visualization Laboratory and KAUST Technology Transfer and Innovation - Terence McElwee, Director, Technology Transfer and Innovation - IP@kaust.edu.sa This technology is part of KAUST\\'s technology commercialization program that seeks to stimulate development and commercial use of KAUST-developed technologies. For more information email us at ip@kaust.edu.sa.

  6. KCC1: First Nanoparticle developed by KAUST Catalysis Center

    KAUST Repository

    Basset, Jean-Marie; Bailey, April Renee; Farago, Amy; McElwee, Terence; Polshettiwar, Vivek; Srinivasan, Madhu

    2010-01-01

    This technology is part of KAUST's technology commercialization program that seeks to stimulate development and commercial use of KAUST-developed technologies. For more information email us at ip@kaust.edu.sa.

  7. Implementation of Summon at KAUST

    KAUST Repository

    Buck, Stephen

    2017-03-09

    Web discovery services has evolved tremendously from the time of its introduction to present day. Their technology has enabled library users to obtain a variety of materials in different format and type faster and farther. Coupled with a myriad of features, users are ‘pampered’ with the options to email, download citations, full text articles, book chapters on different devices such as laptops, desktops and mobile devices (among others). In this session, the speaker will highlight KAUST library’s new discovery service (KORAL powered by Summon) launched in June 2016. Topics include the implementation project, its challenges and lessons learnt and the after-implementation initiatives.

  8. Implementation of Summon at KAUST

    KAUST Repository

    Buck, Stephen; Ramli, Rindra M.

    2017-01-01

    Web discovery services has evolved tremendously from the time of its introduction to present day. Their technology has enabled library users to obtain a variety of materials in different format and type faster and farther. Coupled with a myriad of features, users are ‘pampered’ with the options to email, download citations, full text articles, book chapters on different devices such as laptops, desktops and mobile devices (among others). In this session, the speaker will highlight KAUST library’s new discovery service (KORAL powered by Summon) launched in June 2016. Topics include the implementation project, its challenges and lessons learnt and the after-implementation initiatives.

  9. Marko ja Kaido Tallinnas / Harry Liivrand

    Index Scriptorium Estoniae

    Liivrand, Harry, 1961-

    2003-01-01

    Viviann Napa galeriis (senine Galerie Passage) Harry Liivranna kureeritud Kaido Ole ja Marko Mäetamme näitus "Design Jet 5000". Kunstnikud on viinud Veneetsia biennaalil eksponeeritud kosmoseteemalised maalid digitrüki tehnikasse ning liitnud sarjaga oma Veneetsia näituse kataloogi illustratsioonid

  10. Kaido Kepp : Kindlustuses tulevad väga põnevad ajad / Kaido Kepp ; interv. Kristiina Tamberg

    Index Scriptorium Estoniae

    Kepp, Kaido

    2007-01-01

    Eestis tegevust alustanud rahvusvahelise kindlustuskontserni Royal&SunAlliance juht Eesti kindlustusturu olukorrast, konkurentidest, kindlustuskultuurist ja teenustest, enda juhtimisstiilist. Lisad: Royal&SunAlliance; Kaido Kepp CV

  11. Kaido Ole seintel ja kaante vahel / Valner Valme

    Index Scriptorium Estoniae

    Valme, Valner, 1970-

    2007-01-01

    Kunstnik Kaido Ole (sünd. 1963) eluloolisi andmeid, looming. Eesti Kunstiakadeemia andis välja kataloogi "Ole", toimetaja Eero Epner. Kunstinäitus "Jonas & Kaido" koos Jonas Gasiunasega Vilniuse Vartai galeriis. Näitus "Hümn" Vaal galeriis

  12. A potpourri of results from the KAUST SRI-UQ

    KAUST Repository

    Tempone, Raul

    2016-01-01

    As the KAUST Strategic Research Initiative for Uncertainty Quantification completes its fourth year of existence we recall several results produced during its exciting journey of discovery. These include, among others, contributions on Multi-level

  13. Cloud Computing in KAUST Library: Beyond Remote Hosting

    KAUST Repository

    Yu, Yi

    2013-12-01

    Enterprise computing is the key strategic approach for KAUST to build its modern IT landscape. In such a strategic direction and technical environment, the library tries to establish library technology by catching new trends which help to make the library more efficient and sufficient. This paper focuses on the cloud computing development in the KAUST library, by using real world scenarios and first-hand experiences to describe what cloud computing means for KAUST library. It addresses the difficulties that were met by the library during the implementation process, how cloud computing affects the functional performance and work procedure of the library, how it impacts the style and modal of the library’s technical service and systems administration, how it changes the relationships and cooperation among the involved players (the library, campus IT and vendors), and what the benefits and disadvantages are. The story of cloud computing at KAUST will share the knowledge and lessons that the KAUST library learnt during its development, and will also point out the future direction of cloud computing at KAUST.

  14. John Smith vastab / Kaido Ole, Marko Mäetamm ; interv. Harry Liivrand

    Index Scriptorium Estoniae

    Ole, Kaido

    2003-01-01

    Marko Mäetamm ja Kaido Ole, kelle kosmoseteemaline näitus "Marko and Kaido. By John Smith" on avatud Veneetsia biennaalil räägivad teemadel "koosmaalimine", "kosmoseodüsseia", "maalikunst", "kunstnikuidentiteet", "Veneetsia biennaal", "kuraatori võim", "pseudonüüm", "Eesti kunstiruum", "video" jm.

  15. A potpourri of results from the KAUST SRI-UQ

    KAUST Repository

    Tempone, Raul

    2016-01-08

    As the KAUST Strategic Research Initiative for Uncertainty Quantification completes its fourth year of existence we recall several results produced during its exciting journey of discovery. These include, among others, contributions on Multi-level and Multi-index sampling techniques that address both direct and inverse problems. We may discuss also several techniques for Bayesian Inverse Problems and Optimal Experimental Design.

  16. Kaido Orav sõidab Aafrikasse Zambia lapsi harima / Helve Laasik

    Index Scriptorium Estoniae

    Laasik, Helve, 1958-

    2006-01-01

    Kaido Orav sõidab abiorganisatsiooni Humana kaudu pooleks aastaks vähese kirjaoskusega Zambiasse lapsi õpetama, õpetajaid koolitama ja koole rajama. Eelnevalt läbib ta pooleteiseaastase ettevalmistustsükli Inglismaal

  17. Korterelamud Supilinnas = Apartment buildings in Supilinn / Kaido Kepp ; intervjueerinud Margit Mutso

    Index Scriptorium Estoniae

    Kepp, Kaido

    2012-01-01

    Tartus Meloni t. 28, Oa t. 31 ja 33 asuvate korterelamute arhitektuursest lahendusest. Kergplokkidest elamud on kaetud laudvoodriga, fassaadi keskmine osa on kaetud dekooriga. Arhitektid Kaido Kepp ja Erik Mutso (Arhitektuuriklubi)

  18. Sharing of information and knowledge among staff in King Abdullah University of Science and Technology (KAUST) library

    KAUST Repository

    Ramli, Rindra M.

    2011-01-01

    This paper describes strategies and initiatives undertaken by the King Abdullah University of Science and Technology (KAUST) library in sharing information and knowledge among its staff. KAUST Library adopted several IT platforms to enable staff

  19. BUILDING A NEW GENERATION SCIENCE LIBRARY: THE KAUST STORY

    KAUST Repository

    Al Zahrani, Rashed

    2012-06-01

    If you had the opportunity to build a science library from scratch for a new generation of researchers and students, what would it look like and how would it operate? We will show you the vision and reality of the new King Abdullah University of Science and Technology (KAUST) Library that won the 2011 ALA/AIA Library Architecture award and that for the last three years has been providing a high level of information services to top level international scientists and graduate students. We will describe the major characteristics in contemporary science research, education, and information management that guided the design of our library facility, technical infrastructure, and services. We will give concrete examples and evaluations of our implementation of new information services and tools. And we will end with the challenges still before us, most notably the effective integration of science knowledge management into the workflow of scientific research and enterprise based information technology organization.

  20. Our Journey to Summon and 360: The KAUST experience

    KAUST Repository

    Ramli, Rindra M.

    2017-09-12

    Depicts the journey undertaken by KAUST (King Abdullah University of Science and Technology), an international graduate research university located on the shores of the Red Sea, in implementing Summon as its new webscale discovery layer. We will also describe the implementation of 360 suite of products namely: 360 Core & 360 LINK, 360 Marc. The presentation will cover the early days of library’s foray into discovery layers and the difficulties faced by the library that gave the impetus to embark on the project to evaluate, assess and recommend for a new and robust discovery layer. On top of that, the presenters would elaborate the project timeline (which also include the implementation phase for Summon and 360 Core), the challenges faced by the project team and lessons learnt.

  1. Kunstnikuks pürgija vajab paari õigeaegset impulssi / Kaido Ole, Eva Unt

    Index Scriptorium Estoniae

    Ole, Kaido

    2006-01-01

    Antonia Claudio Carvalho meistriklass "Ava oma silmad/Open Your Eyes" 23.-27. I ja näitus 27. I-9. II Eesti Kunstiakadeemia galeriis. Meistriklassist vestlesid EKA maaliosakonna juhataja Kaido Ole ja maalieriala III kursuse üliõpilane Eva Unt

  2. Implementing an Open Access Policy – Modeling KAUST in the Region

    KAUST Repository

    Baessa, Mohamed A.; Vijayakumar, J.K.

    2014-01-01

    The presentation will discuss different open access approaches, and what can well-fit academic and governmental institutions. As a case study of KAUST, presenters will discuss how it can be initiated in a university set-up, how to get academic stakeholder engaged with support, and how the final stage is reached. Details about the KAUST Open Access Policy for research articles, theses and dissertations and the required tools and workflow to implement the policies will be highlighted.

  3. Implementing an Open Access Policy – Modeling KAUST in the Region

    KAUST Repository

    Baessa, Mohamed A.

    2014-11-12

    The presentation will discuss different open access approaches, and what can well-fit academic and governmental institutions. As a case study of KAUST, presenters will discuss how it can be initiated in a university set-up, how to get academic stakeholder engaged with support, and how the final stage is reached. Details about the KAUST Open Access Policy for research articles, theses and dissertations and the required tools and workflow to implement the policies will be highlighted.

  4. Managing user queries using cloud services: KAUST library experience

    KAUST Repository

    Ramli, Rindra M.

    2017-03-01

    The provision of reference and information services are one of the major activities for academic libraries. Answering questions and providing relevant and timely answers for library users are just one of such services. Questions come in many format: in person, phone, email and even on social media platforms. The type of questions may also differ from simple, directional to complicated ones. One of the challenges for libraries is the capturing and managing of these inquiries. Libraries need to address some of these points: •\\tHow the questions will be captured •\\tHow the questions will be answered •\\tWho will answer these questions •\\tWhat is the turn-around time for answering these questions •\\tWhat kind of statistics to monitor •\\tHow are these statistics communicated to internal library staff and other stakeholders This paper describe the initiatives undertaken by KAUST, a brand new Graduate Research Library located in Saudi Arabia. This initiatives include the implementation of LibAnswers to assist the library in capturing and managing all inquiries. We are tracking inquiries coming in via email or widgets (such as online form), converting received questions into FAQ entries, creating and maintaining a public knowledge base for our users. In addition, it will also describe future plans in store to expand reference services for our library users. KAUST: (King Abdullah University of Science and Technology) is a graduate research university located along the shores of the Red Sea. The university was inaugurated in September 2009. The main areas of study are: Mathematics and Computer Science, Physical Sciences and Life Sciences. The university library is situated at the heart of the campus. It is a digitally born library with collections comprising of print and electronic resources. The library has: •\\t310,000 e-book titles •\\tOver 50,000 e-journal titles •\\tOver 30 scientific databases •\\tAbout 3,500 print titles

  5. To get or not to get: the KAUST library e-resources acquisition experience

    KAUST Repository

    Ramli, Rindra M.

    2014-06-01

    In the challenging times of budget cuts and reviews, libraries are faced with issues, among others, such as justifying acquisition, negotiating deals and reviewing current subscriptions (pertaining to electronic resources). With the rapid increase in growth of electronic resources, libraries have to continuously assess their acquisition models and policies to constantly ensure that they are balancing their budget and users’ needs as well. This paper highlights the role played by Technical and IT department of King Abdullah University of Science and Technology (KAUST) library (Saudi Arabia) in acquiring the electronic resources (electronic books, electronic journals, databases, image and reference) for the community. It will describe the processes during the early days when KAUST library was inaugurated; how electronic resources were acquired and what went through during those days. The paper will elaborate further how the acquisition model has evolved and the various important roles played by the library staff in ensuring that acquisitions/subscriptions are justified, within the budget and provides ROI for the library. King Abdullah University is a graduate research university which opened in September 2009 with its first cohort of 800 graduate students (25% female) taught by 100 faculties. The focus of study and research in the university are: Mathematics and Computer Science, Physical Sciences and Life Sciences. The university library started with 10 staff. The library has a “state-of-the-art learning and information resource center supporting graduate education and advanced scientific research” (KAUST, 2010).

  6. ORCID Integration: Services to Create and Use ORCID IDs at KAUST

    KAUST Repository

    Grenz, Daryl M.

    2015-06-09

    As ORCID IDs become accepted as a global standard, the potential benefits to researchers and institutions of making use of them are multiplying. At King Abdullah University of Science and Technology (KAUST) we adopted the first institutional open access policy in the Arab region in June 2014 and are integrating with ORCID as part of services to researchers that improve the preservation and dissemination of their research. We started by using ORCID IDs to identify authors in our institutional repository. Our next step was to join ORCID as an institutional member and then set up a plan to support our faculty, researchers and students in the creation and use of ORCID identifiers. This presentation will look at the choices made and lessons learned during this process, focusing on the tools we developed to interact with the ORCID member API and the ways in which introducing ORCID has complemented other repository initiatives, such as the implementation of our institutional open access policy.

  7. Milline mentor kõik tuksi keerab? Ja milline on hea mentor? / Marit Pajulaid, Agne Puusaar, Kaido Aettik ; kommenteerinud Tiiu Allikvee

    Index Scriptorium Estoniae

    Pajulaid, Marit

    2010-01-01

    Küsimuste üle, milline peab olema hea mentor ning mida ta peaks ja mida ta ei tohiks teha, arutlevad Fontese pooleaastase mentorprogrammi läbinud Fazer Eesti juhtrühma liige Marit Pajulaid, reklaamibüroo Division personalijuht Agne Puusaar ning endine Kuusakoski juhatuse esimees Kaido Aettik

  8. Working together – Using social media tools / enterprise tools (Sharepoint, Blogs, Wikis, Google Docs/Drive) to enhance staff collaboration – The KAUST library experience

    KAUST Repository

    Ramli, Rindra M.

    2015-06-01

    This paper describes the tools implemented by KAUST library to enhance collaboration among library staff. Highlights the features / functionalities of the implemented tools and their related success / constraints in achieving the desired targets.

  9. Working together – Using social media tools / enterprise tools (Sharepoint, Blogs, Wikis, Google Docs/Drive) to enhance staff collaboration – The KAUST library experience

    KAUST Repository

    Ramli, Rindra M.

    2015-01-01

    This paper describes the tools implemented by KAUST library to enhance collaboration among library staff. Highlights the features / functionalities of the implemented tools and their related success / constraints in achieving the desired targets.

  10. Sharing of information and knowledge among staff in King Abdullah University of Science and Technology (KAUST) library

    KAUST Repository

    Ramli, Rindra M.

    2011-03-01

    This paper describes strategies and initiatives undertaken by the King Abdullah University of Science and Technology (KAUST) library in sharing information and knowledge among its staff. KAUST Library adopted several IT platforms to enable staff to contribute, share, collaborate, extract and act upon knowledge in order to serve our users better. They include: Sharepoint and Google Docs. As Duffy (2000) stated, that “success depends on capitalizing on every available resource including what a company knows and how it uses what it knows”. Therefore, to provide value-added services to our community of researchers and academicians, library staff needs to be equipped with the right skills and tools to be able to act upon users’ inquiries and information needs. KAUST library which was opened in Aug 2009 aims to support education and advanced scientific research. With its state of the art learning and information resource center, the library provides instructional assistance and reference services to its research and academic community. With the influx of information coupled the pervasive use of information technology and Web2.0, the library has to grapple with the issue of information overload. It is important to be able to sieve through the rubbles of information to apply the relevant ones during the point of transaction. Based on our experience in using various IT platforms, this paper will share the impacts of such tools. Lessons learnt and future directions in this area will also be discussed.

  11. An Exploratory study on the use of LibAnswers to Resolve, Track and Monitor Electronic Resources Issues: The KAUST Library experience

    KAUST Repository

    Ramli, Rindra M.

    2017-01-01

    An Exploratory study on KAUST library use of LibAnswers in resolving electronic resources questions received in LibAnswers. It describes the findings of the questions received in LibAnswers. The author made suggestions based on the findings to improve the reference services in responding to e-resources questions.

  12. An Exploratory study on the use of LibAnswers to Resolve, Track and Monitor Electronic Resources Issues: The KAUST Library experience

    KAUST Repository

    Ramli, Rindra M.

    2017-05-03

    An Exploratory study on KAUST library use of LibAnswers in resolving electronic resources questions received in LibAnswers. It describes the findings of the questions received in LibAnswers. The author made suggestions based on the findings to improve the reference services in responding to e-resources questions.

  13. A CRIS in the Desert: The Implementation of Pure at KAUST: A Case Study in Information Exchange

    KAUST Repository

    Grenz, Daryl M.; Lery, Thibaut L.; Ward, Manus; Mastoraki, Eirini; Baessa, Mohamed A.

    2016-01-01

    The integration of research information systems with existing university processes has tended towards information exchange models in which the CRIS ingests information from existing systems and takes on functions that were previously distributed across several independent solutions. This paper draws upon the experience of the implementation of a CRIS at the King Abdullah University of Science and Technology (KAUST) to posit a model in which functions remain distributed so as to take advantage of the strengths of each system. The functions discussed include institutional reporting, publications tracking, preservation of research outputs, provision of public access, researcher identity and profiling, and metrics analysis. The systems reviewed include a CRIS (Pure), a locally developed publications tracking system, a hosted DSpace repository, a locally developed ORCID integration, and a metrics dashboard (PlumX). The interactions between these systems forms a network of services to our research community, with each node connected to several others, and we discuss how we arrived at the current arrangement, as well as its drawbacks and advantages. The still limited use of standard data exchange formats like CERIF XML is discussed as a constraint that increases the costs of adding to and maintaining the network of services. At the same time we look at how increased standardization should make this distributed approach sustainable, allowing institutions like ours to mix and match complementary systems to achieve an optimal set of research information services for our needs.

  14. A CRIS in the Desert: The Implementation of Pure at KAUST: A Case Study in Information Exchange

    KAUST Repository

    Grenz, Daryl M.

    2016-06-10

    The integration of research information systems with existing university processes has tended towards information exchange models in which the CRIS ingests information from existing systems and takes on functions that were previously distributed across several independent solutions. This paper draws upon the experience of the implementation of a CRIS at the King Abdullah University of Science and Technology (KAUST) to posit a model in which functions remain distributed so as to take advantage of the strengths of each system. The functions discussed include institutional reporting, publications tracking, preservation of research outputs, provision of public access, researcher identity and profiling, and metrics analysis. The systems reviewed include a CRIS (Pure), a locally developed publications tracking system, a hosted DSpace repository, a locally developed ORCID integration, and a metrics dashboard (PlumX). The interactions between these systems forms a network of services to our research community, with each node connected to several others, and we discuss how we arrived at the current arrangement, as well as its drawbacks and advantages. The still limited use of standard data exchange formats like CERIF XML is discussed as a constraint that increases the costs of adding to and maintaining the network of services. At the same time we look at how increased standardization should make this distributed approach sustainable, allowing institutions like ours to mix and match complementary systems to achieve an optimal set of research information services for our needs.

  15. In-situ marine monitoring and environmental management of SWRO concentrate discharge: A case study of the KAUST SWRO plant

    KAUST Repository

    Van Der Merwe, Riaan

    2014-06-01

    Concentrate (when discharged to the ocean) may have chronic/acute impacts on marine ecosystems, particularly in the mixing zone around outfalls. The environmental impact of the desalination plant discharges is very site- and volumetric specific, and depends to a great extent on the salinity tolerance of the specific marine microbial communities as well as higher order organisms inhabiting the water column in and around this extreme discharge environment. Scientific studies that aim to grant insight into possible impacts of concentrate discharge are very important, in order to understand how this may affect different marine species when exposed to elevated salinity levels or residual chemicals from the treatment process in the discharge site. The objective of this PhD research was to investigate the potential environmental effects of the concentrate discharge in the near-field area around the submerged discharge of the King Abdullah University of Science and Technology (KAUST) seawater reverse osmosis (SWRO) plant by a combination of biological and hydrological studies. Possible changes in microbial abundance were assessed by using flow cytometric (FCM) analysis on a single-cell level in 107 samples, taken from the discharge area, the feed-water intake area and two control sites. Results indicate that changes in microbial abundance in the near-field area of the KAUST SWRO outfall are minor and appear to bethe result of a dilution effect rather than a direct impact of the concentrate discharge. In order to also investigate potential impacts on higher order organisms, a longterm in-situ salinity tolerance test at the discharge site was conducted on the coral Fungia granulosa and its photophysiology. The corals were exposed to elevated levels of salinity as a direct result of concentrate discharge. Their photosynthetic response after exposure to extreme salinity conditions around the full-scale operating SWRO desalination discharge was measured. A pulse amplitude

  16. Infrastruktuuriteenistus / Kaido Simmermann

    Index Scriptorium Estoniae

    Simmermann, Kaido

    2004-01-01

    Ilmunud ka: 2003 : annual report : [Eesti Raudtee]. - Tallinn, 2004, lk. 29-33; 2003 : godovoi ottshjot : [Eesti Raudtee]. - Tallinn, 2004, lk. 29-33. Ohutuse tagamiseks, rongide liikumiskiiruse, reisijate sõidumugavuste ja raudtee läbilaskevõime tõstmiseks võttis Eesti Raudtee 2003. a. kasutusele infrastruktuuri parandamise muudetud strateegia. Kaart. Diagrammid

  17. KAUST Open Access policy

    KAUST Repository

    Baessa, Mohamed A.

    2017-01-01

    The library plays a critical role in facilitating open access for their researchers, from managing a repository to providing support and information on the OA publication process to their authors. Janis Tyhurst and Dr Imad

  18. KAUST Open Access policy

    KAUST Repository

    Baessa, Mohamed A.

    2017-03-07

    The transition to open access (OA) is being driven by funders, libraries, researchers and publishers around the world, and is having an impact on us all. It is inevitable that different countries, organisations and disciplines are moving at different rates towards an OA model, and it is this that we will focus on in this session. Drawing on experiences from across Europe and the Middle East we will provide perspectives from both a global publisher and institutions based in the region. Taylor & Francis take a flexible, evidence-based approach to open access, providing a choice of publication routes for our authors, and a choice of agreements for our library customers. Carolyn will outline some of the open access developments, opportunities and challenges at Taylor & Francis. The library plays a critical role in facilitating open access for their researchers, from managing a repository to providing support and information on the OA publication process to their authors. Janis Tyhurst and Dr Imad Bachir will each give an overview of how this is being managed by their institution. There will be an opportunity for questions and discussion with the panel.

  19. Exploring off-set pricing models and article deposit terms at King Abdullah University of Science & Technology (KAUST)

    KAUST Repository

    Buck, Stephen

    2018-04-09

    In the ‘normal’ world of retail and commerce you pay for an item and receive the item. In the world of academic journals you prepay for the item and you might receive the item and you might get some money back depending on what journals you did or didn’t receive. In the world of offset pricing you prepay, then you pay again, you sometimes use vouchers, you might get a discount (the following year) then you might get money back, or you might not. Are publishers knowingly placing barriers to off-set models, and not transparently offsetting the APCs to the subscription cost, in order to raise more income? Whether by design or accident it is a complex world which needs a time commitment, which not all librarians can give, to understand fully. The new model of scholarly communication, which leading universities (including KAUST) want to introduce, is based on shifting the subscription costs to publishing costs, not to double the payment channels to the publishers. Can we get to a mutually beneficial position where the author can deposit the accepted version of the article into the Institutional Repository without any embargo period as the institute is agreeing to pay the subscription fee on an ongoing basis? The required model does not adversely affect the vendors’ revenue. This presentation, based on KAUST’’s experience to date, will attempt to explain the different models of offset pricing while outlining KAUST’s dual approach, redirecting subscription money to publishing money and embedding open access terms in understandable language in our license agreements, to the problem. Why we have accepted IoP’s offset offer and not Springer’s, though we were considered among the first timers and important Institutions? Why is this important? Resolving the inherent complexities in offsetting models will save libraries money and also time wasted on tedious and unnecessary administration work. Researchers do not want to know about offsetting agreements nor

  20. Spatial Estimation and Visualization of CO2 Emissions for Campus Sustainability: The Case of King Abdullah University of Science and Technology (KAUST, Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Yusuf A. Adenle

    2017-11-01

    Full Text Available A total of 21 metric tons of CO2 per person in terms of per capita emissions from consumption of energy was recorded in Saudi Arabia in 2011 and forecasts have shown that this emission of CO2 is increasing. This poses the threat of climate change and global warming and therefore the need for the sustainability of the country. The Kingdom of Saudi Arabia’s Vision for 2030 addresses environmental sustainability that includes a reduction in CO2 emissions as well as diversified economic growth. Universities have been regarded as institutions with significant responsibilities to resolve the issues of sustainability as well as serve as role model to society by implementing a sustainability plan. This study established a spatial evaluation, estimation, and visualization of the CO2 emissions of King Abdullah University of Science and Technology (KAUST, Saudi Arabia. The data required for this study were collected from the overall coverage of the university campus buildings by transforming raster data from the satellite image to vector data in the form of polygons, and then multiplying the area by the number of floors of the individual building. ArcGIS 10.3® (ESRI, Redlands, CA, USA software was used for this campus CO2 emissions evaluation and visualization. The overall estimate of the CO2 emissions for the university campus was 127.7-tons CO2 equivalent. The lowest emission was 0.02-tons CO2 equivalent while the maximum value was 20.9-tons of CO2 equivalent. By this ArcGIS-based evaluation, it is evident that geographically integrated model for campus estimation and visualization of CO2 emissions provides the information for decision makers to develop viable strategies for achieving a higher standard in overall campus sustainability and addressing the issue of climate change.

  1. Kaido Kama: oleme esindusdemokraatia kriisis / Kaido Kama ; intervjueerinud Priit Simson

    Index Scriptorium Estoniae

    Kama, Kaido, 1957-

    2009-01-01

    Endine minister, praegu riigikontrolöri nõunik räägib Eesti eurorahade kasutamisest, majandusolukorrast, valimiskampaaniatest, sotsiaalsüsteemist. Autor leiab, et nii Eesti kui ka kogu maailma probleem on enamusdemoktaatia kriisis. Samuti kritiseerib autor Eesti regionaalpoliitikat, mis suunab kõiki inimesi ühemõtteliselt Tallinna suunas

  2. Skype saabub firmadesse / Kaido Einama

    Index Scriptorium Estoniae

    Einama, Kaido, 1971-

    2007-01-01

    Internetisuhtlusfirma Skype on 2006. aasta alguses toonud turule spetsiaalselt firmadele suunatud toote, mis peaks vähendama ettevõtete umbusku ning suurendama suhtlusprogrammi kasutatavust. Lisa: Skype'i peibutised firmadele; Veel internetitelefone

  3. Vabastav raamat kosmilisest totaalsusest / Kaido Floren

    Index Scriptorium Estoniae

    Floren, Kaido

    2000-01-01

    Arvustus: Strugatski, Arkadi, Strugatski, Boriss. Asustatud saar / tlk. Kalle Käsper ja Gohar Käsper-Markosjan. Tln: : Varrak, 1999. Vastukaja : Käsper, Kalle, Käsper-Markosjan, Gohar. Elementaarne, Watson! // Eesti Päevaleht : Arkaadia (2000) 15. jaan., lk. 10

  4. Minu nimi on Earl / Kaido Soorsk

    Index Scriptorium Estoniae

    Soorsk, Kaido, 1973-

    2008-01-01

    Ameerika autodisainerist Harley Earl'ist (1893-1969) ja tema tähtsamatest töödest: Buick Y-Job (1938), LeSabre (1951), Chevrolet Corvette (1953). Harley Earl juhtis General Motorsi Art and Color Section'it, mis 1937. a. nimetati ümber Style Section'iks

  5. 10 kohta veel all / Kaido Haagen

    Index Scriptorium Estoniae

    Haagen, Kaido

    2014-01-01

    Sukeldumiskohti maailmas: Similani saared Tais, Averoy Norras, Tofo Mosambiigis, Punane meri Egiptuses, Sipadani saar Malaisias, Dili Ida-Timoris, Tulamben Balil, Lembeh Indoneesias, Malapascua Filipiinidel, Äntu järved Eestis

  6. Kas noorus on hukas? / Kaido Soorsk

    Index Scriptorium Estoniae

    Soorsk, Kaido, 1973-

    2008-01-01

    Suurbritannia Mehaanikainseneride Ühingu (Institution of Mechanical Engineers) korraldataval iga-aastasel tootearendusvõistlusel masinaehituse- ning autotehnika eriala tudengitele saavutas Tallinna Tehnikaülikooli ja Tallinna Tehnikakõrgkooli tudengite ehitatud vormelauto 2007. a. klassis III 4. koha, 2008. a. klassis I parima uustulnuka tiitli ja 13. koha. Festo 8-st. Juhendasid õppejõud Risto Kõiv ja Janek Luppin

  7. Riigipea institutsioon II aastatuhande viimasel veerandil / Kaido Jaanson

    Index Scriptorium Estoniae

    Jaanson, Kaido, 1940-

    2002-01-01

    Presidendi institutsioonist Lääne-Euroopas pärast Teist maailmasõda. Tabelid: Prantsusmaa 1995. a. presidendivalimised; Soome 2000. a. presidendivalimised; Iiri Vabariigi 1997. a. presidendivalimised (30. oktoober)

  8. Peter Fisk : hoidke servale, mitte keskele / Kaido Einama

    Index Scriptorium Estoniae

    Einama, Kaido, 1971-

    2007-01-01

    Strateegi ja turundaja, Genius Worksi tegevjuhi Peter Fiski esinemisest Tallinna Lauluväljaku uues konverentsikeskuses toimunud innovatsioonikonverentsil InnoEstonia 2007. Vt. samas: Kes on Peter Fisk?

  9. Ümbreilma reisikirä / Kaido Kama

    Index Scriptorium Estoniae

    Kama, Kaido, 1957-

    1999-01-01

    Jahtlaeva "Lennuk" ümbermaailmareisist. Järgneb 9.,16. nov., 2.,14.,30. dets. ; 2000, 13. jaan., 3.,10. veebr., 9.,16.. märts, 13.,27. apr., 25. mai, 22.,29. juuni, 6. juuli, 24. aug., 1.,28. sept., 12.,26. okt., 2.,23. nov., 7. dets ; 2001, 4.,9.,25. jaan., 15. veebr., 6.,13.,22., märts

  10. Hiina mänguasjavabrikud vallutavad mobiilimaailma / Kaido Einama

    Index Scriptorium Estoniae

    Einama, Kaido, 1971-

    2008-01-01

    Ülevaade visiidist Hiina moodsa suurlinna Shanghai elektroonikakauplustesse, kus puututi kokku tuntud kaubamärkide Nokia, Apple ning HTC toodete koopiatega - Nokla, HiPhone, MTC ja ZTC telefonidega. Lisa: Shanghai poodleja spikker

  11. Eesti organisatsioonikultuur on ameerikalik / Maaja Vadi, Kaido Sirel

    Index Scriptorium Estoniae

    Vadi, Maaja, 1955-

    1994-01-01

    Tabelid: W.G. Ouchi organisatsioonikultuuri mudel Jaapani ja Ameerika organisatsioonikultuuri võrdlus. Hindamissüsteem. Rahvuskultuuriline taust. Töötajate värbamine. Karjäär. Otsustamine ja vastutus. Suhtlemine ja traditsioonid

  12. Tähesõjad on tagasi / Merit Kopli, Kaido Kopli

    Index Scriptorium Estoniae

    Kopli, Merit, 1969-

    1999-01-01

    George Lucas ja tema ulmefilmid "Tähesõjad", millest uusim "Star Wars I : The Phantom Menace" tõotab kujuneda 1999.aasta menukaimaks filmiks : Ajalehe lehekülg mitmesuguse infoga filmi maksumuse, tegelaste, režissööri ja esilinastuse kohta

  13. Samm välisilma poole / Kaido Jaanson

    Index Scriptorium Estoniae

    Jaanson, Kaido, 1940-

    2003-01-01

    Rets. rmt.: The Estonian Foreign Policy Yearbook 2003. Eesti välispoliitika aastaraamat. Tallinn, 2003 ; Danish Foreign Policy Yearbook 2003. - Copenhagen: Danish Institute for International Studies, 2003

  14. BUILDING A NEW GENERATION SCIENCE LIBRARY: THE KAUST STORY

    KAUST Repository

    Al Zahrani, Rashed; Branin, Joseph; Yu, Yi

    2012-01-01

    will describe the major characteristics in contemporary science research, education, and information management that guided the design of our library facility, technical infrastructure, and services. We will give concrete examples and evaluations of our

  15. Managing user queries using cloud services: KAUST library experience

    KAUST Repository

    Ramli, Rindra M.; Ba-Rayyan, Faten A.

    2017-01-01

    The provision of reference and information services are one of the major activities for academic libraries. Answering questions and providing relevant and timely answers for library users are just one of such services. Questions come in many format

  16. Our Journey to Summon and 360: The KAUST experience

    KAUST Repository

    Ramli, Rindra M.

    2017-01-01

    to embark on the project to evaluate, assess and recommend for a new and robust discovery layer. On top of that, the presenters would elaborate the project timeline (which also include the implementation phase for Summon and 360 Core), the challenges faced

  17. Juan Linz ja eestlane Aleksander Kesküla / Kaido Jaanson

    Index Scriptorium Estoniae

    Jaanson, Kaido, 1940-

    2002-01-01

    Eestlasest revolutsionääri Aleksander Kesküla elust Hispaanias aastail 1934-1963. Artikli aluseks on A. Kesküla Hispaania-perioodi väheste sõprade, eelkõige tänaseks rahvusvaheliselt tunnustatud sotsioloogi Juan Linz'i meenutused

  18. Maksukohustuse täitmise preventiivne tagamine ehk kuidas õigusriigile kohaselt ennustada / Kaido Künnapas

    Index Scriptorium Estoniae

    Künnapas, Kaido, 1985-

    2018-01-01

    Euroopa Inimõiguste Kohtu kujundatud miinimumstandardid maksude tasumise tagamiseks omandisse sekkumisel, preventiivsete tõkendite süsteemist Eestis ja Ameerika Ühendriikides, riigivastutuse probleemidest preventiivsete tõkendite puhul. Artikkel põhineb autori doktoritööl "Maksukohustuse täitmise preventiivne tagamine enne maksukohustuse tuvastamist: ettevaatuspõhimõte maksumenetluses"

  19. Pimedad ööd kutsuvad häid filme vaatama / Kaido Soom

    Index Scriptorium Estoniae

    Soom, Kaido

    2008-01-01

    12. Pimedate Ööde filmifestivali filmidest, mis jätsid sügavama mulje artikli autorile - Taani mängufilm "Mine rahus, Jamil" (rezh. Omar Shargawi), Suurbritannia -Itaalia - Saksamaa - Hispaania - Poola koostööfilm "See on vaba maailm" (rezh. Ken Loach) ja Šveitsi dokumentaalfilm "Tagane, saatan" (rezh. Peter Entell)

  20. Faktooring käibevahendite finantseerimise vahendina / Ivar Sikk, Kaido Kallas

    Index Scriptorium Estoniae

    Sikk, Ivar

    2002-01-01

    Faktooring on väga paindlik käibevahendite finantseerimise vahend, mis sobib kõikidele ettevõtetele, kes pakuvad või soovivad pakkuda oma kauba või teenuse ostjatele maksetähtaega. Tabelid. Joonised

  1. Vähemusrahvuste kultuuromavalitsuse seadus ja Saksa Kultuuromavalitsus Eesti Vabariigis 1925-1940 / Kaido Laurits

    Index Scriptorium Estoniae

    Laurits, Kaido

    2008-01-01

    Vähemuse kaitse küsimusest. Rahvuslikust kultuurautonoomiast. Vähemusrahvuste õigustest Eesti Vabariigi esimestes aktides. Vähemusrahvuste kultuurautonoomia seadusest, Saksa Kultuuromavalitsuse loomisest ja selle organisatsioonilisest ülesehitusest

  2. Die deutschbaltische Minderheit in der Republik Estland von 1918 bis 1940 / Kaido Laurits

    Index Scriptorium Estoniae

    Laurits, Kaido

    2011-01-01

    Kultuurautonoomia seadusest ja saksa kultuurautonoomiast, baltisaksa haridus- ja kultuurielust. Maal elavatest baltisaksalastest ja nende põllumajanduslikust olukorrast. Linnades leanud baltisakslastest. Rahvustevahelistest suhetest Eestis 1930ndatel aastatel.

  3. To get or not to get: the KAUST library e-resources acquisition experience

    KAUST Repository

    Ramli, Rindra M.; Kabli, Ola

    2014-01-01

    In the challenging times of budget cuts and reviews, libraries are faced with issues, among others, such as justifying acquisition, negotiating deals and reviewing current subscriptions (pertaining to electronic resources). With the rapid increase

  4. KFUPM-KAUST Red Sea model: Digital viscoelastic depth model and synthetic seismic data set

    KAUST Repository

    Al-Shuhail, Abdullatif A.; Mousa, Wail A.; Alkhalifah, Tariq Ali

    2017-01-01

    The Red Sea is geologically interesting due to its unique structures and abundant mineral and petroleum resources, yet no digital geologic models or synthetic seismic data of the Red Sea are publicly available for testing algorithms to image and analyze the area's interesting features. This study compiles a 2D viscoelastic model of the Red Sea and calculates a corresponding multicomponent synthetic seismic data set. The models and data sets are made publicly available for download. We hope this effort will encourage interested researchers to test their processing algorithms on this data set and model and share their results publicly as well.

  5. KFUPM-KAUST Red Sea model: Digital viscoelastic depth model and synthetic seismic data set

    KAUST Repository

    Al-Shuhail, Abdullatif A.

    2017-06-01

    The Red Sea is geologically interesting due to its unique structures and abundant mineral and petroleum resources, yet no digital geologic models or synthetic seismic data of the Red Sea are publicly available for testing algorithms to image and analyze the area\\'s interesting features. This study compiles a 2D viscoelastic model of the Red Sea and calculates a corresponding multicomponent synthetic seismic data set. The models and data sets are made publicly available for download. We hope this effort will encourage interested researchers to test their processing algorithms on this data set and model and share their results publicly as well.

  6. ORCID Integration: Services to Create and Use ORCID IDs at KAUST

    KAUST Repository

    Grenz, Daryl M.; Baessa, Mohamed A.

    2015-01-01

    repository. Our next step was to join ORCID as an institutional member and then set up a plan to support our faculty, researchers and students in the creation and use of ORCID identifiers. This presentation will look at the choices made and lessons learned

  7. Tööettevõtulepingu probleeme : [bakalaureusetöö] / Kaido Loor ; Tartu Ülikool, õigusteaduskond ; juhendaja: Endel Ploom

    Index Scriptorium Estoniae

    Loor, Kaido

    1996-01-01

    Tööettevõtuleping erinevates õigussüsteemides (Rooma õiguses, sõjaeelses Eesti Vabariigis, välisriikides), tööettevõtulepingu mõiste ja põhitunnused kehtivas õiguses; tööettevõtuleping võlaõiguses

  8. Ülemiste City kvartal Tallinnas / Mattias Agabus, Eero Endjärv, Illimar Truverk...[jt.] ; fotod: Kaido Haagen

    Index Scriptorium Estoniae

    2008-01-01

    asendiplaan, 3 korruste plaani, 3 värv. välisvaadet, restorani Mercado sisevaade; projekteerijad: M. Agabus, E. Endjärv, I.Truverk (Agabus, Endjärv & Truverk Arhitektid); hoonete arhitektuurne osa: E. Endjärv; sisearhitektid: K. Lents, H. Kääramees, T. Aunre (restoran Mercado); konstruktorid: Ü. Suvemaa, A. Lehtla, K. Adoberg; maastikuarhitektuur: Ü. Grišakov, M. Agabus, E. Endjärv

  9. Eesti võimalused EL maaelu strateegias 2007-2013, sealhulgas Leader programm / Kaido Koppel, Eha Paas

    Index Scriptorium Estoniae

    Koppel, Kaido

    2005-01-01

    Ilmunud ka: VI Rural Parliament of Estonian Villages : July 21-23, 2005 in Lepanina, Pärnu County. Eestis rakendub Leader programm täies mahus Euroopa Liidu uuel eelarve perioodil ehk alates aastast 2007. Skeem: Maaelu arengu baas 2007-2013

  10. Rahvusooper Estonia annab 5. V oma 99. hooaja viimase etenduse "Luikede järv" / Kaido Padar

    Index Scriptorium Estoniae

    Padar, Kaido

    2005-01-01

    Kella 12-15 on linnaelanikud ja külalised kutsutud hooaega lõpetama ja saatma Estonia maja remonti. Tutvustatakse remondi-ehitusprogrammi, ekraanidel näeb videot Estoniast, lapsed saavad rasvakriidiga joonistada "Unistuste ooperimaja" ja tutvuda kostüümidega, saalis on noorteprojektides osalenute paremate tööde näitus, saab pildistada ja filmida teatri ruume jpm.

  11. Exploring off-set pricing models and article deposit terms at King Abdullah University of Science & Technology (KAUST)

    KAUST Repository

    Buck, Stephen; Vijayakumar, J.K.

    2018-01-01

    -set models, and not transparently offsetting the APCs to the subscription cost, in order to raise more income? Whether by design or accident it is a complex world which needs a time commitment, which not all librarians can give, to understand fully

  12. 28 clear sentences / Tõnis Saadoja

    Index Scriptorium Estoniae

    Saadoja, Tõnis, 1980-

    2011-01-01

    Näitusest "Kaido Ole. Handsome Hero and Plenty of Still Lifes" ("Kaido Ole. Kena kangelane ja küllaga vaikelusid") Kumu Kunstimuuseumis 27.01.-15.04.2012. Kunstnikust ja tema loomingust. Video "Monologue" Kaido Olest tegi Flo Kasearu

  13. Krõps kirikus teenis esikoha : Kaido Veermäe püüab ideid ja kütab emotsioone / Anneli Aasmäe

    Index Scriptorium Estoniae

    Aasmäe, Anneli, 1973-

    1999-01-01

    Režissöör Andrus Tuisu reklaamiklipp "Vigur krõps - kirik" võitis reklaamfilmide festivalil "The Mobius Advertising Awards 1998" Chicagos esimese koha. Idee autor reklaamiagentuurist Kontuur Leo Burnett jagab muljeid

  14. Eesti Ajaloomuuseumi, Maarjamäe lossi tallihoone renoveerimine = Renovation of the Estonian History Museum's Maarjamäe palace stables / Jaak Huimerind, Tarmo Piirmets ; kommenteerinud Kaido Kivi

    Index Scriptorium Estoniae

    Huimerind, Jaak, 1957-

    2015-01-01

    Eesti Ajaloomuuseumi Maarjamäe lossi renoveeritud tallihoone Tallinnas Pirita tee 66, valminud 2014. Arhitekt Jaak Huimerind (Studio Paralleel OÜ), sisearhitekt ja näituse kujundaja Tarmo Piirmets (Pink OÜ). Eesti Kultuurkapitali Arhitektuuri sihtkapitali renoveerimispreemia 2014

  15. Töötajate õigused maksejõuetu tööandja ettevõtte üleminekul : kas ebaõnnestunud harmoneerimine? / Kaido Künnapas

    Index Scriptorium Estoniae

    Künnapas, Kaido, 1985-

    2011-01-01

    2009. aastal jõustunud töölepingu seaduse §-s 112 sisalduva töölepingute ülemineku reeglistiku vastavusest Euroopa Liidu õigusele ning olulisematest positiivsetest ja negatiivsetest arengusuundadest asjaomase reeglistiku muutumisel Eestis

  16. John Smithi kaks palet / Johannes Saar

    Index Scriptorium Estoniae

    Saar, Johannes, 1965-

    2003-01-01

    Näitus "John Smith. Marko ja Kaido" Tallinna Kunstihoones. Kaido Ole ja Marko Mäetamm esindavad rühmitusena "John Smith" Eestit 2003. a. Veneetsia biennaalil. Ilmunud ka kogumikus "Päevast päeva", lk. 90-96

  17. Tornimäe kaksiktornid Tallinnas. Konkursi "Aasta betoonehitis 2007" nominent / Meeli Truu, Juhan Idnurm, Jaan Port...[jt.

    Index Scriptorium Estoniae

    2008-01-01

    AS Nord Projekt; konstruktorid: Juhan Idnurm, Jaan Port, Kaido Kuusiku (Nord Projekt AS), Indrek Heinloo (E-Inseneribüroo OÜ), Matis Teeäär (Neoprojekt OÜ), Kaido Pärl (TAA-Konsult); ehitajad: Lemminkäinen Eesti AS, AS Merko Ehitus; betooni ja betoonelementide tarnijad: AS Rudus Eesti, AS Betoneks

  18. Rahvuspaviljon kui lakmuspaber / Reet Varblane

    Index Scriptorium Estoniae

    Varblane, Reet, 1952-

    2003-01-01

    50. Veneetsia biennaal "Unistused ja konfliktid". Kuraator Francesco Bonami. Võrdlus 49. Veneetsia biennaaliga. Šveitsi paviljonis näidatud Emanuelle Antille'i filmist "Angels Camp", iisraeli kunstniku Michal Rovneri ja Luksemburgi esindava Su-Mei Tse (rahvusväljapaneku preemia) ruumist, Eesti väljapanekust "Marko und Kaido" - Marko Mäetamm ja Kaido Ole

  19. Kadriorus jagati riiklikke autasusid / Tõnu Anton

    Index Scriptorium Estoniae

    Anton, Tõnu, 1953-

    1999-01-01

    Seoses Eesti Vabariigi 81. aastapäevaga said Valgetähe teenetemärgid juristid Tõnu Anton, Rait Maruste, Kaido Pihlakas ja Luule Käis. Kommenteerib Riigikohtu halduskolleegiumi esimees Tõnu Anton

  20. Kunstnike liidu uus kunstigalerii Hop / Juta Kivimäe

    Index Scriptorium Estoniae

    Kivimäe, Juta, 1952-

    2006-01-01

    Eesti Kunstiakadeemias Kaido Ole juhendamisel maali õppiva sakslase Benjamin Badocki ja Kadri Mälgu juhendamisel ehtekunsti õppiva austraallanna Teresa Lane'i ühisnäitus "I like reality" Hopi galeriis 21.-30. V

  1. Eesti Energia esindused = Eesti Energia branches / Andres Labi, Janno Roos

    Index Scriptorium Estoniae

    Labi, Andres, 1977-

    2013-01-01

    Eesti Energia klienditeeninduse kontorite sisekujundusest. Autorid: Janno Roos, Andres Labi ja Liisa Põime (Ruumilabor). Visuaalne identiteet: Tank.Teenuste disain: Urmas Pastarus. ESLi aastapreemiate žürii esimehe Kaido Kivi ning žürii liikme Raivo Puusepa arvamused

  2. Tallinnas Narva mnt. 7 asuva kohviku Zebra sisekujundus / Tiiu Truus, Tiiu Prisko, Mati Veermets...[jt.

    Index Scriptorium Estoniae

    2006-01-01

    põhiplaan, 11 värv. vaadet; fotod: Kalle Veesaar; laes olevate dekoratiivsete lippude graafiline kujundus on Tiiu Priskolt ja Mati Veermetsalt, tualettruumi looduskivist valamu ja põrandavaasi autor on Kaido Kivi

  3. Koolis tulistamise järelmid: korralikud kriisikavad ja õpetajatele rohkem õigusi / Joosep Värk

    Index Scriptorium Estoniae

    Värk, Joosep

    2015-01-01

    Vestlusest Haridus- ja Teadusministeeriumi koolivõrgu osakonna konsultandi Jürgen Rakaselja, Politsei- ja Piirivalveameti arendusosakonna valmisoleku ja reageerimise büroo juhi Marti Magnuse ja Rocca al Mare Kooli direktori Kaido Kreintaaliga

  4. GAZ - slishkom vremennaja alternativa / Roman Vikulov

    Index Scriptorium Estoniae

    Vikulov, Roman

    2005-01-01

    Narva linna küttekomisjoni poolt organiseeritud seminarist, kus osales ka Põhjamaade juhtivasse energeetikakompaniisse kuuluva kontserni Fortum Termest arengudirektor Kaido-Paul Bõstrov ja Vene Föderatsiooni majandusministeeriumi riiklik ekspert, akadeemik Vladimir Borovkov

  5. Leningradi aktsioonid / Sandra Jõgeva

    Index Scriptorium Estoniae

    Jõgeva, Sandra, 1976-

    2006-01-01

    Eesti kunstnike väljapanekust "Empty Spaces and their Occupants" 12.-24. augustini 2006 a. toimuval Peterburi Maneezhi 6. rahvusvahelisel eksperimentaalkunsti festivalil, kuraator Maksim Surin. Osalevad Kaido Ole, Merike Estna, Meeland Sepp jt

  6. Tootest olulisemaks saab ärimudel. Kandiline arbuus tavalisest 30 korda kallim / Ain Alvela ; kommenteerinud Janek Kalvi

    Index Scriptorium Estoniae

    Alvela, Ain, 1967-

    2011-01-01

    Eesti Arengufondi juhatuse esimehe Ott Pärna, ASi Kalev Chocolate Factory juhataja Kaido Kaare ja ASi Balsnack International Holding juhatuse esimehe Elmar Rusingu ettekannetest toiduainetööstuse aastakonverentsil "Uue tõusu ootuses". Graafik

  7. Pop / Tõnu Kaalep

    Index Scriptorium Estoniae

    Kaalep, Tõnu, 1966-2018

    2007-01-01

    Heliplaatidest: Wilco "Sky Blue Sky", Traffic "Traffic", The Cinematic Orchestra "Ma Fleur", Static-X "Cannibal", DJ Kentaro "Enter", Erinevad esitajad "Biitpiraadid 2: Kitarristide röövretk", Kaido Kirikmäe "Lintprii"

  8. Oskari juht loovutab peagi vastvõidetud aktsiapaki / Aldo Parik ; interv. Hans Väre

    Index Scriptorium Estoniae

    Parik, Aldo

    2007-01-01

    Saarepeedil tegutseva lihatööstuse Oskar tegevjuht ja omanik Aldo Parik suurendas oma osalust 100%-ni, kuid kavatseb lähiajal aktsiate kontrollpakist loobuda. Lisa: Taust. Arvamust avaldab Wõro Kommertsi juhatuse esimees Kaido Kaare

  9. Doktor Haageni preparaadid / Kalev Vapper

    Index Scriptorium Estoniae

    Vapper, Kalev, 1982-

    2008-01-01

    Mõtteid ja assotsiatsioone Kaido Haageni kaks nädalat pärast pommitamist Gruusias tehtud fotoseeriat vaadates. Fotosid eksponeeriti näitusel "Seinad 080808" Disaini- ja Arhitektuurigaleriis Tallinnas

  10. Sem prioritetov Tallinna

    Index Scriptorium Estoniae

    2003-01-01

    Tallinna linnakantselei Eurointegratsioonibüroo juhataja Hedi Pika, projektijuhi Tõnu Karu ja Tallinna alalise esindaja Brüsselis Kaido Sireli tööst Euroopa Liidu struktuurifondide projektide realiseerimisel

  11. Stephen Kingi tee tumeda tornini võttis 30 aastat / Raul Sulbi

    Index Scriptorium Estoniae

    Sulbi, Raul

    2007-01-01

    Stephen Kingi triloogiast "Tume torn" (Tallinn : Pegasus, 2006-2007) : Laskur : [romaan] / tõlkija Mart Kalvet ; Kolm saatusekaarti / [tõlkinud Kaido Haavandi] ; Ahermaad / [tõlkinud Matti Piirimaa] ;

  12. Kunstnikele tasuta monitorid / Kirsti Vainküla

    Index Scriptorium Estoniae

    Vainküla, Kirsti, 1972-

    1998-01-01

    Ideegrupp Interface jagas 10-le eesti kunstnikule arvutimonitorid, mille need kunstiliselt kujundavad. Monitori said Agur Kruusing, Marko Mäetamm, Kaido Ole, Martin Pedanik, Urmas Puhkan, Jüri Roosa, Jasper Zoova

  13. Baruto : dopinguproov polnud korrektne / Oliver Lomp

    Index Scriptorium Estoniae

    Lomp, Oliver

    2008-01-01

    Jaapni sumoproffide üldkoosolekul andsid kõik 70 eliitdivisjonidesse kuuluvat maadlejat allkirja avaldusele, kus väjendati nördimust ebakorrektsete marihuaana testimisprotseduuride pärast. Kaido Höövelson (Baruto) selgitas protesti tagamaid

  14. Digimaks ei hakka põhjustama guugeldamisreise / Dmitri Jegorov

    Index Scriptorium Estoniae

    Jegorov, Dmitri

    2017-01-01

    Eesti digimajanduse maksustamise muutuste mõjust. Vastus Kaido Künnapas, Mihkel Miidla ja Paul Künnapi artiklile "Kas pärast digimaksu kehtestamist tuleb guugeldamiseks minna Rootsi reisile?". Eesti Päevaleht, 2017, 9. okt.

  15. Combustion-driven oscillation in a furnace with multispud-type gas burners. 4th Report. Effects of position of secondary air guide sleeve and openness of secondary air guide vane on combustion oscillation condition; Multispud gata gas turner ni okeru nensho shindo. 4. Nijigen kuki sleeve ichi oyobi nijigen kuki vane kaido no shindo reiki ni oyobosu eikyo

    Energy Technology Data Exchange (ETDEWEB)

    Akiyama, I.; Okiura, K.; Baba, A.; Orimoto, M. [Babcock-Hitachi K.K., Tokyo (Japan)

    1994-07-25

    Effects of the position of a secondary air guide sleeve and the openness of a secondary air guide vane on combustion oscillation conditions were studied experimentally for multispud-type gas burners. Pressure fluctuation in furnaces was analyzed with the previously reported resonance factor which was proposed as an index to represent the degree of combustion oscillation. As a result, the combustion oscillation region was largely affected by both position of a guide sleeve and openness of a guide vane. As the openness having large effect on the ratio of primary and secondary air/tertiary air and the position hardly having effect on the ratio were adjusted skillfully, the burner with no combustion oscillation region was achieved in its normal operation range. In addition, as the effect of preheating combustion air was arranged with a standard flow rate or mass flow flux of air, it was suggested the combustion oscillation region due to preheating can be described with the same manner as that due to no preheating. 5 refs., 8 figs.

  16. Water and Energy Consumption at King Abdullah University of Science and Technology

    KAUST Repository

    Wiche Latorre, Pia Alexandra

    2012-05-01

    Saudi Arabia is the greatest exporter of oil in the world and also the country with greatest desalination capacity. It is considered a rich country but not a developed one. Because water is scarce while energy is abundant, it becomes important to evaluate the environmental performance of populations in Saudi Arabia with regards to these two aspects. King Abdullah University of Science and Technology (KAUST) is a gated community in Saudi Arabia with high living standards where water and energy are free of cost (no constraint over use). Four environmental sustainability indicators were used to determine the environmental performance of KAUST in comparison to other countries. It was found that per capita, KAUST is between the five greatest water and energy consumers in the world. Important factors to this result are the fact that KAUST is still under construction, that the peak capacity for permanent residents has not yet been reached and that there is little control over the water and energy systems at KAUST. It was concluded that KAUST should reduce its water and energy consumption per capita. To this means, some proposed solutions were to have wide-spread awareness-raising campaigns to all people working and living in KAUST, and to improve control over air conditioning control systems.

  17. When Library and Archival Science Methods Converge and Diverge: KAUST’s Multi-Disciplinary Approach to the Management of its Audiovisual Heritage

    KAUST Repository

    Kenosi, Lekoko; Graves, Chris; Bukhari, Duaa

    2015-01-01

    Libraries and Archives have long recognized the important role played by audiovisual records in the development of an informed global citizen and the King Abdullah University of Science and Technology (KAUST) is no exception. Lying on the banks

  18. Recommendation Report: EJournals/EBooks A-Z Management System

    KAUST Repository

    Ramli, Rindra M.

    2014-01-01

    This is a recommendation report for KAUST Library on the Ejournals / EBooks AZ Management systems project. It briefly described the issues faced by the ERM Team, project plan overview and the project findings as well as the recommendation(s).

  19. Using the IR as a Research Data Registry

    KAUST Repository

    Grenz, Daryl M.; Mastoraki, Eirini; Wang, Han; Baessa, Mohamed A.

    2018-01-01

    As data and software become increasingly common research outputs, universities have an opportunity to expand their existing efforts to record affiliated publications so that they also capture information about research data releases. At KAUST we

  20. Electronic Resources Management Project Presentation 2012

    KAUST Repository

    Ramli, Rindra M.

    2012-01-01

    This presentation describes the electronic resources management project undertaken by the KAUST library. The objectives of this project is to migrate information from MS Sharepoint to Millennium ERM module. One of the advantages of this migration

  1. Optimal Experimental Design for Large-Scale Bayesian Inverse Problems

    KAUST Repository

    Ghattas, Omar

    2014-01-01

    We develop a Bayesian framework for the optimal experimental design of the shock tube experiments which are being carried out at the KAUST Clean Combustion Research Center. The unknown parameters are the pre-exponential parameters and the activation

  2. The establishment phases of ETD program in a brand new University

    KAUST Repository

    Baessa, Mohamed A.

    2014-07-24

    For many Universities, ETD is a combination of digitized documents and digitally born documents. But at brand new Universities like King Abdullah University of Science and Technology (KAUST), or more specifically for the libraries that born digitally, est

  3. Optimal Design of Shock Tube Experiments for Parameter Inference

    KAUST Repository

    Bisetti, Fabrizio; Knio, Omar

    2014-01-01

    We develop a Bayesian framework for the optimal experimental design of the shock tube experiments which are being carried out at the KAUST Clean Combustion Research Center. The unknown parameters are the pre-exponential parameters and the activation

  4. The establishment phases of ETD program in a brand new University

    KAUST Repository

    Baessa, Mohamed A.; Vijayakumar, J.K.

    2014-01-01

    For many Universities, ETD is a combination of digitized documents and digitally born documents. But at brand new Universities like King Abdullah University of Science and Technology (KAUST), or more specifically for the libraries that born

  5. Gathering by the Red Sea highlights links between environment and epigenetics

    KAUST Repository

    Li, Mo; Borrelli, Emiliana; Magistretti, Pierre J.; Izpisua Belmonte, Juan Carlos; Sassone-Corsi, Paolo; Orlando, Valerio

    2017-01-01

    , and how the environment may impinge on epigenetic control, are topics of growing debate. Those themes were the focus of the inaugural international King Abdullah University of Science and Technology (KAUST) Research Conference on Environmental Epigenetics

  6. Effect of Temperature, Pressure and Equivalence Ratio on Ignition Delay in Ignition Quality Tester (IQT): Diesel,n-Heptane, andiso-Octane Fuels under Low Temperature Conditions

    KAUST Repository

    Yang, Seung Yeon; Naser, Nimal; Chung, Suk-Ho; Cha, Junepyo

    2015-01-01

    -octane in relatively low temperature conditions to simulate unsteady spray ignition behavior. A KAUST Research ignition quality tester (KR-IQT) was utilized, which has a feature of varying temperature, pressure and equivalence ratio using a variable displacement fuel

  7. Nanocomposite Membrane via Magnetite Nanoparticle Assembly

    KAUST Repository

    Xie, Yihui

    2012-01-01

    discussions and suggestions. I also want to extend my gratitude to the staff from the KAUST Core Lab for Advanced Nanofabrication, Imaging and Characterization, especially Dr. Ali Reza Behzad, Dr. Rachid Sougrat, and Dr. Long Chen, for their assistance

  8. Comparative metagenomics of the Red Sea

    KAUST Repository

    Mineta, Katsuhiko

    2016-01-01

    started monthly samplings of the metagenomes in the Red Sea under KAUST-CCF project. In collaboration with Kitasato University, we also collected the metagenome data from the ocean in Japan, which shows contrasting features to the Red Sea. Therefore

  9. Identity of a brand new library

    KAUST Repository

    Vijayakumar, J.K.

    2017-01-01

    King Abdullah University of Science and Technology (KAUST) Library in Saudi Arabia aspires to be one of the great new-generation libraries in the field of scientific research. Its services and systems support a digitally born collection, 97

  10. Computational Study of Stratified Combustion in an Optical Diesel Engine

    KAUST Repository

    Jaasim, Mohammed; Hernandez Perez, Francisco; Vallinayagam, R.; Vedharaj, S.; Johansson, Bengt; Im, Hong G.

    2017-01-01

    Full cycle simulations of KAUST optical diesel engine were conducted in order to provide insights into the details of fuel spray, mixing, and combustion characteristics at different start of injection (SOI) conditions. Although optical diagnostics

  11. Kunstimuuseumi viimane näitus Rotermanni soolalaos

    Index Scriptorium Estoniae

    2005-01-01

    13. maist Marko Mäetamme ja Kaido Ole "Suur projekt". 18. V muusikaline live-keskkond "Museum of Sleep / Uinuv muuseum", hüvastijätt soolalaoga Ki wa, Joel Tammiku, Tanel Paliale, Masina, Porti, El Roboticos Digitablosi ja Fabrique'i ning Villu Jõgeva ja Kaarel Kurismaa objektide osavõtul

  12. Täna kell 18.30 avatakse Okupatsioonide muuseumis...

    Index Scriptorium Estoniae

    2004-01-01

    Linnakultuuriaineline näitus "Paraad". Keskne idee on seotud rula kui eluhoiakuga. Osalevad Tuukka & Kätlin Kaila ning Vaughan Baker (London), Jani Tolin ja Freeman (Helsingi), Aadam Kaarma, Anu Samarüütel, Tarrvi Laamann, Marko Mäetamm & Kaido Ole, Lazer, Väike J, Veronika Valk, DJ Critical

  13. Vabadus võtta vabalt / Maria-Kristiina Soomre

    Index Scriptorium Estoniae

    Soomre, Maria-Kristiina, 1978-

    2004-01-01

    Tänavakunstinäitus "Paraad" Eesti Lähimineviku Okupatsioonide Muuseumis. Osalevad Tuukka & Kätlin Kaila ning Vaughan Baker (London), Jani Tolin ja Freeman (Helsingi), Aadam Kaarma, Anu Samarüütel, Tarrvi Laamann, Marko Mäetamm & Kaido Ole, Lazer, Väike J, Veronika Valk, Kaarel Kulbin, DJ Critical

  14. Maal ei ole surnud / Jaan Elken

    Index Scriptorium Estoniae

    Elken, Jaan, 1954-

    2001-01-01

    Põhjamaade ja Baltikumi I maalibiennaal Rootsis Väsbys. Biennaali Rootsi-poolne kuraator ja kujundaja Ricardo Donoso, Eesti komplekti koostas Mare Pedanik. Eksponeeritud on Tiit Pääsukese, Ado Lille, Andres Toltsi, Kaido Ole, Jaan Elkeni tööd. Näituse ülevaade, eraldi peatutud Leedu ja Läti kunstnikel

  15. Hotell "Telegraaf" Tallinnas Vene t 9 / Martin Aunin, Riho Märtson, Külli Salum...[jt.

    Index Scriptorium Estoniae

    2007-01-01

    I ja III korruse plaan, 2 välisvaadet, 4 sisevaadet; fotod: Tiit Veermäe, Kaido Haagen, Arne Maasik; endise Kommertspanga (ehitatud 1874. a. arhitekt P. Schreiberi projekti järgi N. Thamme juhtimisel) ja hilisema Tallinna Telegraafi hoonesse rajatud hotell, projekteerija EA Reng

  16. Kõik on nii nagu enne, aga miski pole enam endine / Martin Rünk

    Index Scriptorium Estoniae

    Rünk, Martin

    2010-01-01

    Anders Härmi kuraatoriprojekt "Next to Nothing" ("Eimillestki edasi") Eesti Kaasaegse Kunsti Muuseumis 22. augustini 2010. Pikemalt Martin Creedi (Suurbritannia), Laura Tootsi, Triin Tamme, Dénes Farkasi, Neeme Külma ja Kaido Ole töödest

  17. Unustage ainulaadsus, maalikunst on nüüd kunstihoones keelatud / Johannes Saar

    Index Scriptorium Estoniae

    Saar, Johannes, 1965-

    2005-01-01

    Anders Härmi kureeritud rahvusvahelisest maalinäitusest "Maalimine keelatud" Tallinna Kunstihoones. Lätlase Ritums Ivanovsi, itaallase Davide LaRocca, eestlaste Tõnis Saadoja, Marko Mäetamme, Kaido Ole ja Margarete Fuksi töödest näitusel

  18. Büroo Ignite = Ignite office / Priit Põldme, Reet Sepp

    Index Scriptorium Estoniae

    Põldme, Priit, 1971-

    2013-01-01

    Büroo Ignite (Tatari 25, Tallinn) sisekujundusest. Sisearhitektid Priit Põldme ja Reet Sepp (SAB Joonprojekt). Arhitektid Heiki Taras ja Ahti Luhaäär (Arhitektibüroo Pilter ja Taras). Sisearhitekti ja ESLi aastapreemiate žürii esimehe Kaido Kivi arvamus

  19. Kontori ja klubimaailma sümbioos / Ell-Maaja Randküla

    Index Scriptorium Estoniae

    Randküla, Ell-Maaja, 1939-2016

    2005-01-01

    Büroohoone Jungent Tallinnas Paldiski mnt. 11. Sisekujundus: Jan Joonas Graps ja Ken-Kristjan Ruut, OÜ Jan & Ken. Pilgupüüdjaks büroos on ka Kaido Ole suureformaadilised maalid. K.-K. Ruudust ja J. J. Grapsist, nende tähtsamad tööd. Ill.: 3 plaani, 15 värv. vaadet

  20. 10 aastat - 30 ettevõtet : KPMG kogemus tasakaalus tulemuskaardiga / Jüri Sakkeus

    Index Scriptorium Estoniae

    Sakkeus, Jüri

    2008-01-01

    Tasakaalus tulemuskaardi koostamise ja rakendamise nõuded, selle plussid ja miinused ning mõju ettevõtte arengule. Vt. samas: Tarmo Noop. Loon süsteemi, mis töötab ise; Kaido Kangur. Kas teate, millal teie äri kokku kukub?; Marko Rillo. Tasakaalus tulemuskaardi sobivusest ja mittesobivusest. Skeemid

  1. India ja Lääne kultuur ühendavad käed

    Index Scriptorium Estoniae

    2002-01-01

    Suvetuurist "Indian experience" (peakorraldajaks DJ ja muusik Kaido Kirikmäe), mis toimub 6. juunil Viljandi kultuurikolledzhis, 7. juunil Pärnu Sütevaka humanitaargümnaasiumi hoovil, 8. juunil Haapsalu kõlakojas ning 9. juunil Tallinnas

  2. Burkhardt plaanib rajada Rail Balticat / Liis Kängsepp

    Index Scriptorium Estoniae

    Kängsepp, Liis, 1981-

    2007-01-01

    Eesti Raudteest loobuma pidanud Edward Burkhardt hakkab arendama Rail Balticat ning otsib võimalust panna Eesti ja Soome vahele käima vagunipraam. Vt. samas: Raudtee müüjad endiselt nördinud. Küsimustele vastab Eesti Raudtee uus juht Kaido Simmermann

  3. Zebra - sõbralik ja lillelõhnaline / Ell-Maaja Randküla

    Index Scriptorium Estoniae

    Randküla, Ell-Maaja, 1939-2016

    2006-01-01

    Tallinnas Narva mnt. 7 asuva kohviku Zebra sisekujundus. Sisearhitekt Tiiu Truus. Ehitus: AS KMG Ehitus. Materjalidest on kasutatud triibulise mustriga puitu Zebrano ja looduskivi. Laes on dekoratiivsed lipud, mille graafiline kujundus on Tiiu Priskolt ja Mati Veermetsalt. Tualettruumi looduskivist valamu ja põrandavaasi autor on Kaido Kivi. Ill.: põhiplaan, 11 värv. vaadet

  4. Kahe aastaga suurte sekka / Mark Buckton

    Index Scriptorium Estoniae

    Buckton, Mark

    2006-01-01

    Kaido Höövelson (maadlejanimega Baruto) on esimene eestlane, kes on jälje jätnud Jaapani iidses võitluskunstis sumos. Artikli autor on Suurbritannia Sumoühingu persident ja ajakirja Sumo Fan Magazine peatoimetaja

  5. Kumu Kunstimuuseum / Pekka Vapaavuori, Pia Sabelström, Pille Lausmäe

    Index Scriptorium Estoniae

    Vapaavuori, Pekka, 1962-

    2006-01-01

    II ja V korruse plaan, 2 välis- ja 5 sisevaadet; fotod: Kaido Haagen; projekteerija: Arkkitehtitoimisto Vapaavuori OY, 7 kaasautorit loetletud; sisekujundus: P. Sabelström; mööbel: P. Lausmäe, maastik: DIA Arhitektuur

  6. Muuseumiseinte vahel tuksleb linn / Kiwa

    Index Scriptorium Estoniae

    Kiwa, pseud., 1975-

    2008-01-01

    Näitus "Koht, mis paneb liikuma" Kumu Kunstimuuseumis. Grafitikunstnike Antoni, Uku ja Remi ruumiinstallatsioonist "Ajaviil". Reet Ausi, Ville Hyvöneni, HULA ja Tartu kõrgema kunstikooli tudengite ruumiinstallatsioonist "Üle prahi". Raoul Kurvitza arvutikunsti teosest "Pentatonic Color System II". Eksponeeritakse ka Maarit Murka ja Kaido Ole töid

  7. Comments on The Art of Collecting / Katarina Meister, Lylian Meister, Tiina Sarapu ...[jt.

    Index Scriptorium Estoniae

    2013-01-01

    6. Tallinna rakenduskunsti triennaal "Kogumise kunst" satelliitnäituse kuraator Tiina Sarapu, näitusel osalejad Katarina Meister, Lylian Meister, Marit Ilison, Krista Leesi ja Jaanus Samma ning näituse külastaja, maalikunstnik Kaido Ole näitusest ja kogumise kogemusest

  8. Kinnisvaragurude ümarlaud / interv. Jaanika Merilo

    Index Scriptorium Estoniae

    2007-01-01

    Järg. Profit nr. 3 lk. 18-21. Eesti kinnisvaraturu olukorrast, vestlusringis osalevad investeerimisfirma EE-REIT juhatuse liige Ain Kivisaar, Arco Vara Eesti tegevjuht Kaido Kangur, Hansapanga makromajanduse analüütik Maris Lauri ja ASYIT Ehituse kinnisvaraosakonna müügijuht Tõnu Toompark

  9. Hotelli Radisson SAS mantra : jah, ma saan! / Kai Vare

    Index Scriptorium Estoniae

    Vare, Kai, 1968-

    2004-01-01

    Radisson SAS hotell Tallinnas on kliendirahulolu-uuringute järgi keti hotellide seas esimeste hulgas. Hotelli direktor Kaido Ojaperv ja müügijuht Ann-Kai Tõrs Radisson SAS-i standarditest, kliendi sajaprotsendilise rahulolu tagamise põhimõtetest, personali valikust, koolitusest. Kommenteerib Sandra Dimitrovich

  10. Foorumi ärikeskus Tallinnas / Hanno Grossschmidt, Tomomi Hayashi

    Index Scriptorium Estoniae

    Grossschmidt, Hanno, 1973-

    2007-01-01

    asendiplaan, I korruse plaan, lõige, 4 värv. välis- ja 2 sisevaadet (restoran, äritänav); fotod: Kaido Haagen, Margus Tammik; projekteerija HG Arhitektuur; sisekujundajad: äritänav - Kohvi OÜ, Argentiina restoran - Ruumilabor OÜ

  11. Kalevi rooli asub endine lihatööstur / Kaisa Tahlfeld

    Index Scriptorium Estoniae

    Tahlfeld, Kaisa

    2010-01-01

    Endine Atria juht Kaido Kaare saab Kalev Chocolate Factory uueks juhiks. Kaare arvates võiksid Eesti magusatööstuse ambitsioonid ulatuda Eestist väljapoole, ta näeb võimalusi suurendada koostöös Orkla grupi ettevõtetega Kalevi tootmisefektiivsust ja jätkata tootearendust

  12. Kergplokkidest Jämera tüüpmaja Merirahu eramurajoonis / Ivi-Els Schneider, Piret Anier

    Index Scriptorium Estoniae

    Schneider, Ivi-Els, 1945-

    2005-01-01

    I ja II korruse plaan, välisvaade, 10 sisevaadet, värv.; ümberprojekteerimine: arhitekt Piret Anier, AB Zokkel, sisearhitekt Ivi-Els Schneideri jooniste järgi on valmistatud ka enamik mööblist; fotod: Kaido Haagen

  13. Saku Suurhall Rocca al Mares = Saku Suurhall in Rocca al Mare / Inga Raukas

    Index Scriptorium Estoniae

    Raukas, Inga, 1967-

    2001-01-01

    Peaprojekteerija, detailplaneering: Nord Projekt AS. Arhitektid Esa Viitanen (Soome), Andres Kariste, kaastöö: Meeli Truu, Loomet Raudsepp. Sisekujundus: Eero Jürgenson, Maarja Valk-Falk, Tambet Pedak, ARS Interjöörprojekt. Konstruktsioonid: Kaido Kuusiku, Tiit Arumäe, Aive Sau, Jaan Port. Projekteerimise projektijuht Andres Mikker. Projekt 1999-2001, valmis 2001. 9 ill

  14. Saare jonniga idealist / Lemmi Kann

    Index Scriptorium Estoniae

    Kann, Lemmi

    2008-01-01

    Maxima OÜ tegevjuhist Margus Pärnast. Lisad: Elulugu; Tasub teada. Kommenteerivad: TOP Auto juhatuse esimees Felor Pärnpuu, Sales-Star ASi juhatuse esimees Tiina Aas, psühhiaater Jüri Ennet ning ASi Mobec müügijuht Kaido Sumberg. Vt. samas: Karmi käega õppejõud Pärn

  15. Sõjast väsinud maa

    Index Scriptorium Estoniae

    2004-01-01

    Oma kogemustest Bagrami lennubaasis Afganistanis räägivad Eesti Päästemeeskonna demineerimismissiooni liikmed Jaanus Vahersalu, Jaan Ohtra, Kaukko Kiisk, Toomas Sims, Tõnu Mägi, Raido Taalmann, Indrek Samm, Kalvar Tammine, Kaido Kaurit, Rauno Saareleht ja Pille Volmerson

  16. Nurgatagused rütmid peidus tööstushoonete vahel / Urmas Oja

    Index Scriptorium Estoniae

    Oja, Urmas, 1981-2012

    2005-01-01

    Luku-Experdi peahoonest Tartu mnt. 74 Tallinnas. Projekteerija: AB Zero OÜ. Arhitekt Hindrek Kesler. Ehitus: XI 2004-VIII 2005. Lk 39 Luku-Experdi juhatuse esimehe Kaido Sõmeri kommentaar "Hoone sümboliseerib turvatunnet". Ill.: 5 värv. välisvaadet

  17. Hotelli Telegraaf sisekujundus. Tallinn, Vene 9 / Külli Salum, Riina Harik, Martin Aunin

    Index Scriptorium Estoniae

    Salum, Külli, 1971-

    2008-01-01

    I ja II korruse plaan, värv. välisvaade, 18 sisevaadet; fotod: Kaido Haagen; juurdeehituse arhitekt: M. Aunin. Sisearhitektid K. Salum ja R. Harik pälvis Eesti Sisearhitektide Liidu 2007. a. ajaloolise interjööri preemia

  18. Partsi otsus Langi kohta määrab valitsuse saatuse / Tuuli Koch

    Index Scriptorium Estoniae

    Koch, Tuuli

    2005-01-01

    Peaministri otsus, kas esitada Rein Lang välisministri kandidaadiks või mitte, osutub valitsuskriisi võtmeküsimuseks. Peaminister peab vajalikuks veel kord kandidaadiga kohtuda. Vt. samas lühiintervjuud Rein Langiga. Kommenteerivad politoloog Kaido Jaanson, MK Estonija peatoimetaja Pavel Ivanov ja Euroopa Parlamendi liige Marianne Mikko

  19. Vankumatu Andersen / Harry Liivrand

    Index Scriptorium Estoniae

    Liivrand, Harry, 1961-

    2005-01-01

    Areen tähistas Anderseni juubeliaastat erinumbri ja illustratsioonidega eesti kunstnikelt: Valli Lember-Bogatkina, Evald Okas, Jüri Arrak, Kaido Ole, Laurentsius, Ülle Meister, Regina Lukk-Toompere, Piret Raud, Marko Mäetamm. Vt. H. C. Andersen. Vankumatu tinasõdur, Eesti Ekspress, 30. juuni, lk. B1-13

  20. Jõhvi kunstikoolis tehti märulit / Tiia Linnard

    Index Scriptorium Estoniae

    Linnard, Tiia, 1962-

    2002-01-01

    Tartu Ülikooli maalikunsti 6 tudengit ja õppejud Jüri Kask tegid Jõhvi kunstikoolis action paintingut (grupimaalimine). Jaan Elkeni kommentaarid action painting tüüpi kunsti ajaloost ja enda grupiviisilisest maalimisest 1999. a. koos Marko Mäetamme ja Kaido Olega.

  1. Eestlased riisusid Balti fotovõistlusel koore

    Index Scriptorium Estoniae

    2011-01-01

    Eesti, Läti ja Leedu fotovõistlusest, kus valiti Baltikumi parimad loodusfotod ja maaelu kajastavad fotod. Osales 259 fotograafi. Parim loodusfoto oli Kaido Haageni "Kus sa oled, mu sõber" ning parim foto maaelu kategoorias Arne Aderi "Jõuluks koju"

  2. Graafikatriennaalist kunstitriennaaliks / Harry Liivrand

    Index Scriptorium Estoniae

    Liivrand, Harry, 1961-

    2004-01-01

    Tallinna XIII graafikatriennaalist. Peateemaks maapagu ja eksiilisolek. Eksiiliteemat kommenteerivad David Kiehl (New Yorgi Whitney muuseumi kuraator), Maaretta Jaukkuri (Helsingi Kiasma muuseumi kuraator), Irina Cios (Bukaresti kunstiteadlane), Silvina Der-Meguerditchian (argentiina kunstnik). Parimaks väljapanekuks Sirje Helme kuraatorinäitus "Teine naaber" Tallinna Kunstihoones ja Kunstihoone galeriis. Marko Mäetamme ja Kaido Ole 100 betoonkohvri projektist. Triennaali preemiasaajad

  3. John Smith iz Stuttgarta pereselilsja v Rapla. Sledujushtshaja stantsija - Veneetsia / Ilja Sundelevitsh

    Index Scriptorium Estoniae

    Sundelevitsh, Ilja

    2003-01-01

    John Smithi (Marko Mäetamm ja Kaido Ole) näitusest Tallinna Kunstihoones. John Smithi biograafia. Sirje Helme koostatud näitusest "Leidlaps" galeriis 008 (Tallinna Viru keskuses kaupluse Sity Sokos tühjaksjäänud ruumides). Esile tõstetud Jüri Kase töid

  4. John Smith - eesti kunstnik / Ants Juske

    Index Scriptorium Estoniae

    Juske, Ants, 1956-2016

    2006-01-01

    Marko Mäetamme ja Kaido Ole kollektiivsest loomingust, mida esitatakse John Smithi autorinime all, mõnda ka salapärase J. Smithi nn. biograafiast. Illustratsiooniks J. Smith'i "Jumalate maailm I (fragment). Õli, lõuend, 2002. Erakogu

  5. Eesti Post otsib võimalusi frantsiisikontorite avamiseks / Kadri Haavajõe

    Index Scriptorium Estoniae

    Haavajõe, Kadri

    2008-01-01

    Frantsiisilepingu alusel saab osutada postiteenuseid kohapealsete teenindajate abil, kelle koolituse ja tasustamise tagab Eesti Post. Frantsiisikontoritest on soovi avaldanud Laekvere ja Tamsalu vald. Vt. samas lk. 11: Kaido Padar. Frantsiisikontor - mugav postiteenus Sinu lähedal. Eesti Posti kommunikatsiooni- ja turundusjuht postiteenuste pakkumisest maapiirkondades

  6. Prokuratuur saatis Amigo peksjad kohtusse / Rasmus Kagge

    Index Scriptorium Estoniae

    Kagge, Rasmus, 1977-

    2007-01-01

    Ilmunud ka: Postimees : na russkom jazõke 16. nov. lk. 5. Tallinna ööklubi Amigo peksmisskandaali uurimisest - prokurör Saskia Kask esitas ööklubi vahetuse vanemale Kaido Reinsoole ja Skorpioni turvatöötajale Valeera Manninenile süüdistused kahe kliendi peksmises ja saatis nad kohtu alla. Vt. samas intervjuud Saskia Kasega: Prokurör: Postimehest oli suur abi; Peksmisvideo kadumises kaks kahtlusalust. Lisa: Skandaali kronoloogia

  7. Uus kaasaegse kunsti näitusepaik Riias / Inga Lace ; interv. Sandra Jõgeva

    Index Scriptorium Estoniae

    Lace, Inga

    2008-01-01

    Riia Kunstiruumi (Riga Art Space) turundusjuht Inga Lace Raekoja platsi all asuvast uuest näitusepaigast, selle tööpõhimõtetest ning eesti kunstnike - Jaan Tooniku ja Andrus Joonase näitus suures saalis, Kaido Ole ja Tõnis Saadoja näitus väikses saalis- vastuvõtust Lätis. Septembris avatakse Johannes Saare kureeritud rahvusvaheline projekt "Halb nali"

  8. Vaikuse ääremail / Teet Veispak

    Index Scriptorium Estoniae

    Veispak, Teet, 1955-

    2006-01-01

    2006. a. Tallinnas Kaasaegse Kunsti Eesti Keskuselt ilmunud Andreas Trosseki toimetatud artiklikogumikust "Uue nimetaja otsinguid aastal 2000+n : lisandusi eesti kunstiloole", mis sisaldab 2005. a. novembris peetud ettekannete päeval "Roheline, toores ja lõikamata. Noor eesti kunst uue sajandi alguses" esitatud ettekandeid. Anneli Porri, Elin Kardi ja Kaido Ole artiklitest, kogumikus on veel Rael Arteli ja Kristjan Mändmaa artiklid

  9. Eesti hallhüljes ja konnad nüüd ilmakuulsad / Ulvar Käärt

    Index Scriptorium Estoniae

    Käärt, Ulvar, 1982-

    2011-01-01

    Kaido Haageni veealune ülesvõte hallhülgest pälvis 3. koha konkursil Ocean Views 2011 ning vees tehtud pilt kahest kärnkonnast märgiti veealuse käitumise kategoorias auhinnaga ära konkursil Beneath The Sea 2011. K. Haageni rändnäitust "Silmad vees II" näeb Kuressaare gümnaasiumi ujulas

  10. Kuldala elamurajoon Rae vallas Harjumaal / Lembit-Kaur Stöör, Margus Maiste, Raivo Kotov...[jt.

    Index Scriptorium Estoniae

    2008-01-01

    joonised: vaade, I-IV korruse plaan (2), planeeringu makett, 5 värv. fotot: 3 välis- ja 2 sisevaadet; fotod: Kaido Haagen; arhitektuurne projekt: KOKO Arhitektid.; autorid: L.-K. Stöör, M. Maiste, R. Kotov, T. Kimmel, hoonete projekteerimine: L.-K. Stöör, M. Maiste, Olga Batuhtina, maastikuarhitektuur: Margit Kärner

  11. Tallinna XIII graafikatriennaali grand prix' pälvis leedu graafik Egle Kuckaite

    Index Scriptorium Estoniae

    2004-01-01

    Kolm võrdset preemiat: Sang-gon Chung Lõuna-Koreast, Krishs Salmanis Lätist ja Joanne Soroka Shotimaalt. Diplomid: Anonymous Boh ja Eve Kiiler Eestist, Pete Nevin Inglismaalt, Hanna Oinonen Soomest ja venetsueela-soome kunstnik Sandra Vina de Karila. Tallinna linna preemia: John Smith (Marko Mäetamm & Kaido Ole) Eestist. Eesti Kunstimuuseumi preemia: Markus Lampinen Soomest. Eesti Panga preemia: Leonards Laganovskis Lätist

  12. Täna avatakse Kotkas Eesti nüüdiskunsti näitused

    Index Scriptorium Estoniae

    2005-01-01

    Eksponeeritud John Smithi uued poliitilised tõlgendused "Brezhnev", "Hitler" ja "Holocaust", Mare Mikofi "Ene" (2003). Näitusel esinevast 12 kunstnikust 7 (Kaido Ole, Mari Roosvalt, Leonhard Lapin, Hannes Starkopf, Jaan Toomik, Vergo Vernik, Jaan Elken) kuulub rühmitusse Ruum 312A. Kotka linnaraamatukogus on eksponeeritud Rait Rosina ja Helina Loidi maalid, Haukkavuori vaatlustornis on Ly Lestbergi isikunäitus "Elysion" ja tema uus video

  13. Eile sai Eesti Kunstimuuseumi asutamisest 86 aastat ning Tartu Kunstimuuseumi asutamisest 65 aastat

    Index Scriptorium Estoniae

    2005-01-01

    Kumu ettekannetepäev "Roheline, toores ja lõikamata. Noor eesti kunst uue sajandi alguses" sarjast "Lisandusi eesti kunstiloole". Esinesid Karin Laansoo, Irit Rogoff, Kaido Ole, Kristjan Mändmaa, Rael Artel. Esitleti raamatut "22 + Noored eesti kunstnikud. Young Estonian Artists". 18. XI kirjutatakse alla Jaapani valitsuse kultuuritoetusleping, mis on suunatud Kumu varustamiseks kaasaegse audiogiidi süsteemiga, esitlustehnika ja maalikonserveerimislabori tehnikaga

  14. Separation, Characterization and Fouling Potential of Sludge Waters from Different Biological Wastewater Treatment Processes

    KAUST Repository

    Xue, Jinkai

    2011-07-01

    The major limitation, which hinders the wider application of membrane technology and increases the operating costs of membranes involved in wastewater treatment plants, is membrane fouling induced by organic matter. Extracellular polymeric products (EPS) and soluble microbial products (SMP) are the two most mentioned major foulants in publications, for which the debate on precise definitions seems to be endless. Therefore, a concept of sludge water, which conceptually covers both EPS and SMP, has been developed in this research. A standard procedure of sludge water separation, which is centrifugation at 4000g for 15 min followed by 1.2μm glass fiber filter filtration, was established based on separation experiments with membrane tank sludge from the KAUST MBR wastewater treatment plant. Afterwards, sludge waters from the KAUST MBR WWTP anoxic tank, aerobic tank and membrane tank as well as sludge waters from the Jeddah WWTP anoxic tank, aerobic tank and secondary effluent were produced through the previously developed standard procedure. The obtained sludge water samples were thereafter characterized with TOC/COD, LC-­‐OCD and F-­‐EEM, which showed that KAUST anoxic/ aerobic /membrane tank sludge waters had similar characteristics for all investigated parameters, yet the influent naturally had a higher DOC and biopolymer concentration. Moreover, lower TOC/COD, negligible biopolymers and low levels of humics were found in KAUST effluent. Compared with the KAUST MBR WWTP, the Jeddah WWTP’s sludge waters generally had higher DOC and biopolymer concentrations. To investigate sludge water fouling potential, the KAUST membrane tank sludge water as well as the Jeddah secondary effluent were filtrated through a membrane array consisting of an ultrafiltration (UF) Millipore RC10kDa at the first step followed by a nanofiltration (NF) KOCH Acid/Base stable NF200 at the second step. It was found that cake layer and standard blocking occurred simultaneously during both

  15. Benchmarked Library Websites Comparative Study

    KAUST Repository

    Ramli, Rindra M.; Tyhurst, Janis

    2015-01-01

    This presentation provides an analysis of services provided by the benchmarked library websites. The exploratory study includes comparison of these websites against a list of criterion and presents a list of services that are most commonly deployed by the selected websites. In addition to that, the investigators proposed a list of services that could be provided via the KAUST library website.

  16. Electronic Resources Management Project Presentation 2012

    KAUST Repository

    Ramli, Rindra M.

    2012-11-05

    This presentation describes the electronic resources management project undertaken by the KAUST library. The objectives of this project is to migrate information from MS Sharepoint to Millennium ERM module. One of the advantages of this migration is to consolidate all electronic resources into a single and centralized location. This would allow for better information sharing among library staff.

  17. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.

    2015-01-01

    We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  18. When Library and Archival Science Methods Converge and Diverge: KAUST’s Multi-Disciplinary Approach to the Management of its Audiovisual Heritage

    KAUST Repository

    Kenosi, Lekoko

    2015-07-16

    Libraries and Archives have long recognized the important role played by audiovisual records in the development of an informed global citizen and the King Abdullah University of Science and Technology (KAUST) is no exception. Lying on the banks of the Red Sea, KAUST has a state of the art library housing professional library and archives teams committed to the processing of digital audiovisual records created within and outside the University. This commitment, however, sometimes obscures the fundamental divergences unique to the two disciplines on the acquisition, cataloguing, access and long-term preservation of audiovisual records. This dichotomy is not isolated to KAUST but replicates itself in many settings that have employed Librarians and Archivists to manage their audiovisual collections. Using the KAUST audiovisual collections as a case study the authors of this paper will take the reader through the journey of managing KAUST’s digital audiovisual collection. Several theoretical and methodological areas of convergence and divergence will be highlighted as well as suggestions on the way forward for the IFLA and ICA working committees on the management of audiovisual records.

  19. Hydrolytically stable fluorinated metal-organic frameworks for energy-efficient dehydration

    KAUST Repository

    Cadiau, Amandine; Belmabkhout, Youssef; Adil, Karim; Bhatt, Prashant; Pillai, Renjith S.; Shkurenko, Aleksander; Martineau-Corcos, Charlotte; Maurin, Guillaume; Eddaoudi, Mohamed

    2017-01-01

    fluorinated metal-organic framework, AlFFIVE-1-Ni (KAUST-8), with a periodic array of open metal coordination sites and fluorine moieties within the contracted square-shaped one-dimensional channel. This material selectively removed water vapor from gas

  20. A computational study of ethylene–air sooting flames: Effects of large polycyclic aromatic hydrocarbons

    KAUST Repository

    Selvaraj, Prabhu; Arias, Paul G.; Lee, Bok Jik; Im, Hong G.; Wang, Yu; Gao, Yang; Park, Sungwoo; Sarathy, Mani; Lu, Tianfeng; Chung, Suk-Ho

    2015-01-01

    formation to various chemical pathways for large polycyclic aromatic hydrocarbons (PAH). The gas-phase chemical mechanism adopted the KAUST-Aramco PAH Mech 1.0, which utilized the AramcoMech 1.3 for gas-phase reactions validated for up to C2 fuels

  1. Single Cell Genomics in Marine Omics

    KAUST Repository

    Kodzius, Rimantas

    2014-09-10

    Kingdom of Saudi Arabia invests heavily to both in infrastructure and science. King Abdullah University of Science and Technology (KAUST) is a modern and international university close to the Red Sea, with the focus on water, food, energy, and the environment.

  2. Benchmarking and scaling studies of pseudospectral code Tarang ...

    Indian Academy of Sciences (India)

    are transformed from the Fourier space to the real space, multiplied with each other, and then transformed ... Science and Technology (KAUST). The HPC ... cessors (resources) by the same amount takes approximately the same time (see figure 1). ... We are in the process of implementing 'pencil decomposition' on Tarang.

  3. Single Cell Genomics in Marine Omics

    KAUST Repository

    Kodzius, Rimantas; Gojobori, Takashi

    2014-01-01

    Kingdom of Saudi Arabia invests heavily to both in infrastructure and science. King Abdullah University of Science and Technology (KAUST) is a modern and international university close to the Red Sea, with the focus on water, food, energy, and the environment.

  4. Red Sea as a source for bioprospecting

    KAUST Repository

    Kodzius, Rimantas

    2015-01-01

    King-Abdullah University of Science and Technology (KAUST) is located on the shores of the Red Sea in Saudi Arabia. The Red Sea is well known for its unique environment, harboring various microbes capable of surviving in salty brines. We collected

  5. Enabling High Performance Large Scale Dense Problems through KBLAS

    KAUST Repository

    Abdelfattah, Ahmad; Keyes, David E.; Ltaief, Hatem

    2014-01-01

    KBLAS (KAUST BLAS) is a small library that provides highly optimized BLAS routines on systems accelerated with GPUs. KBLAS is entirely written in CUDA C, and targets NVIDIA GPUs with compute capability 2.0 (Fermi) or higher. The current focus

  6. DDMGD: the database of text-mined associations between genes methylated in diseases from different species

    KAUST Repository

    Raies, A. B.; Mansour, H.; Incitti, R.; Bajic, Vladimir B.

    2014-01-01

    ://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we

  7. Conference/Symposium: 2017 Princeton-Combustion Institute Summer School on Combustion

    Science.gov (United States)

    2018-02-07

    Technology (KAUST). On behalf of all the attendees, the organizers of the Summer School express their profound gratitude to the lecturers, sponsors...professors. Personally, I want to thank you, Professor Law, and express my gratitude for the tremendous arrangement, great munificence, and the new

  8. Connecting the pieces: using ORCIDs to improve research impact and repositories

    KAUST Repository

    Baessa, Mohamed A.

    2015-05-19

    Quantitative data are crucial in the assessment of research impact in the academic world. However, as a young university created in 2009, King Abdullah University of Science and Technology (KAUST) needs to aggregate bibliometrics from researchers coming from diverse origins, not necessarily with the proper affiliations. In this context, the University has launched an institutional repository in September 2012 with the objectives of creating a home for the intellectual outputs of KAUST researchers. Later, the university adopted the first mandated institutional open access policy in the Arab region, effective June 31, 2014. Several projects were then initiated in order to accurately identify the research being done by KAUST authors and bring it into the repository in accordance with the open access policy. Integration with ORCID has been a key element in this process and the best way to ensure data quality for researcher’s scientific contributions. It included the systematic inclusion and creation, if necessary, of ORCID identifiers in the existing repository system, an institutional membership in ORCID, and the creation of dedicated integration tools. In addition and in cooperation with the Office of Research Evaluation, the Library worked at implementing a Current Research Information System (CRIS) as a standardized common resource to monitor KAUST research outputs. We will present our findings about the CRIS implementation, the ORCID API, the repository statistics as well as our approach in conducting the assessment of research impact in terms of usage by the global research community.

  9. Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences

    KAUST Repository

    Kalkatawi, Manal M.; Rangkuti, Farania; Schramm, Michael C.; Jankovic, Boris R.; Kamau, Allan; Chowdhary, Rajesh; Archer, John A.C.; Bajic, Vladimir B.

    2011-01-01

    . These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity

  10. Connecting the pieces: Using ORCIDs to improve research impact and repositories.

    Science.gov (United States)

    Baessa, Mohamed; Lery, Thibaut; Grenz, Daryl; Vijayakumar, J K

    2015-01-01

    Quantitative data are crucial in the assessment of research impact in the academic world. However, as a young university created in 2009, King Abdullah University of Science and Technology (KAUST) needs to aggregate bibliometrics from researchers coming from diverse origins, not necessarily with the proper affiliations. In this context, the University has launched an institutional repository in September 2012 with the objectives of creating a home for the intellectual outputs of KAUST researchers. Later, the university adopted the first mandated institutional open access policy in the Arab region, effective June 31, 2014. Several projects were then initiated in order to accurately identify the research being done by KAUST authors and bring it into the repository in accordance with the open access policy. Integration with ORCID has been a key element in this process and the best way to ensure data quality for researcher's scientific contributions. It included the systematic inclusion and creation, if necessary, of ORCID identifiers in the existing repository system, an institutional membership in ORCID, and the creation of dedicated integration tools. In addition and in cooperation with the Office of Research Evaluation, the Library worked at implementing a Current Research Information System (CRIS) as a standardized common resource to monitor KAUST research outputs. We will present our findings about the CRIS implementation, the ORCID API, the repository statistics as well as our approach in conducting the assessment of research impact in terms of usage by the global research community.

  11. Uus inkvisitsioon - põletatakse Siiri Sisask / Kati Murutar

    Index Scriptorium Estoniae

    Murutar, Kati, 1967-

    1998-01-01

    Siiri Sisaski kontserdist Esku kirikus. Vastukajad: Kivi, A. Kas Eestis põletatakse nõidu?; Jürjo, Villu. Kõigil on õigus oma kodu kaitsta // Postimees (1998) 1. sept., lk. 8. (Kirjad); Jaanson, Kaido. Pühakoda on pühakoda; Jürjo, Villu. Küsimus on vabaduses öelda ei // Postimees (1998) 3. sept., lk. 8. (Kirjad) ; Uluots, Kristiina. Sisaski kirikukontserdi asjus // Postimees (1998) 4. sept., lk. 8 (Kirjad); Bahovski, Erkki. Pühadus ja haige rahvas // Postimees (1998) 6. sept., lk. 3

  12. Эстонские фотографы получили большую часть призов на балтийском фотоконкурсе

    Index Scriptorium Estoniae

    2011-01-01

    4.-5. novembril Riias toimunud Baltimaade Loodusfoto Festivalil (Baltic Nature Photo Festival) anti üle esimese Baltimaade loodus- ja talufotode konkursi auhinnad. Võidukad olid Eesti piltnikud. Baltimaade loodusfoto Grand Prix võitis Kaido Haagen fotoga «Kus sa oled, mu sõber?», Maailma looduse foto Grand Prix sai Silver Kommusaar fotoga «Tormipilv» ja Baltimaade talufoto võistluse Grand Prix sai Arne Ader fotoga «Jõuluks koju!». Konkursid korraldas Eestis tegutsev MTÜ Institute of Photography

  13. Me aiaäärne tsivilisatsioon / Andri Ksenofontov

    Index Scriptorium Estoniae

    Ksenofontov, Andri, 1962-

    2008-01-01

    Gerhard Richteri näitus "Ülevaade" 6. VI-17. VIII ja Eha Komissarovi kureeritud eesti kunstnike linnakeskkonna-teemaline näitus "Koht, mis paneb liikuma" 20. VI-17. VIII Kumu Kunstimuuseumis. Lühidalt Tõnis Saadoja Gerhard Richteri portreede seeriast "Mainstream" Kumu Kunstimuuseumis. Maarit Murka töödest, Kaarel Nurga fotodest, Anton Kooviti, Uku ja Remi grafititoast, Raoul Kurvitza arvutiinstallatsioonist "Pentatonic Color System II" (helilooja Ariel Lagle), Reet Ausi, Marit Ahvena,Ville Hyvöneni, Hula, EKA moedisaini ja Tartu Kõrgema Kunstikooli tekstiili- ja fotoosakonna projektist "Üle prahi", Kaido Ole installatsioonist "Koosolek"

  14. 15 tähtteost Eesti kunsti 15 aastast / Harry Liivrand

    Index Scriptorium Estoniae

    Liivrand, Harry, 1961-

    2006-01-01

    Kunstiteosed, mis on märgilise tähendusega nii nende loojate loomingus kui eesti kunstiajaloo kontekstis: Raoul Kurvitz "Ararat", Jaan Toomik "...16. mai-31. mai 1992", Jüri Ojaver "Nišš. Image", Raul Rajangu "Playboy House", Jaan Toomik "Tantsides koju", Ado Lill "Nimetu 55", Kai Kaljo "Luuser", Mark Raidpere sari "Io", Ene-Liis Semper "FF/Rew", Laurentsius & AD "Roos XXII", Mare Tralla "Sing with me!", Peeter Allik"Ma nägin seda", Kaido Ole "Tüdruk ja poiss", Jaan Elken "Video Kills a Radio Star", Andres Tali "Pastoraalne pastishsh"

  15. Tööpuudus hiilib kikivarvul Võrumaale / Arved Breidaks

    Index Scriptorium Estoniae

    Breidaks, Arved, 1975-

    2008-01-01

    Võrumaal on töötute arv eelmise aastaga võrreldes tõusma hakanud: mullu suvel maakonnas registreeritud 3,9%-line töötuse määr asendus tänavu juuli lõpus 5,4%-lise töötusega. Lisa: Töötus Võrumaal. Vt. samas: Kuidas iseloomustate olukorda Võrumaa tööjõuturul? Vastavad Martin Arula (AS Toftan), Kaido Mäesalu (AS Suwem), Meelis Munski (AS Semuehitus), Indrek Klampe (OÜ Selista Ehitus), Andres Visanpuu (Võru TÜ)

  16. Käsitöö ja ühistöö. Tallinna diakonisside haigla kabelist Pikva Miikaeli kabeliks

    Index Scriptorium Estoniae

    2006-01-01

    1891. a. arhitekt Erwin Bernhardi projekti järgi valminud puitkabeli teisaldamisest Pikva mõisa aladele. Teisaldustöid tegi OÜ Kuukaar. Projekti töörühm: Illar Kannelmäe, Mare Kelpmann, Reet Talima, Kaido Ole, Lauri Sillak, Mati Raal, Merike Kallas. Andres Sild mõõdistas ja inventeeris kabeli, Jaanus Vipper restaureeris aknad ja uksed, Tõnu Vainküla orelikapi ja pingid, Indrek Joala paigaldas konstruktsiooniosasid, Tõnu Aru ja Eve Ester jäädvustasid kabeli taastamise. Kabel pühitseti 2. XI 2005

  17. Uudised : Muusikakonkurss. No stress. M&3. Tsensuur. Tähtpäev

    Index Scriptorium Estoniae

    2005-01-01

    Viljandi Kultuuriakadeemia korraldatud muusikakonkursist "Muusikatriaad" 8.-10. märtsini Viljandis. Eesti plaadifirma Kuurortrecords andis 1. märtsil välja uue kogumikalbumi "Music From the Land and from near the Sea: Far-away Sound from Estonia, Latvia and Iceland". Kuurortrecordsi esindaja Kaido Kirikmäe esineb oma duoga Hea Rannik 4. märtsil Reykjavikis. Trahvid tõusust ebasündsate sõnavõttude eest. Rulers of Deep (M. Meri, P. Julm) tähistab 5. tegutsemisaastat

  18. Easy Access to HPC Resources through the Application GUI

    KAUST Repository

    van Waveren, Matthijs

    2016-11-01

    The computing environment at the King Abdullah University of Science and Technology (KAUST) is growing in size and complexity. KAUST hosts the tenth fastest supercomputer in the world (Shaheen II) and several HPC clusters. Researchers can be inhibited by the complexity, as they need to learn new languages and execute many tasks in order to access the HPC clusters and the supercomputer. In order to simplify the access, we have developed an interface between the applications and the clusters and supercomputer that automates the transfer of input data and job submission and also the retrieval of results to the researcher’s local workstation. The innovation is that the user now submits his jobs from within the application GUI on his workstation, and does not have to directly log into the clusters or supercomputer anymore. This article details the solution and its benefits to the researchers.

  19. Direct numerical simulations of reacting flows with detailed chemistry using many-core/GPU acceleration

    KAUST Repository

    Herná ndez Pé rez, Francisco E.; Mukhadiyev, Nurzhan; Xu, Xiao; Sow, Aliou; Lee, Bok Jik; Sankaran, Ramanan; Im, Hong G.

    2018-01-01

    A new direct numerical simulation (DNS) code for multi-component gaseous reacting flows has been developed at KAUST, with the state-of-the-art programming model for next generation high performance computing platforms. The code, named KAUST Adaptive Reacting Flows Solver (KARFS), employs the MPI+X programming, and relies on Kokkos for “X” for performance portability to multi-core, many-core and GPUs, providing innovative software development while maintaining backward compatibility with established parallel models and legacy code. The capability and potential of KARFS to perform DNS of reacting flows with large, detailed reaction mechanisms is demonstrated with various model problems involving ignition and turbulent flame propagations with varying degrees of chemical complexities.

  20. Direct numerical simulations of reacting flows with detailed chemistry using many-core/GPU acceleration

    KAUST Repository

    Hernández Pérez, Francisco E.

    2018-03-29

    A new direct numerical simulation (DNS) code for multi-component gaseous reacting flows has been developed at KAUST, with the state-of-the-art programming model for next generation high performance computing platforms. The code, named KAUST Adaptive Reacting Flows Solver (KARFS), employs the MPI+X programming, and relies on Kokkos for “X” for performance portability to multi-core, many-core and GPUs, providing innovative software development while maintaining backward compatibility with established parallel models and legacy code. The capability and potential of KARFS to perform DNS of reacting flows with large, detailed reaction mechanisms is demonstrated with various model problems involving ignition and turbulent flame propagations with varying degrees of chemical complexities.

  1. SBOLme: a Repository of SBOL Parts for Metabolic Engineering

    KAUST Repository

    Kuwahara, Hiroyuki

    2017-01-12

    The Synthetic Biology Open Language (SBOL) is a community-driven open language to promote standardization in synthetic biology. To support the use of SBOL in metabolic engineering, we developed SBOLme, the first open-access repository of SBOL 2-compliant biochemical parts for a wide range of metabolic engineering applications. The URL of our repository is http://www.cbrc.kaust.edu.sa/sbolme.

  2. Pure- and mixed-gas propylene/propane permeation properties of spiro- and triptycene-based microporous polyimides

    KAUST Repository

    Swaidan, Ramy J.; Ghanem, Bader; Swaidan, Raja; Litwiller, Eric; Pinnau, Ingo

    2015-01-01

    Solution-processable polyimides of intrinsic microporosity (PIM-PIs) comprising relatively inflexible and contorted backbones have demonstrated outstanding molecular-sieving behavior in membrane-based separation of gas/gas pairs. In this work, the effects of systematically increasing intra-chain rigidity on the propylene/propane separation properties were compared for PIM-PIs made from 2,3,5,6-tetramethyl-1,4-phenylene diamine (TMPD) and (i) spiro-centered dianhyride (SPDA-TMPD or PIM-PI-1) and (ii) 9,10-diisopropyltriptycene-based dianhydride (TPDA-TMPD or KAUST PI-1). Pure-gas experiments at 2 bar and 35 oC showed significant increases in C3H6 permeability and C3H6/C3H8 selectivity by transitioning from PIM-PI-1 (P(C3H6)=393 Barrer, α(C3H6/C3H8)=6) to KAUST-PI-1 (P(C3H6)=817 Barrer, α(C3H6/C3H8)=16), positioning KAUST-PI-1 considerably above the experimentally observed pure-gas C3H6/C3H8 polymer upper bound. However, 50:50 C3H6/C3H8 mixed-gas feeds induced significant losses in C3H6 permeability and C3H6/C3H8 selectivity relative to the 2 bar pure-gas data for PIM-PI-1 and KAUST-PI-1 as the C3H6/C3H8 selectivity dropped from 6 to 3 and 16 to 5, respectively, at 2 bar C3H6 partial pressure due to plasticization and competitive sorption.

  3. Robust and scalable hierarchical matrix-based fast direct solver and preconditioner for the numerical solution of elliptic partial differential equations

    KAUST Repository

    Chavez Chavez, Gustavo Ivan

    2017-01-01

    Numerical experiments corroborate the robustness, accuracy, and complexity claims and provide a baseline of the performance and memory footprint by comparisons with competing approaches such as the multigrid solver hypre, and the STRUMPACK implementation of the multifrontal factorization with hierarchically semi-separable matrices. The companion implementation can utilize many thousands of cores of Shaheen, KAUST's Haswell-based Cray XC-40 supercomputer, and compares favorably with other implementations of hierarchical solvers in terms of time-to-solution and memory consumption.

  4. Benchmarking and scaling studies of pseudospectral code Tarang for turbulence simulations

    KAUST Repository

    VERMA, MAHENDRA K

    2013-09-21

    Tarang is a general-purpose pseudospectral parallel code for simulating flows involving fluids, magnetohydrodynamics, and Rayleigh–Bénard convection in turbulence and instability regimes. In this paper we present code validation and benchmarking results of Tarang. We performed our simulations on 10243, 20483, and 40963 grids using the HPC system of IIT Kanpur and Shaheen of KAUST. We observe good ‘weak’ and ‘strong’ scaling for Tarang on these systems.

  5. Discover yourself - Making your online information searchable

    KAUST Repository

    Martin, Jose

    2015-11-08

    The slides used during the presentation where KAUST Library shows 2 different approaches to making the information available in the Library websites searchable via the Catalog. This enables users to search for information about not only resources, but also the services provided by the Library. The first approach is based on using Encore and the OAI-PMH protocol, and the second one uses Google\\'s Custom Search Engine.

  6. Benchmarking and scaling studies of pseudospectral code Tarang for turbulence simulations

    KAUST Repository

    VERMA, MAHENDRA K; CHATTERJEE, ANANDO; REDDY, K SANDEEP; YADAV, RAKESH K; PAUL, SUPRIYO; CHANDRA, MANI; Samtaney, Ravi

    2013-01-01

    Tarang is a general-purpose pseudospectral parallel code for simulating flows involving fluids, magnetohydrodynamics, and Rayleigh–Bénard convection in turbulence and instability regimes. In this paper we present code validation and benchmarking results of Tarang. We performed our simulations on 10243, 20483, and 40963 grids using the HPC system of IIT Kanpur and Shaheen of KAUST. We observe good ‘weak’ and ‘strong’ scaling for Tarang on these systems.

  7. Discover yourself - Making your online information searchable

    KAUST Repository

    Martin, Jose

    2015-01-01

    The slides used during the presentation where KAUST Library shows 2 different approaches to making the information available in the Library websites searchable via the Catalog. This enables users to search for information about not only resources, but also the services provided by the Library. The first approach is based on using Encore and the OAI-PMH protocol, and the second one uses Google's Custom Search Engine.

  8. Pure- and mixed-gas propylene/propane permeation properties of spiro- and triptycene-based microporous polyimides

    KAUST Repository

    Swaidan, Ramy Jawdat

    2015-06-03

    Solution-processable polyimides of intrinsic microporosity (PIM-PIs) comprising relatively inflexible and contorted backbones have demonstrated outstanding molecular-sieving behavior in membrane-based separation of gas/gas pairs. In this work, the effects of systematically increasing intra-chain rigidity on the propylene/propane separation properties were compared for PIM-PIs made from 2,3,5,6-tetramethyl-1,4-phenylene diamine (TMPD) and (i) spiro-centered dianhyride (SPDA-TMPD or PIM-PI-1) and (ii) 9,10-diisopropyltriptycene-based dianhydride (TPDA-TMPD or KAUST PI-1). Pure-gas experiments at 2 bar and 35 oC showed significant increases in C3H6 permeability and C3H6/C3H8 selectivity by transitioning from PIM-PI-1 (P(C3H6)=393 Barrer, α(C3H6/C3H8)=6) to KAUST-PI-1 (P(C3H6)=817 Barrer, α(C3H6/C3H8)=16), positioning KAUST-PI-1 considerably above the experimentally observed pure-gas C3H6/C3H8 polymer upper bound. However, 50:50 C3H6/C3H8 mixed-gas feeds induced significant losses in C3H6 permeability and C3H6/C3H8 selectivity relative to the 2 bar pure-gas data for PIM-PI-1 and KAUST-PI-1 as the C3H6/C3H8 selectivity dropped from 6 to 3 and 16 to 5, respectively, at 2 bar C3H6 partial pressure due to plasticization and competitive sorption.

  9. Raamatupidamise tarkvarade võrdlus

    Index Scriptorium Estoniae

    2004-01-01

    Ilmunud ka: Buhgalterskije Novosti, nr. 8, 2004, lk. 44-49. Järg Raamatupidamisuudised nr. 8 lk. 49-52. Oma ettevõtete poolt müüdavat tarkvara tutvustavad Reimo Möll Excellent Business Solutions Eesti AS-ist (FirstOffice HansaWorld SBE); Helen Märtsoo Hansa Business Solutions AS-ist (HansaRaama); Allan Vähejaus Vallaste ja Partnerid OÜ-st (Joosep); Andres Kert Merit Tarkvara AS-ist (Merit Aktiva, Microsoft Navision); Kaido Rasva Ecosoft OÜ-st (RAMIX-START); Raivo Viitas Systec AS-ist (SAF); Imbi Rooste Gaiasoft AS-ist (Verp 6.1; Verp 6.2e). Tabelid

  10. Teatri aastaauhindade laureaadid 2008

    Index Scriptorium Estoniae

    2008-01-01

    Tiit Ojasoo - lavastajaauhind, Silver Vahtre, Krista Tool ja Margus Vaigur - kunstniku auhind, Piret Laurimaa - naisnäitleja auhind, Üllar Saaremäe - meesnäitleja auhind, Tiina Tauraite - naiskõrvalosa auhind, Taavi Teplenkov - meeskõrvalosa auhind, Mart Koldits - sõnalavastuse eriauhind, Dmitri Bertman ja Mart Madiste - muusikalavastuse auhind, Vitali Nikolajev - muusikalavastuse eriauhind, Marina Kesler - balletilavastuse auhind, Oksana Titova - tantsulavastuse auhind, Ivika Sillar - kriitikaauhind, Külli Teetamm ja Tambet Tuisk - Ants Lauteri näitlejaauhind, Heli Veskus - Georg Otsa auhind, Finn Poulsen - Salme Reegi auhind, Elo Soode - Natalie Mei auhind, Aarne Üksküla - Priit Põldroosi auhind, Maimu Berg - Aleksander Kurtna auhind, Laura Peterson - Kristallkingakese auhind, Liina Laigu, Kaido Päästel ja Juhan Rumm - teatritöötaja auhind

  11. Eesti teatri aastaauhinnad 2007

    Index Scriptorium Estoniae

    2008-01-01

    Tiit Ojasoo - lavastajaauhind, Silver Vahtre, Krista Tool ja Margus Vaigur - kunstniku auhind, Piret Laurimaa - naisnäitleja auhind, Üllar Saaremäe - meesnäitleja auhind, Tiina Tauraite - naiskõrvalosa auhind, Taavi Teplenkov - meeskõrvalosa auhind, Mart Koldits - sõnalavastuse eriauhind, Dmitri Bertman ja Mart Madiste - muusikalavastuse auhind, Vitali Nikolajev - muusikalavastuse eriauhind, Marina Kesler - balletilavastuse auhind, Oksana Titova - tantsulavastuse auhind, Ivika Sillar - kriitikaauhind, Külli Teetamm ja Tambet Tuisk - Ants Lauteri näitlejaauhind, Heli Veskus - Georg Otsa auhind, Finn Poulsen - Salme Reegi auhind, Elo Soode - Natalie Mei auhind, Aarne Üksküla - Priit Põldroosi auhind, Maimu Berg - Aleksander Kurtna auhind, Laura Peterson - Kristallkingakese auhind, Liina Laigu, Kaido Päästel ja Juhan Rumm - teatritöötaja auhind

  12. Academic Libraries’ Role in Improving Institutions Research Impact

    KAUST Repository

    Tamarkin, Molly; Vijayakumar, J.K.; Baessa, Mohamed A.; Grenz, Daryl M.

    2015-01-01

    In the changing landscape of scientific research and scholarly communication, importance of “quality in research”, “reviewed research” and “reviewed publications” in qualifying for the ratings and rankings are widely discussed. While publishing the research pieces in peer-reviewed and highly ranked journals are increasingly important, there are different methods and tools to be in place at Institutional level to increase researchers’ profile and the ranking of the institutions. As a young research based university created in 2009, King Abdullah University of Science and Technology (KAUST) focuses on the bibliometrics and altemetrics tools, author affiliations, author naming and plug-ins to different search engines, research evaluation systems as well as to research repositories. The University has launched an institutional repository in September 2012 as a home for the intellectual outputs of KAUST researchers, and then adopted the first institutional open access mandate in the Arab region effective June 31, 2014. Integration with ORCID became a key element in this process and the best way to ensure data quality for researcher’s scientific contributions systematically. We will present the inclusion and creation of ORCID identifiers in the existing systems as an institutional member to ORCID, and the creation of dedicated integration tools with Current Research Information System (CRIS) as a standardized common resource to monitor KAUST research outputs. We will also present our experiences in awareness programs, trainings, outreach, implementation of systems and tools like PlumX, as well as our approach in improving the research impact and profiling our Institution’s research to the world.

  13. Academic Libraries’ Role in Improving Institutions Research Impact

    KAUST Repository

    Tamarkin, Molly

    2015-11-11

    In the changing landscape of scientific research and scholarly communication, importance of “quality in research”, “reviewed research” and “reviewed publications” in qualifying for the ratings and rankings are widely discussed. While publishing the research pieces in peer-reviewed and highly ranked journals are increasingly important, there are different methods and tools to be in place at Institutional level to increase researchers’ profile and the ranking of the institutions. As a young research based university created in 2009, King Abdullah University of Science and Technology (KAUST) focuses on the bibliometrics and altemetrics tools, author affiliations, author naming and plug-ins to different search engines, research evaluation systems as well as to research repositories. The University has launched an institutional repository in September 2012 as a home for the intellectual outputs of KAUST researchers, and then adopted the first institutional open access mandate in the Arab region effective June 31, 2014. Integration with ORCID became a key element in this process and the best way to ensure data quality for researcher’s scientific contributions systematically. We will present the inclusion and creation of ORCID identifiers in the existing systems as an institutional member to ORCID, and the creation of dedicated integration tools with Current Research Information System (CRIS) as a standardized common resource to monitor KAUST research outputs. We will also present our experiences in awareness programs, trainings, outreach, implementation of systems and tools like PlumX, as well as our approach in improving the research impact and profiling our Institution’s research to the world.

  14. Gathering by the Red Sea highlights links between environment and epigenetics

    KAUST Repository

    Li, Mo

    2017-06-06

    The number of conferences on epigenetics has been increasing in the past decade, underscoring the impact of the field on a variety of areas in biology and medicine. However, the mechanistic role of the epigenome in adaptation and inheritance, and how the environment may impinge on epigenetic control, are topics of growing debate. Those themes were the focus of the inaugural international King Abdullah University of Science and Technology (KAUST) Research Conference on Environmental Epigenetics in Saudi Arabia, where more than 100 participants from 19 countries enjoyed vibrant scientific discussions and a pleasant February breeze from the Red Sea.

  15. Boron Removal from Seawater by Thin-Film Composite Reverse Osmosis Membranes

    KAUST Repository

    Al Sunbul, Yasmeen

    2018-04-01

    Reverse Osmosis membranes have been successfully proven to remove almost 99% of chemicals dissolved in seawater. However, removal of certain trace elements, such as boron is challenging and relatively low for seawater reverse osmosis desalination plants compared to thermal desalination plants. Boron is naturally occurring and is present in seawater at an average concentration of 4.5-5 mg/L. While boron is a vital element, its toxicity has been proven on crops, animals and possibly humans. Additionally, boron should be removed to comply with the current guideline value of 0.5 mg/L, for drinking water, issued by the World Health Organization (WHO), which is barely attained by a single-pass process seawater reverse osmosis plant. Currently, multipass reverse osmosis membrane operations with pH modifications are the only valid method for boron removal. However, this is not economically efficient as it requires higher energy and chemicals consumptions. The objective of this study was to investigate boron removal by commercial TFC RO membranes in addition to custom-made KAUST-synthesized TFC membrane. Five membrane samples were examined: Toray, Sepro, Koch, and KAUST in-house synthesized membrane. Three different feed pH conditions were used: pH6, pH8, and pH10. Filtration experiments were conducted in two parts. In experiment 1, all five membranes were examined for boron rejection in a dead-end permeation system, whereas in experiment 2 the two membranes with the highest boron rejection from experiment 1 were tested in a cross-flow system. Permeate and feed samples were taken continuously and analyzed for boron concentration, rejection calculation. Membrane surfaces were characterized according to hydrophilicity, roughness and surface charge. The results showed for all the tested membranes that boron rejection increased as the feed pH increased. KAUST, defect-free TFC, showed the highest performance for boron rejection for all pH conditions, although, it shows the

  16. Buying success, Saudi style

    Science.gov (United States)

    Durrani, Matin

    2009-11-01

    Oil - it is what has made Saudi Arabia rich. Without this black gold, none of the country's shopping malls, luxury hotels, six-lane highways or the airconditioned comfort that keeps the terrible heat at bay would be possible. From the first deposits harvested in the early 1950s, Saudi Arabia is now the world's leading exporter of petroleum, which accounts for nearly three-quarters of government revenue. And without the wealth from oil, the huge new King Abdullah University of Science and Technology (KAUST), built on hard, desert soil in less than two years, would have been impossible.

  17. Assessment of AOD variability over Saudi Arabia using MODIS Deep Blue products

    International Nuclear Information System (INIS)

    Butt, Mohsin Jamil; Assiri, Mazen Ebraheem; Ali, Md. Arfan

    2017-01-01

    The aim of this study is to investigate the variability of aerosol over The Kingdom of Saudi Arabia. For this analysis, Moderate Resolution Imaging Spectroradiometer (MODIS) Deep Blue (DB) Aerosol Optical Depth (AOD) product from Terra and Aqua satellites for the years 2000–2013 is used. The product is validated using AERONET data from ground stations, which are situated at Solar Village Riyadh and King Abdullah University of Science and Technology (KAUST) Jeddah. The results show that both Terra and Aqua satellites exhibit a tendency to show the spatial variation of AOD with Aqua being better than Terra to represent the ground based AOD measurements over the study region. The results also show that the eastern, central, and southern regions of the country have a high concentration of AOD during the study period. The validation results show the highest correlation coefficient between Aqua and KAUST data with a value of 0.79, whilst the Aqua and Solar Village based AOD indicates the lowest Root Mean Square Error (RMSE) and Mean Absolute Error (MAE) values which are, 0.17 and 0.12 respectively. Furthermore, the Relative Mean Bias (RMB) based analysis show that the DB algorithm overestimates the AOD when using Terra and Solar Village data, while it underestimates the AOD when using Aqua with Solar Village and KAUST data. The RMB value for Aqua and Solar Village data indicates that the DB algorithm is close to normal in the study region. - Highlights: • The significance of aerosol in the Kingdom of Saudi Arabia is addressed. • MODIS (Terra and Aqua), AERONET and ground based sand event data is used. • MODIS DB product is used to prepare annual aerosol maps and monthly AOD variability. • A comparison is made between Terra and Aqua AOD product over bright surface. • MODIS DB AOD product is validated using AERONET data at Solar Village and KAUST. - This research highlighted the aerosol variability over The Kingdom of Saudi Arabia by using Satellite, AERONET

  18. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece

    2012-11-28

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  19. Simplifying the Access to HPC Resources by Integrating them in the Application GUI

    KAUST Repository

    van Waveren, Matthijs

    2016-06-22

    The computing landscape of KAUST is increasing in complexity. Researchers have access to the 9th fastest supercomputer in the world (Shaheen II) and several other HPC clusters. They work on local Windows, Mac, or Linux workstations. In order to facilitate the access of the HPC systems, we have developed interfaces to several research applications that automate input data transfer, job submission and retrieval of results. The user now submits his jobs to the cluster from within the application GUI on his workstation, and does not have to physically go onto the cluster anymore.

  20. CFD Modeling of a Multiphase Gravity Separator Vessel

    KAUST Repository

    Narayan, Gautham

    2017-05-23

    The poster highlights a CFD study that incorporates a combined Eulerian multi-fluid multiphase and a Population Balance Model (PBM) to study the flow inside a typical multiphase gravity separator vessel (GSV) found in oil and gas industry. The simulations were performed using Ansys Fluent CFD package running on KAUST supercomputer, Shaheen. Also, a highlight of a scalability study is presented. The effect of I/O bottlenecks and using Hierarchical Data Format (HDF5) for collective and independent parallel reading of case file is presented. This work is an outcome of a research collaboration on an Aramco project on Shaheen.

  1. CFD Modeling of a Multiphase Gravity Separator Vessel

    KAUST Repository

    Narayan, Gautham; Khurram, Rooh Ul Amin; Elsaadawy, Ehab

    2017-01-01

    The poster highlights a CFD study that incorporates a combined Eulerian multi-fluid multiphase and a Population Balance Model (PBM) to study the flow inside a typical multiphase gravity separator vessel (GSV) found in oil and gas industry. The simulations were performed using Ansys Fluent CFD package running on KAUST supercomputer, Shaheen. Also, a highlight of a scalability study is presented. The effect of I/O bottlenecks and using Hierarchical Data Format (HDF5) for collective and independent parallel reading of case file is presented. This work is an outcome of a research collaboration on an Aramco project on Shaheen.

  2. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece; Rashid, Mamoon; Pain, Arnab

    2012-01-01

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  3. Optimization and analysis of decision trees and rules: Dynamic programming approach

    KAUST Repository

    Alkhalid, Abdulaziz

    2013-08-01

    This paper is devoted to the consideration of software system Dagger created in KAUST. This system is based on extensions of dynamic programming. It allows sequential optimization of decision trees and rules relative to different cost functions, derivation of relationships between two cost functions (in particular, between number of misclassifications and depth of decision trees), and between cost and uncertainty of decision trees. We describe features of Dagger and consider examples of this systems work on decision tables from UCI Machine Learning Repository. We also use Dagger to compare 16 different greedy algorithms for decision tree construction. © 2013 Taylor and Francis Group, LLC.

  4. From red to green: building and managing the scientific electronic collections for a new Sci-Tech University Library

    KAUST Repository

    Al Zahrani, Rashed

    2013-08-01

    Electronic resources have evolved to become one of the most important resources within the library’s collection. The growths of these resources and the players involved within this area have provided library users with another alternative to obtain information. When implemented correctly with library assistance (library trainings, reference consultations and so forth), library users can access these electronic resources anywhere in the world with relative ease as long as there is an internet connection. Geographic barriers are no longer an issue and information can be obtained in a just-in-time manner. This paper describes how KAUST library built its electronic resources and how they grew into what it is today. Issues such as manpower, expertise level, budget, ERM tools, library-vendor relations and library-user communication will also be elaborated in the paper. Despite its drawbacks, KAUST library has managed to overcome most of them and strived to improve certain areas of concern. The paper will also describe the library’s ERM future directions and strategic planning. KAUST University was opened in September 2009 and it started out with its first cohort of 800 graduate students (25% female) taught by 100 faculties. The main areas of study focus on science and engineering divisions consisting mainly of: Mathematics and Computer Science, Physical Sciences and Life Sciences. From a demographic snapshot taken in 2010, 36% of the student body came from Saudi Arabia and the Middle East, 34% from Asia, 21% from Americas, 5% from Europe and 4% from Africa (alZahrani, R. , Branin, J. and Yi , 2012). The university library, when first started, had about 10 staff. The library is known to have a “state-of-the-art learning and information resource center supporting graduate education and advanced scientific research” (KAUST, 2010). The library subscribed to major science databases, electronic journals and books. It also offers a myriad of services from document

  5. Identity of a brand new library

    KAUST Repository

    Vijayakumar, J.K.

    2017-03-16

    King Abdullah University of Science and Technology (KAUST) Library in Saudi Arabia aspires to be one of the great new-generation libraries in the field of scientific research. Its services and systems support a digitally born collection, 97% of their collection is electronic. The spectacular library facility with lots of space for collaboration and its collections remains open twenty-four hours, every day of the year and is facilitated by a staff coming from 12 different nationalities. It has an Open Access mandate, the first in the Middle East region, and runs a successful digital research repository.

  6. Optimization and analysis of decision trees and rules: Dynamic programming approach

    KAUST Repository

    Alkhalid, Abdulaziz; Amin, Talha M.; Chikalov, Igor; Hussain, Shahid; Moshkov, Mikhail; Zielosko, Beata

    2013-01-01

    This paper is devoted to the consideration of software system Dagger created in KAUST. This system is based on extensions of dynamic programming. It allows sequential optimization of decision trees and rules relative to different cost functions, derivation of relationships between two cost functions (in particular, between number of misclassifications and depth of decision trees), and between cost and uncertainty of decision trees. We describe features of Dagger and consider examples of this systems work on decision tables from UCI Machine Learning Repository. We also use Dagger to compare 16 different greedy algorithms for decision tree construction. © 2013 Taylor and Francis Group, LLC.

  7. Continuous Shearlet Tight Frames

    KAUST Repository

    Grohs, Philipp

    2010-10-22

    Based on the shearlet transform we present a general construction of continuous tight frames for L2(ℝ2) from any sufficiently smooth function with anisotropic moments. This includes for example compactly supported systems, piecewise polynomial systems, or both. From our earlier results in Grohs (Technical report, KAUST, 2009) it follows that these systems enjoy the same desirable approximation properties for directional data as the previous bandlimited and very specific constructions due to Kutyniok and Labate (Trans. Am. Math. Soc. 361:2719-2754, 2009). We also show that the representation formulas we derive are in a sense optimal for the shearlet transform. © 2010 Springer Science+Business Media, LLC.

  8. Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia

    KAUST Repository

    Lai, PokYui

    2012-06-08

    A slow-growing, strictly aerobic, Gram-negative, coccus bacterial strain, designated KAUST100406-0324T, was isolated from sea-floor sediment collected from the Red Sea, Saudi Arabia. The catalase- and oxidase-positive strain was non-sporulating and only slightly halophilic. Optimum growth occurred at 20-25 °C and at pH values ranging from 7.0 to 8.0. The major cellular fatty acids of the strain were unsaturated C18: 1ω6c and/or C18:1ω7c, C18:1ω7c 11-methyl and C16:1ω7c and/or C16:1ω6c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. Ubiquinone 10 was the predominant lipoquinone. The DNA G+C content of strain KAUST100406-0324T was 64.0 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that the novel strain belonged to the family Rhodobacteraceae of the class Alphaproteobacteria but formed a distinct evolutionary lineage from other bacterial species with validly published names. The 16S rRNA gene sequence of the novel strain was distantly related, but formed a monophyletic cluster with, those of bacteria from two moderately halophilic genera, Hwanghaeicola and Maribius. The similarity of the sequence between the novel strain KAUST100406-0324T and the type strains Hwanghaeicola aestuarii Y26T (accession number FJ230842), Maribius pelagius B5-6T (DQ514326) and Maribius salinus CL-SP27T (AY906863) were 94.5 %, 95.2 % and 95.3 %, respectively. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we propose that this strain represents a novel species of a new genus in the family Rhodobacteraceae, for which the name of Profundibacterium mesophilum gen. nov., sp. nov. was proposed, with KAUST100406-0324T (= JCM 17872T = NRRL B-59665T) as the type strain. © 2013 IUMS.

  9. Development of the Red Sea Biogeographic Information System

    KAUST Repository

    Machda, Fahmi

    2010-05-01

    Marine studies, surveys, and observational activities are continuously generating new and diverse data, which are hard to keep track of with tables and spreadsheets. Integrated data and information management systems that collect, analyze, and combine data are needed in order to provide a comprehensive picture of marine environments under study. For these reasons, we started to develop the Red Sea Biogeographic Information System (RBIS) at King Abdullah University of Science and Technology (KAUST) as a web application utilizing the most updated Web 2.0 technologies. RBIS is designed to have an easily accessible interface that is able to host and display research activities conducted in the Red Sea. Its data model is designed to deal with any kind of marine data. For its data structure, RBIS is organizing the data into three main categories: biological data, physicochemical data, and human activities. Spatial distribution of these data is visualized on a Google-Maps mashup. Dynamic charts are used to visualize the statistics of the data. With these functionalities, data model, and data structure, RBIS is able to organize, visualize, and do instantly combined analyses of research data from the Red Sea. The current version is accessible at http://www.kaust.edu.sa/rbis. © 2010 IEEE.

  10. DANNP: an efficient artificial neural network pruning tool

    KAUST Repository

    AlShahrani, Mona; Soufan, Othman; Magana-Mora, Arturo; Bajic, Vladimir B.

    2017-01-01

    Although the ANN pruning algorithms are not entirely parallelizable, DANNP was able to speed up the ANN pruning up to eight times on a 32-core machine, compared to the serial implementations. To assess the impact of the ANN pruning by DANNP tool, we used 16 datasets from different domains. In eight out of the 16 datasets, DANNP significantly reduced the number of weights by 70%–99%, while maintaining a competitive or better model performance compared to the unpruned ANN. Finally, we used a naïve Bayes classifier derived with the features selected as a byproduct of the ANN pruning and demonstrated that its accuracy is comparable to those obtained by the classifiers trained with the features selected by several state-of-the-art FS methods. The FS ranking methodology proposed in this study allows the users to identify the most discriminant features of the problem at hand. To the best of our knowledge, DANNP (publicly available at www.cbrc.kaust.edu.sa/dannp) is the only available and on-line accessible tool that provides multiple parallelized ANN pruning options. Datasets and DANNP code can be obtained at www.cbrc.kaust.edu.sa/dannp/data.php and https://doi.org/10.5281/zenodo.1001086.

  11. Stabilization of flow past a rounded cylinder

    Science.gov (United States)

    Samtaney, Ravi; Zhang, Wei

    2016-11-01

    We perform global linear stability analysis on low-Re flow past a rounded cylinder. The cylinder corners are rounded with a radius R, normalized as R+ = R / D where D is the cylinder diameter, and its effect on the flow stability characteristics is investigated. We compute the critical Reynolds number (Recr) for the onset of first instability, and quantify the perturbation growth rate for the super-critical flows. It is found that the flow can be stabilized by partially rounding the cylinder. Compared with the square and circular cylinders, the partially rounded cylinder has a higher Recr , attaining a maximum at around R+ = 0 . 30 , and the perturbation growth rate of the super-critical flows is reduced for Re R+ -> 0 . 00), while only the near-wake backflow is crucial for circular-like cylinders (R+ -> 0 . 50). The stability analysis results are also verified with those of the direct simulations and very good agreement is achieved. Supported by the KAUST Office of Competitive Research Funds under Award No. URF/1/1394-01. The supercomputer Shaheen at KAUST was utilized for the simulations.

  12. Impact of Subgrid Scale Models and Heat Loss on Large Eddy Simulations of a Premixed Jet Burner Using Flamelet-Generated Manifolds

    Science.gov (United States)

    Hernandez Perez, Francisco E.; Im, Hong G.; Lee, Bok Jik; Fancello, Alessio; Donini, Andrea; van Oijen, Jeroen A.; de Goey, L. Philip H.

    2017-11-01

    Large eddy simulations (LES) of a turbulent premixed jet flame in a confined chamber are performed employing the flamelet-generated manifold (FGM) method for tabulation of chemical kinetics and thermochemical properties, as well as the OpenFOAM framework for computational fluid dynamics. The burner has been experimentally studied by Lammel et al. (2011) and features an off-center nozzle, feeding a preheated lean methane-air mixture with an equivalence ratio of 0.71 and mean velocity of 90 m/s, at 573 K and atmospheric pressure. Conductive heat loss is accounted for in the FGM tabulation via burner-stabilized flamelets and the subgrid-scale (SGS) turbulence-chemistry interaction is modeled via presumed filtered density functions. The impact of heat loss inclusion as well as SGS modeling for both the SGS stresses and SGS variance of progress variable on the numerical results is investigated. Comparisons of the LES results against measurements show a significant improvement in the prediction of temperature when heat losses are incorporated into FGM. While further enhancements in the LES results are accomplished by using SGS models based on transported quantities and/or dynamically computed coefficients as compared to the Smagorinsky model, heat loss inclusion is more relevant. This research was sponsored by King Abdullah University of Science and Technology (KAUST) and made use of computational resources at KAUST Supercomputing Laboratory.

  13. Seabed Filter Feasibility Study of Om Almisk Island

    KAUST Repository

    Sesler, Kathryn

    2012-06-01

    Freshwater access has always been and is continuing to be a severe problem in desert coastal regions, despite the fact that they have an unlimited supply of easily accessible saline water. Water desalination plants are well established and heavily relied upon throughout the Middle East, Saudi Arabia in particular. However, water desalination tends to be a very expensive and energy intensive solution to the problem. The transition from using open water intake systems and all of the pretreatment processes that they require, to using seabed water filters as an intake, would potentially reduce the lifetime costs, energy consumption, and environmental impacts commonly associated with water desalination. This is because the filtration process that the seabed filter generates, serves as sufficient pretreatment for seawater as well as eliminating any risk of entrainment or impingement of marine organisms. The main objective of this research is to conduct a feasibility study on Om Almisk Island, an island off the coast of King Abdullah University of Science and Technology (KAUST), to determine if it would be a suitable location to construct a seabed water filter as a replacement for the current open water intake. The Om Almisk Island site was evaluated through collection of sand samples over a radial grid around Om Almisk Island and sample analysis using grain size distribution, porosity, and hydraulic conductivity. The lack of mud, high hydraulic conductivity, proximity to KAUST, and the shallow waters of the sandy apron surrounding Om Almisk Island make this an ideal location for a seabed water filter to be used as an intake and pretreatment for the KAUST desalination plant. This location also has low tide change and the presence of benthic macrofauna to create bioturbation in the sediments, which could inhibit the growth of a schmutzdecke. If this biological layer forms, it could drastically reduce the hydraulic conductivity of the system. Due to the high hydraulic

  14. A comprehensive detailed kinetic mechanism for the simulation of transportation fuels

    KAUST Repository

    Mehl, Marco; Zhang, Kuiwen; Wagnon, Scott; Kukkadapu, Goutham; Westbrook, Charles K.; Pitz, William J.; Zhang, Yinjia; Curran, Henry J.; Al Rachidi, Mariam; Atef, Nour; Sarathy, Mani; Ahmed, Ahfaz

    2017-01-01

    This work presents a recently compiled comprehensive model for transportations fuels resulting from the collaboration of three research groups: LLNL, NUI Galway and KAUST. In the past 5 years new fundamental calculations led to significant improvements in the fidelity of detailed kinetic models of important surrogate components (e.g. n-heptane, iso-octane, toluene…) improving predictions of the combustion behavior of pure components and mixtures. By extending the newly adopted reaction rate rules, mechanisms for components that were not included in the previous LLNL gasoline and diesel surrogate mechanisms were developed (e.g. polyalkylated aromatics, cycloalkanes, components from bio-logical sources…). The major features of this updated and extended model are presented together with validation comparisons, examples of applications and future directions.

  15. Using the IR as a Research Data Registry

    KAUST Repository

    Grenz, Daryl M.

    2018-05-01

    As data and software become increasingly common research outputs, universities have an opportunity to expand their existing efforts to record affiliated publications so that they also capture information about research data releases. At KAUST we have taken several steps to put our repository on a path towards becoming a reliable registry for information about the existence and location of research data released by affiliated researchers. These included developing a process to retrospectively retrieve and register information about datasets with machine-readable relationships to publications already in the repository, and updates to our active publications tracking procedures so that data availability statements are retrieved at the time of harvesting and checked for references to research data. The presentation will conclude by discussing how these efforts help put the repository in a position to provide expanded services in support of improved research data management, including access to and preservation of research data not explicitly linked to a formal publication.

  16. Teaching numerical methods with IPython notebooks and inquiry-based learning

    KAUST Repository

    Ketcheson, David I.

    2014-01-01

    A course in numerical methods should teach both the mathematical theory of numerical analysis and the craft of implementing numerical algorithms. The IPython notebook provides a single medium in which mathematics, explanations, executable code, and visualizations can be combined, and with which the student can interact in order to learn both the theory and the craft of numerical methods. The use of notebooks also lends itself naturally to inquiry-based learning methods. I discuss the motivation and practice of teaching a course based on the use of IPython notebooks and inquiry-based learning, including some specific practical aspects. The discussion is based on my experience teaching a Masters-level course in numerical analysis at King Abdullah University of Science and Technology (KAUST), but is intended to be useful for those who teach at other levels or in industry.

  17. Reduced Gasoline Surrogate (Toluene/n-Heptane/iso-Octane) Chemical Kinetic Model for Compression Ignition Simulations

    KAUST Repository

    Sarathy, Mani

    2018-04-03

    Toluene primary reference fuel (TPRF) (mixture of toluene, iso-octane and heptane) is a suitable surrogate to represent a wide spectrum of real fuels with varying octane sensitivity. Investigating different surrogates in engine simulations is a prerequisite to identify the best matching mixture. However, running 3D engine simulations using detailed models is currently impossible and reduction of detailed models is essential. This work presents an AramcoMech reduced kinetic model developed at King Abdullah University of Science and Technology (KAUST) for simulating complex TPRF surrogate blends. A semi-decoupling approach was used together with species and reaction lumping to obtain a reduced kinetic model. The model was widely validated against experimental data including shock tube ignition delay times and premixed laminar flame speeds. Finally, the model was utilized to simulate the combustion of a low reactivity gasoline fuel under partially premixed combustion conditions.

  18. A metal-organic framework-based splitter for separating propylene from propane

    KAUST Repository

    Cadiau, Amandine

    2016-07-07

    The chemical industry is dependent on the olefin/paraffin separation, which is mainly accomplished by using energy-intensive processes. We report the use of reticular chemistry for the fabrication of a chemically stable fluorinated metal-organic framework (MOF) material (NbOFFIVE-1-Ni, also referred to as KAUST-7). The bridging of Ni(II)-pyrazine square-grid layers with (NbOF5)2- pillars afforded the construction of a three-dimensional MOF, enclosing a periodic array of fluoride anions in contracted square-shaped channels. The judiciously selected bulkier (NbOF5)2- caused the looked-for hindrance of the previously free-rotating pyrazine moieties, delimiting the pore system and dictating the pore aperture size and its maximum opening. The restricted MOF window resulted in the selective molecular exclusion of propane from propylene at atmospheric pressure, as evidenced through multiple cyclic mixed-gas adsorption and calorimetric studies.

  19. SVAMP: Sequence variation analysis, maps and phylogeny

    KAUST Repository

    Naeem, Raeece

    2014-04-03

    Summary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima\\'s D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents. Availability and implementation: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp. © The Author 2014.

  20. Optimal Design and Model Validation for Combustion Experiments in a Shock Tube

    KAUST Repository

    Long, Quan

    2014-01-06

    We develop a Bayesian framework for the optimal experimental design of the shock tube experiments which are being carried out at the KAUST Clean Combustion Center. The unknown parameters are the pre-exponential parameters and the activation energies in the reaction rate functions. The control parameters are the initial hydrogen concentration and the temperature. First, we build a polynomial based surrogate model for the observable related to the reactions in the shock tube. Second, we use a novel MAP based approach to estimate the expected information gain in the proposed experiments and select the best experimental set-ups corresponding to the optimal expected information gains. Third, we use the synthetic data to carry out virtual validation of our methodology.

  1. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species

    KAUST Repository

    Salhi, Adil; Negrã o, Só nia; Essack, Magbubah; Morton, Mitchell J. L.; Bougouffa, Salim; Mohamad Razali, Rozaimi; Radovanovic, Aleksandar; Marchand, Benoit; Kulmanov, Maxat; Hoehndorf, Robert; Tester, Mark A.; Bajic, Vladimir B.

    2017-01-01

    Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.

  2. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species

    KAUST Repository

    Salhi, Adil

    2017-07-14

    Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.

  3. DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail; Soufan, Othman; Essack, Magbubah; Kalnis, Panos; Bajic, Vladimir B.

    2016-01-01

    DASPfind is a computational method for finding reliable new interactions between drugs and proteins. We show over six different DTI datasets that DASPfind outperforms other state-of-the-art methods when the single top-ranked predictions are considered, or when a drug with no known targets or with few known targets is considered. We illustrate the usefulness and practicality of DASPfind by predicting novel DTIs for the Ion Channel dataset. The validated predictions suggest that DASPfind can be used as an efficient method to identify correct DTIs, thus reducing the cost of necessary experimental verifications in the process of drug discovery. DASPfind can be accessed online at: http://​www.​cbrc.​kaust.​edu.​sa/​daspfind.

  4. Hydrolytically stable fluorinated metal-organic frameworks for energy-efficient dehydration

    KAUST Repository

    Cadiau, Amandine

    2017-05-18

    Natural gas must be dehydrated before it can be transported and used, but conventional drying agents such as activated alumina or inorganic molecular sieves require an energy-intensive desiccant-regeneration step. We report a hydrolytically stable fluorinated metal-organic framework, AlFFIVE-1-Ni (KAUST-8), with a periodic array of open metal coordination sites and fluorine moieties within the contracted square-shaped one-dimensional channel. This material selectively removed water vapor from gas streams containing CO2, N2, CH4, and higher hydrocarbons typical of natural gas, as well as selectively removed both H2O and CO2 in N2-containing streams. The complete desorption of the adsorbed water molecules contained by the AlFFIVE-1-Ni sorbent requires relatively moderate temperature (~105°C) and about half the energy input for commonly used desiccants.

  5. Reduced Gasoline Surrogate (Toluene/n-Heptane/iso-Octane) Chemical Kinetic Model for Compression Ignition Simulations

    KAUST Repository

    Sarathy, Mani; Atef, Nour; Alfazazi, Adamu; Badra, Jihad; Zhang, Yu; Tzanetakis, Tom; Pei, Yuanjiang

    2018-01-01

    Toluene primary reference fuel (TPRF) (mixture of toluene, iso-octane and heptane) is a suitable surrogate to represent a wide spectrum of real fuels with varying octane sensitivity. Investigating different surrogates in engine simulations is a prerequisite to identify the best matching mixture. However, running 3D engine simulations using detailed models is currently impossible and reduction of detailed models is essential. This work presents an AramcoMech reduced kinetic model developed at King Abdullah University of Science and Technology (KAUST) for simulating complex TPRF surrogate blends. A semi-decoupling approach was used together with species and reaction lumping to obtain a reduced kinetic model. The model was widely validated against experimental data including shock tube ignition delay times and premixed laminar flame speeds. Finally, the model was utilized to simulate the combustion of a low reactivity gasoline fuel under partially premixed combustion conditions.

  6. Connecting the pieces: using ORCIDs to improve research impact and repositories

    KAUST Repository

    Baessa, Mohamed A.; Lery, Thibaut L.; Vijayakumar, J.K.; Grenz, Daryl M.

    2015-01-01

    Integration with ORCID has been a key element in this process and the best way to ensure data quality for researcher’s scientific contributions. It included the systematic inclusion and creation, if necessary, of ORCID identifiers in the existing repository system, an institutional membership in ORCID, and the creation of dedicated integration tools. In addition and in cooperation with the Office of Research Evaluation, the Library worked at implementing a Current Research Information System (CRIS) as a standardized common resource to monitor KAUST research outputs. We will present our findings about the CRIS implementation, the ORCID API, the repository statistics as well as our approach in conducting the assessment of research impact in terms of usage by the global research community.

  7. Intakes and outfalls for seawater reverse-osmosis desalination facilities innovations and environmental impacts

    CERN Document Server

    Jones, Burton; Maliva, Robert

    2015-01-01

    The book assembles the latest research on new design techniques in water supplies using desalinated seawater. The authors examine the diverse issues related to the intakes and outfalls of these facilities. They clarify how and why these key components of the facilities impact the cost of operation and subsequently the cost of water supplied to the consumers. The book consists of contributed articles from a number of experts in the field who presented their findings at the “Desalination Intakes and Outfalls” workshop held at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia in October, 2013. The book integrates coverage relevant to a wide variety of researchers and professionals in the general fields of environmental engineering and sustainable development.

  8. FDM 3D printed coffee glove embedded with flexible electronic

    KAUST Repository

    Bahri, Meznan

    2017-10-31

    With the advances in 3D printing technology, Flexible Electronics can now be exploited to form the so-called “Embedded Electronics”. This paper describes experiences learned from a research project which ran during summer 2016 at KAUST, in collaboration with the Electrical and Computer Engineering Department at Effat University, and aimed at creating a heating coffee glove product operating on double alkaline batteries using Kapton© as a flexible substrate for the circuit. The circuit and its batteries are encapsulated in a 3D printed glove, designed using SolidWorks©. The proposed methodology and techniques applied during this work could be further used in implementing other technologies, such as thermoelectric coolers head patches, smart garments, and flexible smartphones. Limitation and recommendation of the present methodology are also discussed.

  9. A comprehensive detailed kinetic mechanism for the simulation of transportation fuels

    KAUST Repository

    Mehl, Marco

    2017-02-27

    This work presents a recently compiled comprehensive model for transportations fuels resulting from the collaboration of three research groups: LLNL, NUI Galway and KAUST. In the past 5 years new fundamental calculations led to significant improvements in the fidelity of detailed kinetic models of important surrogate components (e.g. n-heptane, iso-octane, toluene…) improving predictions of the combustion behavior of pure components and mixtures. By extending the newly adopted reaction rate rules, mechanisms for components that were not included in the previous LLNL gasoline and diesel surrogate mechanisms were developed (e.g. polyalkylated aromatics, cycloalkanes, components from bio-logical sources…). The major features of this updated and extended model are presented together with validation comparisons, examples of applications and future directions.

  10. Single-cell technologies in molecular marine studies

    KAUST Repository

    Kodzius, Rimantas

    2015-01-24

    Middle Eastern countries are experiencing a renaissance, with heavy investment in both in infrastructure and science. King Abdullah University of Science and Technology (KAUST) is a new and modern university in Saudi Arabia. At the Computational Bioscience Research Center (CBRC) we are working on exploring the Red Sea and beyond, collaborating with Japanese and other research centers. We are using the environment to collect and analyze the microorganisms present. The platform being established at CBRC allows to process samples in a pipeline. The pipeline components consist of sample collection, processing and sequencing, following the in silico analysis, determining the gene functions, identifying the organisms. The genomes of microorganisms of interest are targeted modified by genome editing technology such as CRISPR and desired properties are selected by single cell instrumentation. The final output is to identify valuable microorganisms with production of bio-energy, nutrients, the food and fine chemicals.

  11. Optimal Design of Shock Tube Experiments for Parameter Inference

    KAUST Repository

    Bisetti, Fabrizio

    2014-01-06

    We develop a Bayesian framework for the optimal experimental design of the shock tube experiments which are being carried out at the KAUST Clean Combustion Research Center. The unknown parameters are the pre-exponential parameters and the activation energies in the reaction rate expressions. The control parameters are the initial mixture composition and the temperature. The approach is based on first building a polynomial based surrogate model for the observables relevant to the shock tube experiments. Based on these surrogates, a novel MAP based approach is used to estimate the expected information gain in the proposed experiments, and to select the best experimental set-ups yielding the optimal expected information gains. The validity of the approach is tested using synthetic data generated by sampling the PC surrogate. We finally outline a methodology for validation using actual laboratory experiments, and extending experimental design methodology to the cases where the control parameters are noisy.

  12. Nano Antenna Integrated Diode (Rectenna) For Infrared Energy Harvesting

    KAUST Repository

    Gadalla, Mena N.

    2013-01-01

    40% without it) which in turn improves the coupled power by 40 times. Nano antennas were fabricated in house using Electron beam lithography with a precise gap of 50nm. In addition, THz diode was designed, fabricated and integrated to the nano antennas to rectify the enhanced THz signal. The integration of the nano diode required a precise overlap of the two arms of the antenna in the rage of 100nm. In order to overcome two arms overlap fabrication challenges, three layer alignment technique was used to produce precise overlap.The THz rectifier was electrically tested and shown high sensitivity and rectification ability without any bias. Finally, nano antenna integrated diode is under optical testing using   a   10.6μm   𝐶𝑜2 laser at Electro-Optics Lab, Prince Sultan Advanced Technologies Research Institute (PSATRI), King Saud University due to the unavailability of the measurement setup in KAUST.

  13. Optimal Experimental Design for Large-Scale Bayesian Inverse Problems

    KAUST Repository

    Ghattas, Omar

    2014-01-06

    We develop a Bayesian framework for the optimal experimental design of the shock tube experiments which are being carried out at the KAUST Clean Combustion Research Center. The unknown parameters are the pre-exponential parameters and the activation energies in the reaction rate expressions. The control parameters are the initial mixture composition and the temperature. The approach is based on first building a polynomial based surrogate model for the observables relevant to the shock tube experiments. Based on these surrogates, a novel MAP based approach is used to estimate the expected information gain in the proposed experiments, and to select the best experimental set-ups yielding the optimal expected information gains. The validity of the approach is tested using synthetic data generated by sampling the PC surrogate. We finally outline a methodology for validation using actual laboratory experiments, and extending experimental design methodology to the cases where the control parameters are noisy.

  14. Comparative metagenomics of the Red Sea

    KAUST Repository

    Mineta, Katsuhiko

    2016-01-26

    Metagenome produces a tremendous amount of data that comes from the organisms living in the environments. This big data enables us to examine not only microbial genes but also the community structure, interaction and adaptation mechanisms at the specific location and condition. The Red Sea has several unique characteristics such as high salinity, high temperature and low nutrition. These features must contribute to form the unique microbial community during the evolutionary process. Since 2014, we started monthly samplings of the metagenomes in the Red Sea under KAUST-CCF project. In collaboration with Kitasato University, we also collected the metagenome data from the ocean in Japan, which shows contrasting features to the Red Sea. Therefore, the comparative metagenomics of those data provides a comprehensive view of the Red Sea microbes, leading to identify key microbes, genes and networks related to those environmental differences.

  15. Knowledge Exploration from Big Data in Biomedicine

    KAUST Repository

    Bajic, Vladimir B.

    2016-01-27

    The last few decades have witnessed an enormous accumulation of data and information in various forms in the domain of Biomedicine. To search for accurate and rich information on any particular topic in this domain appears challenging. The main reasons are that a) useful pieces of information are scattered across numerous sources, b) data is contained in a variety of formats, c) data/information are not indexed with standard identifiers, d) a lot of information is in a free text format, and e) frequently the information needed is not explicitly presented in any single data/information source. This situation requires new approaches to search for, extract and explore the desired information. We will present a system developed at KAUST that addresses some of these challenges. This system is a representative of a technological solution to what can be named Next Generation Knowledge Mining Systems for the biomedical domain.

  16. Eesti kunsti superego, ego ja id / Andri Ksenofontov

    Index Scriptorium Estoniae

    Ksenofontov, Andri, 1962-

    2007-01-01

    Graafikanäitus "Kohanemised" Rahvusraamatukogus. JP Kaljoneni (sünd. 1976, Soome) fotonäitus "Integrations" Draakoni galeriis. Jevgeni Klimovi (1946-1996) fotonäitus Venemaa saatkonna galeriis. Nikolai Kormashovi portree-etüüdide väljapanek Haus galeriis. Jaan Elkeni popmuusikast inspireeritud maalinäitus Hobusepea galeriis. Näitus "Skulptuur räägib : võim ja vabadus" Tallinna Kunstihoones. Tanja Muravskaja video ja fotoseeria "Positsioonid" ning Kristina Normani videoinstallatsioon "Monoliit. Eternal Mix" Noorte kunstnike biennaalil Rüütelkonna hoones. Kaido Ole väljapanek "Hümn" Vaal-galeriis. Anu Pennaneni video "Sõprus" Kumus. Flo Kasearu video "Mulgi reisid" ja näitus ArtDepoo Galeriis. Eeva Käsperi klaasinäitus "Õrn. Salvestatud mõjutused" Hop galeriis. EKA metallikunsti ja skulptuuri eriala üliõpilaste kollektiivse alateadvusliku joonistamise näitus "Entroopia" Pikk t. 42 ja muud

  17. Robust and scalable hierarchical matrix-based fast direct solver and preconditioner for the numerical solution of elliptic partial differential equations

    KAUST Repository

    Chavez, Gustavo Ivan

    2017-07-10

    This dissertation introduces a novel fast direct solver and preconditioner for the solution of block tridiagonal linear systems that arise from the discretization of elliptic partial differential equations on a Cartesian product mesh, such as the variable-coefficient Poisson equation, the convection-diffusion equation, and the wave Helmholtz equation in heterogeneous media. The algorithm extends the traditional cyclic reduction method with hierarchical matrix techniques. The resulting method exposes substantial concurrency, and its arithmetic operations and memory consumption grow only log-linearly with problem size, assuming bounded rank of off-diagonal matrix blocks, even for problems with arbitrary coefficient structure. The method can be used as a standalone direct solver with tunable accuracy, or as a black-box preconditioner in conjunction with Krylov methods. The challenges that distinguish this work from other thrusts in this active field are the hybrid distributed-shared parallelism that can demonstrate the algorithm at large-scale, full three-dimensionality, and the three stressors of the current state-of-the-art multigrid technology: high wavenumber Helmholtz (indefiniteness), high Reynolds convection (nonsymmetry), and high contrast diffusion (inhomogeneity). Numerical experiments corroborate the robustness, accuracy, and complexity claims and provide a baseline of the performance and memory footprint by comparisons with competing approaches such as the multigrid solver hypre, and the STRUMPACK implementation of the multifrontal factorization with hierarchically semi-separable matrices. The companion implementation can utilize many thousands of cores of Shaheen, KAUST\\'s Haswell-based Cray XC-40 supercomputer, and compares favorably with other implementations of hierarchical solvers in terms of time-to-solution and memory consumption.

  18. Flow cytometric assessment of microbial abundance in the near-field area of seawater reverse osmosis concentrate discharge

    KAUST Repository

    Van Der Merwe, Riaan

    2014-06-01

    The discharge of concentrate and other process waters from seawater reverse osmosis (SWRO) plant operations into the marine environment may adversely affect water quality in the near-field area surrounding the outfall. The main concerns are the increase in salt concentration in receiving waters, which results in a density increase and potential water stratification near the outfall, and possible increases in turbidity, e.g., due to the discharge of filter backwash waters. Changes in ambient water quality may affect microbial abundance in the area, for example by hindering the photosynthesis process or disrupting biogenesis. It is widely accepted that marine biodiversity is lower in more extreme conditions, such as high salinity environments. As aquatic microbial communities respond very rapidly to changes in their environment, they can be used as indicators for monitoring ambient water quality. The objective of this study was to assess possible changes in microbial abundance as a result of concentrate discharge into the near-field area (<. 25. m) surrounding the outfall of the King Abdullah University of Science and Technology (KAUST) SWRO plant. Flow cytometric (FCM) analysis was conducted in order to rapidly determine microbial abundance on a single-cell level in 107 samples, taken by diving, from the discharge area, the intake area and two control sites. FCM analysis combined the measurement of distinct scatter of cells and particles, autofluorescence of cyanobacteria and algae, and fluorescence after staining of nucleic acids with SYBR® Green for a total bacterial count. The results indicate that changes in microbial abundance in the near-field area of the KAUST SWRO outfall are minor and appear to be the result of a dilution effect rather than a direct impact of the concentrate discharge. © 2014 Elsevier B.V.

  19. Genetical, cytological and physiological studies on the induced mutants with special regard to effective methods for obtaining useful mutants in perennial woody plant

    International Nuclear Information System (INIS)

    Kukimura, H.; Ikeda, F.; Fujita, H.; Maeta, T.; Nakajima, K.; Katagiri, K.; Nakahira, K.; Somegou, M.

    1976-01-01

    The plants studied included apple trees, cryptomeria (japanese cedar) and mulberry. In apple, dwarf and compact types of mutants from cv. Fuji were found to be graft incompatible on Maruba-kaido(Malus prunifolia) rootstock. In Sunki mandarin(Citrus sunki), the number of nucellar embryo per seed was affected by gamma-irradiation, and morphological mutants from nucellar seedlings were obtained at high rate by irradiation at floral bud stage with 2kR exposure. In Cryptomeria, re-irradiated waxless mutants by gamma-rays showed very high rate of somatic mutation when compared to other morphological mutants. Pollen sterility and pollen shaped PMC were found in the most of gamma-induced-mutants. Mutants forming pollen shaped PMC had a genetical tendency of continuous male flower bud formation for a longer term. With mulberry, time of sprouting of induced mutants differed from the originals. Ability of root initiation of semi-softwood cuttings in morphological mutants were tested. Cytochimera induction were found at considerably high rate when actively growing diploid plants were irradiated by gamma-rays. Eight kinds of cytochimeras were induced. Frequency of 2-4-4 was extremely high(approx. 50%), then 4-2-2 and 2-4-2 chimeras followed. Seven kinds were induced by semi-acute irradiation(200R/h), while 4 kinds by acute irradiation(5kR/h). By breeding test it was cleared that the elongate and entire leaf was sexually transmissible, whereas the 'dwarf' was not obvious and the 'marginally curledleaf' was not transmissible. Pyronin-methylgreen staining method proved to be useful in some morphological mutants to distinguish the histo-genetical differences which exist in the shoot apex.

  20. Physical and chemical properties of deposited airborne particulates over the Arabian Red Sea coastal plain

    Science.gov (United States)

    Engelbrecht, Johann P.; Stenchikov, Georgiy; Jish Prakash, P.; Lersch, Traci; Anisimov, Anatolii; Shevchenko, Illia

    2017-09-01

    Mineral dust is the most abundant aerosol, having a profound impact on the global energy budget. This research continues our previous studies performed on surface soils in the Arabian Peninsula, focusing on the mineralogical, physical and chemical composition of dust deposits from the atmosphere at the Arabian Red Sea coast. For this purpose, aerosols deposited from the atmosphere are collected during 2015 at six sites on the campus of the King Abdullah University of Science and Technology (KAUST) situated on the Red Sea coastal plain of Saudi Arabia and subjected to the same chemical and mineralogical analysis we conducted on soil samples. Frisbee deposition samplers with foam inserts were used to collect dust and other deposits, for the period December 2014 to December 2015. The average deposition rate measured at KAUST for this period was 14 g m-2 per month, with lowest values in winter and increased deposition rates in August to October. The particle size distributions provide assessments of particle size fractions in the dust deposits.X-ray diffraction (XRD) analysis of a subset of samples confirms variable amounts of quartz, feldspars, micas, and halite, with lesser amounts of gypsum, calcite, dolomite, hematite, and amphibole. Freeze-dried samples were re-suspended onto the Teflon® filters for elemental analysis by X-ray fluorescence (XRF), while splits from each sample were analyzed for water-soluble cations and anions by ion chromatography. The dust deposits along the Red Sea coast are considered to be a mixture of dust emissions from local soils and soils imported from distal dust sources. Airborne mineral concentrations are greatest at or close to dust sources, compared to those through medium- and long-range transport. It is not possible to identify the exact origin of deposition samples from the mineralogical and chemical results alone. These aerosol data are the first of their kind from the Red Sea region. They will help assess their potential

  1. Physical and chemical properties of deposited airborne particulates over the Arabian Red Sea coastal plain

    KAUST Repository

    Engelbrecht, Johann

    2017-09-27

    Mineral dust is the most abundant aerosol, having a profound impact on the global energy budget. This research continues our previous studies performed on surface soils in the Arabian Peninsula, focusing on the mineralogical, physical and chemical composition of dust deposits from the atmosphere at the Arabian Red Sea coast. For this purpose, aerosols deposited from the atmosphere are collected during 2015 at six sites on the campus of the King Abdullah University of Science and Technology (KAUST) situated on the Red Sea coastal plain of Saudi Arabia and subjected to the same chemical and mineralogical analysis we conducted on soil samples. Frisbee deposition samplers with foam inserts were used to collect dust and other deposits, for the period December 2014 to December 2015. The average deposition rate measured at KAUST for this period was 14 g m−2 per month, with lowest values in winter and increased deposition rates in August to October. The particle size distributions provide assessments of  < 10 and  < 2.5 µm dust deposition rates, and it is suggested that these represent proxies for PM10 (coarse) and PM2. 5 (fine) particle size fractions in the dust deposits. X-ray diffraction (XRD) analysis of a subset of samples confirms variable amounts of quartz, feldspars, micas, and halite, with lesser amounts of gypsum, calcite, dolomite, hematite, and amphibole. Freeze-dried samples were re-suspended onto the Teflon® filters for elemental analysis by X-ray fluorescence (XRF), while splits from each sample were analyzed for water-soluble cations and anions by ion chromatography. The dust deposits along the Red Sea coast are considered to be a mixture of dust emissions from local soils and soils imported from distal dust sources. Airborne mineral concentrations are greatest at or close to dust sources, compared to those through medium- and long-range transport. It is not possible to identify the exact origin of deposition samples from the

  2. DANNP: an efficient artificial neural network pruning tool

    KAUST Repository

    Alshahrani, Mona

    2017-11-06

    available at www.cbrc.kaust.edu.sa/dannp) is the only available and on-line accessible tool that provides multiple parallelized ANN pruning options. Datasets and DANNP code can be obtained at www.cbrc.kaust.edu.sa/dannp/data.php and https://doi.org/10.5281/zenodo.1001086.

  3. Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants.

    Science.gov (United States)

    Magana-Mora, Arturo; Ashoor, Haitham; Jankovic, Boris R; Kamau, Allan; Awara, Karim; Chowdhary, Rajesh; Archer, John A C; Bajic, Vladimir B

    2013-01-01

    In higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for signals within genomic sequences of plants that correspond to TISs. Our tool requires only genome sequence, not expressed sequences. Its sensitivity/specificity is for A.t. (90.75%/92.2%), for Vitis vinifera (66.8%/94.4%) and for Populus trichocarpa (81.6%/94.4%), which suggests that our tool can be used in annotation of different plant genomes. We provide a list of features used in our model. Further study of these features may improve our understanding of mechanisms of the translation initiation. Our tool is implemented as an artificial neural network. It is available as a web-based tool and, together with the source code, the list of features, and data used for model development, is accessible at http://cbrc.kaust.edu.sa/dts.

  4. Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text

    KAUST Repository

    Bin Raies, Arwa

    2013-10-16

    Background:In a number of diseases, certain genes are reported to be strongly methylated and thus can serve as diagnostic markers in many cases. Scientific literature in digital form is an important source of information about methylated genes implicated in particular diseases. The large volume of the electronic text makes it difficult and impractical to search for this information manually.Methodology:We developed a novel text mining methodology based on a new concept of position weight matrices (PWMs) for text representation and feature generation. We applied PWMs in conjunction with the document-term matrix to extract with high accuracy associations between methylated genes and diseases from free text. The performance results are based on large manually-classified data. Additionally, we developed a web-tool, DEMGD, which automates extraction of these associations from free text. DEMGD presents the extracted associations in summary tables and full reports in addition to evidence tagging of text with respect to genes, diseases and methylation words. The methodology we developed in this study can be applied to similar association extraction problems from free text.Conclusion:The new methodology developed in this study allows for efficient identification of associations between concepts. Our method applied to methylated genes in different diseases is implemented as a Web-tool, DEMGD, which is freely available at http://www.cbrc.kaust.edu.sa/demgd/. The data is available for online browsing and download. © 2013 Bin Raies et al.

  5. FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

    KAUST Repository

    Alam, Tanvir

    2016-10-12

    Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna

  6. OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models

    KAUST Repository

    Magana-Mora, Arturo

    2017-06-14

    Classification problems from different domains vary in complexity, size, and imbalance of the number of samples from different classes. Although several classification models have been proposed, selecting the right model and parameters for a given classification task to achieve good performance is not trivial. Therefore, there is a constant interest in developing novel robust and efficient models suitable for a great variety of data. Here, we propose OmniGA, a framework for the optimization of omnivariate decision trees based on a parallel genetic algorithm, coupled with deep learning structure and ensemble learning methods. The performance of the OmniGA framework is evaluated on 12 different datasets taken mainly from biomedical problems and compared with the results obtained by several robust and commonly used machine-learning models with optimized parameters. The results show that OmniGA systematically outperformed these models for all the considered datasets, reducing the F score error in the range from 100% to 2.25%, compared to the best performing model. This demonstrates that OmniGA produces robust models with improved performance. OmniGA code and datasets are available at www.cbrc.kaust.edu.sa/omniga/.

  7. DDMGD: the database of text-mined associations between genes methylated in diseases from different species

    KAUST Repository

    Raies, A. B.

    2014-11-14

    Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD\\'s scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases.

  8. DESM: portal for microbial knowledge exploration systems

    KAUST Repository

    Salhi, Adil

    2015-11-05

    Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.

  9. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

    KAUST Repository

    Chen, Peng

    2013-07-23

    Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. © 2013 Wiley Periodicals, Inc.

  10. PyClaw: Accessible, Extensible, Scalable Tools for Wave Propagation Problems

    KAUST Repository

    Ketcheson, David I.

    2012-08-15

    Development of scientific software involves tradeoffs between ease of use, generality, and performance. We describe the design of a general hyperbolic PDE solver that can be operated with the convenience of MATLAB yet achieves efficiency near that of hand-coded Fortran and scales to the largest supercomputers. This is achieved by using Python for most of the code while employing automatically wrapped Fortran kernels for computationally intensive routines, and using Python bindings to interface with a parallel computing library and other numerical packages. The software described here is PyClaw, a Python-based structured grid solver for general systems of hyperbolic PDEs [K. T. Mandli et al., PyClaw Software, Version 1.0, http://numerics.kaust.edu.sa/pyclaw/ (2011)]. PyClaw provides a powerful and intuitive interface to the algorithms of the existing Fortran codes Clawpack and SharpClaw, simplifying code development and use while providing massive parallelism and scalable solvers via the PETSc library. The package is further augmented by use of PyWENO for generation of efficient high-order weighted essentially nonoscillatory reconstruction code. The simplicity, capability, and performance of this approach are demonstrated through application to example problems in shallow water flow, compressible flow, and elasticity.

  11. An Experimental and Numerical Study of N-Dodecane/Butanol Blends for Compression Ignition Engines

    KAUST Repository

    Wakale, Anil Bhaurao; Mohamed, Samah; Naser, Nimal; Jaasim, Mohammed; Banerjee, Raja; Im, Hong G.; Sarathy, Mani

    2018-01-01

    Alcohols are potential blending agents for diesel that can be effectively used in compression ignition engines. This work investigates the use of n-butanol as a blending component for diesel fuel using experiments and simulations. Dodecane was selected as a surrogate for diesel fuel and various concentrations of n-butanol were added to study ignition characteristics. Ignition delay times for different n-butanol/dodecane blends were measured using the ignition quality tester at KAUST (KR-IQT). The experiments were conducted at pressure of 21 and 18 bar, temperature ranging from 703-843 K and global equivalence ratio of 0.85. A skeletal mechanism for n-dodecane and n-butanol blends with 203 species was developed for numerical simulations. The mechanism was developed by combining n-dodecane skeletal mechanism containing 106 species and a detailed mechanism for all the butanol isomers. The new mixture mechanism was validated for various pressure, temperature and equivalence ratio using a 0-D homogeneous reactor model from CHEMKIN for pure base fuels (n-dodecane and butanol). Computational fluid dynamics (CFD) code, CONVERGE was used to further validate the new mechanism. The new mechanism was able to reproduce the experimental results from IQT at different pressure and temperature conditions.

  12. FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

    KAUST Repository

    Alam, Tanvir; Uludag, Mahmut; Essack, Magbubah; Salhi, Adil; Ashoor, Haitham; Hanks, John B.; Kapfer, Craig Eric; Mineta, Katsuhiko; Gojobori, Takashi; Bajic, Vladimir B.

    2016-01-01

    Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna

  13. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.

    2015-11-19

    Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for practical applications. Here we present the expanded and enhanced version of HOCOMOCO (http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco10), the collection of models of DNA patterns, recognized by transcription factors. HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs. Furthermore, we introduce the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs. The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data. To facilitate a practical application, all HOCOMOCO models are linked to gene and protein databases (Entrez Gene, HGNC, UniProt) and accompanied by precomputed score thresholds. Finally, we provide command-line tools for PWM and diPWM threshold estimation and motif finding in nucleotide sequences.

  14. Red Sea as a source for bioprospecting

    KAUST Repository

    Kodzius, Rimantas

    2015-12-12

    King-Abdullah University of Science and Technology (KAUST) is located on the shores of the Red Sea in Saudi Arabia. The Red Sea is well known for its unique environment, harboring various microbes capable of surviving in salty brines. We collected sediment samples from brine pool adjacent to the Thuwal cold seeps in the Red Sea. The taxonomic analysis showed the diversity and abundance of bacterial and archaeal operational taxonomic units (OUT). Recently we established in the laboratory a microdroplet technology to encapsulate single cells. This technology enables us to analyze single-cell genomes and perform the high-throughput screening. The genomes of both cultivable and uncultivable organisms can be analyzed. We envision the collection of complimentary data, obtained by various techniques, such as single-cell genomics, metagenomics, and transcriptomics. That will enable us not only to understand the environment and microorganism communities but also will allow to discover the previously unknown genes, pathways, and whole genomes. These data will facilitate the enhancement of biological and chemical producers, and pave the way for bioprospecting.

  15. Role of library's subscription licenses in promoting open access to scientific research

    KAUST Repository

    Buck, Stephen

    2018-04-30

    This presentation, based on KAUST’’s experience to date, will attempt to explain the different ways of bringing Open Access models to scientific Publisher’s licenses. Our dual approach with offset pricing is to redirect subscription money to publishing money and embed green open access deposition terms in understandable language in our license agreements. Resolving the inherent complexities in open access publishing, repository depositions and offsetting models will save libraries money and also time wasted on tedious and unnecessary administration work. Researchers will also save their time with overall clarity and transparency. This will enable trust and, where mistakes are made, and there inevitably will be with untried models, we can learn from these mistakes and make better, more robust services with auto deposition of our articles to our repository fed by Publishers’ themselves. The plan is to cover all Publishers with OA license terms for KAUST author’s right while continuing our subscription to them. There are marketing campaigns, awareness sessions are planned, in addition to establishing Libguides to help researchers, in addition to manage offset pricing models.

  16. DDMGD: the database of text-mined associations between genes methylated in diseases from different species.

    Science.gov (United States)

    Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir B

    2015-01-01

    Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Computational Study of Stratified Combustion in an Optical Diesel Engine

    KAUST Repository

    Jaasim, Mohammed

    2017-03-28

    Full cycle simulations of KAUST optical diesel engine were conducted in order to provide insights into the details of fuel spray, mixing, and combustion characteristics at different start of injection (SOI) conditions. Although optical diagnostics provide valuable information, the high fidelity simulations with matched parametric conditions improve fundamental understanding of relevant physical and chemical processes by accessing additional observables such as the local mixture distribution, intermediate species concentrations, and detailed chemical reaction rates. Commercial software, CONVERGE™, was used as the main simulation tool, with the Reynolds averaged Navier-Stokes (RANS) turbulence model and the multi-zone (SAGE) combustion model to compute the chemical reaction terms. SOI is varied from late compression ignition (CI) to early partially premixed combustion (PPC) conditions. The simulation results revealed a stronger correlation between fuel injection timing and combustion phasing for late SOI conditions, whereas the combustion phasing starts to decouple from SOI for early SOI cases. The predictions are consistent with the experimental observations, in terms of the overall trends in combustion and emission characteristics, while the high fidelity simulations provided further insights into the effects of mixture stratifications resulting from different SOI conditions.

  18. Compare local pocket and global protein structure models by small structure patterns

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/

  19. HCVpro: Hepatitis C virus protein interaction database

    KAUST Repository

    Kwofie, Samuel K.

    2011-12-01

    It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

  20. Role of library's subscription licenses in promoting open access to scientific research

    KAUST Repository

    Buck, Stephen

    2018-01-01

    This presentation, based on KAUST’’s experience to date, will attempt to explain the different ways of bringing Open Access models to scientific Publisher’s licenses. Our dual approach with offset pricing is to redirect subscription money to publishing money and embed green open access deposition terms in understandable language in our license agreements. Resolving the inherent complexities in open access publishing, repository depositions and offsetting models will save libraries money and also time wasted on tedious and unnecessary administration work. Researchers will also save their time with overall clarity and transparency. This will enable trust and, where mistakes are made, and there inevitably will be with untried models, we can learn from these mistakes and make better, more robust services with auto deposition of our articles to our repository fed by Publishers’ themselves. The plan is to cover all Publishers with OA license terms for KAUST author’s right while continuing our subscription to them. There are marketing campaigns, awareness sessions are planned, in addition to establishing Libguides to help researchers, in addition to manage offset pricing models.

  1. Neuro-symbolic representation learning on biological knowledge graphs.

    Science.gov (United States)

    Alshahrani, Mona; Khan, Mohammad Asif; Maddouri, Omar; Kinjo, Akira R; Queralt-Rosinach, Núria; Hoehndorf, Robert

    2017-09-01

    Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. https://github.com/bio-ontology-research-group/walking-rdf-and-owl. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  2. Neuro-symbolic representation learning on biological knowledge graphs

    KAUST Repository

    Alshahrani, Mona

    2017-04-21

    Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge.We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of SemanticWeb based knowledge bases in biology to use in machine learning and data analytics.https://github.com/bio-ontology-research-group/walking-rdf-and-owl.robert.hoehndorf@kaust.edu.sa.Supplementary data are available at Bioinformatics online.

  3. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

    KAUST Repository

    Chen, Peng; Li, Jinyan; Limsoon, Wong; Kuwahara, Hiroyuki; Huang, Jianhua Z.; Gao, Xin

    2013-01-01

    Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. © 2013 Wiley Periodicals, Inc.

  4. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

    KAUST Repository

    Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Yevshin, Ivan S.; Sharipov, Ruslan N.; Fedorova, Alla D.; Rumynskiy, Eugene I.; Medvedeva, Yulia A.; Magana-Mora, Arturo; Bajic, Vladimir B.; Papatsenko, Dmitry A.; Kolpakov, Fedor A.; Makeev, Vsevolod J.

    2017-01-01

    We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database. HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.

  5. OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models

    KAUST Repository

    Magana-Mora, Arturo; Bajic, Vladimir B.

    2017-01-01

    Classification problems from different domains vary in complexity, size, and imbalance of the number of samples from different classes. Although several classification models have been proposed, selecting the right model and parameters for a given classification task to achieve good performance is not trivial. Therefore, there is a constant interest in developing novel robust and efficient models suitable for a great variety of data. Here, we propose OmniGA, a framework for the optimization of omnivariate decision trees based on a parallel genetic algorithm, coupled with deep learning structure and ensemble learning methods. The performance of the OmniGA framework is evaluated on 12 different datasets taken mainly from biomedical problems and compared with the results obtained by several robust and commonly used machine-learning models with optimized parameters. The results show that OmniGA systematically outperformed these models for all the considered datasets, reducing the F score error in the range from 100% to 2.25%, compared to the best performing model. This demonstrates that OmniGA produces robust models with improved performance. OmniGA code and datasets are available at www.cbrc.kaust.edu.sa/omniga/.

  6. Comparing the Richtmyer-Meshkov instability of thermal and ion-species interfaces in two-fluid plasmas

    Science.gov (United States)

    Wheatley, Vincent; Bond, Daryl; Li, Yuan; Samtaney, Ravi; Pullin, Dale

    2017-11-01

    The Richtmyer-Meshkov instability (RMI) of a shock accelerated perturbed density interface is important in both inertial confinement fusion and astrophysics, where the materials involved are typically in the plasma state. Initial density interfaces can be due to either temperature or ion-species discontinuities. If the Atwood number of the interfaces and specific heat ratios of the fluids are matched, these two cases behave similarly when modeled using the equations of either hydrodynamics or magnetohydrodynamics. In the two-fluid ion-electron plasma model, however, there is a significant difference between them: In the thermal interface case, there is a discontinuity in electron density that is also subject to the RMI, while for the ion-species interface case there is not. It will be shown via ideal two-fluid plasma simulations that this causes substantial differences in the dynamics of the flow between the two cases. This work was partially supported by the KAUST Office of Sponsored Research under Award URF/1/2162-01.

  7. ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

    Science.gov (United States)

    Hungler, Arnaud; Momin, Afaque; Diederichs, Kay; Arold, Stefan, T.

    2016-01-01

    Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for ‘crystallization and preliminary X-ray analysis’ publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. PMID:27980519

  8. DWFS: A Wrapper Feature Selection Tool Based on a Parallel Genetic Algorithm

    KAUST Repository

    Soufan, Othman

    2015-02-26

    Many scientific problems can be formulated as classification tasks. Data that harbor relevant information are usually described by a large number of features. Frequently, many of these features are irrelevant for the class prediction. The efficient implementation of classification models requires identification of suitable combinations of features. The smaller number of features reduces the problem\\'s dimensionality and may result in higher classification performance. We developed DWFS, a web-based tool that allows for efficient selection of features for a variety of problems. DWFS follows the wrapper paradigm and applies a search strategy based on Genetic Algorithms (GAs). A parallel GA implementation examines and evaluates simultaneously large number of candidate collections of features. DWFS also integrates various filteringmethods thatmay be applied as a pre-processing step in the feature selection process. Furthermore, weights and parameters in the fitness function of GA can be adjusted according to the application requirements. Experiments using heterogeneous datasets from different biomedical applications demonstrate that DWFS is fast and leads to a significant reduction of the number of features without sacrificing performance as compared to several widely used existing methods. DWFS can be accessed online at www.cbrc.kaust.edu.sa/dwfs.

  9. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

    Science.gov (United States)

    Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

    2013-01-01

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. PMID:23175603

  10. A framework for dense triangular matrix kernels on various manycore architectures

    KAUST Repository

    Charara, Ali

    2017-06-06

    We present a new high-performance framework for dense triangular Basic Linear Algebra Subroutines (BLAS) kernels, ie, triangular matrix-matrix multiplication (TRMM) and triangular solve (TRSM), on various manycore architectures. This is an extension of a previous work on a single GPU by the same authors, presented at the EuroPar\\'16 conference, in which we demonstrated the effectiveness of recursive formulations in enhancing the performance of these kernels. In this paper, the performance of triangular BLAS kernels on a single GPU is further enhanced by implementing customized in-place CUDA kernels for TRMM and TRSM, which are called at the bottom of the recursion. In addition, a multi-GPU implementation of TRMM and TRSM is proposed and we show an almost linear performance scaling, as the number of GPUs increases. Finally, the algorithmic recursive formulation of these triangular BLAS kernels is in fact oblivious to the targeted hardware architecture. We, therefore, port these recursive kernels to homogeneous x86 hardware architectures by relying on the vendor optimized BLAS implementations. Results reported on various hardware architectures highlight a significant performance improvement against state-of-the-art implementations. These new kernels are freely available in the KAUST BLAS (KBLAS) open-source library at https://github.com/ecrc/kblas.

  11. DEEPre: sequence-based enzyme EC number prediction by deep learning

    KAUST Repository

    Li, Yu

    2017-10-20

    Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manuallycrafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre\\'s ability to capture the functional difference of enzyme isoforms.The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.

  12. Numerical Simulations of High Reactivity Gasoline Fuel Sprays under Vaporizing and Reactive Conditions

    KAUST Repository

    Mohan, Balaji; Jaasim, Mohammed; Ahmed, Ahfaz; Hernandez Perez, Francisco; Sim, Jaeheon; Roberts, William L.; Sarathy, Mani; Im, Hong G.

    2018-01-01

    Gasoline compression ignition (GCI) engines are becoming more popular alternative for conventional spark engines to harvest the advantage of high volatility. Recent experimental study demonstrated that high reactivity gasoline fuel can be operated in a conventional mixing controlled combustion mode producing lower soot emissions than that of diesel fuel under similar efficiency and NOx level [1]. Therefore, there is much interest in using gasoline-like fuels in compression ignition engines. In order to improve the fidelity of simulation-based GCI combustion system development, it is mandatory to enhance the prediction of spray combustion of gasoline-like fuels. The purpose of this study is to model the spray characteristics of high reactivity gasoline fuels and validate the models with experimental results obtained through an optically accessible constant volume vessel under vaporizing [2] and reactive conditions [3]. For reacting cases, a comparison of PRF and KAUST multi-component surrogate (KMCS) mechanism was done to obtain good agreement with the experimental ignition delay. From this study, some recommendations were proposed for GCI combustion modelling framework using gasoline like fuels.

  13. PyClaw: Accessible, Extensible, Scalable Tools for Wave Propagation Problems

    KAUST Repository

    Ketcheson, David I.; Mandli, Kyle; Ahmadia, Aron; Alghamdi, Amal; de Luna, Manuel Quezada; Parsani, Matteo; Knepley, Matthew G.; Emmett, Matthew

    2012-01-01

    Development of scientific software involves tradeoffs between ease of use, generality, and performance. We describe the design of a general hyperbolic PDE solver that can be operated with the convenience of MATLAB yet achieves efficiency near that of hand-coded Fortran and scales to the largest supercomputers. This is achieved by using Python for most of the code while employing automatically wrapped Fortran kernels for computationally intensive routines, and using Python bindings to interface with a parallel computing library and other numerical packages. The software described here is PyClaw, a Python-based structured grid solver for general systems of hyperbolic PDEs [K. T. Mandli et al., PyClaw Software, Version 1.0, http://numerics.kaust.edu.sa/pyclaw/ (2011)]. PyClaw provides a powerful and intuitive interface to the algorithms of the existing Fortran codes Clawpack and SharpClaw, simplifying code development and use while providing massive parallelism and scalable solvers via the PETSc library. The package is further augmented by use of PyWENO for generation of efficient high-order weighted essentially nonoscillatory reconstruction code. The simplicity, capability, and performance of this approach are demonstrated through application to example problems in shallow water flow, compressible flow, and elasticity.

  14. The future of the CAVE

    KAUST Repository

    DeFanti, Thomas; Acevedo-Feliz, Daniel; Ainsworth, Richard; Brown, Maxine; Cutchin, Steven; Dawe, Gregory; Doerr, Kai-Uwe; Johnson, Andrew; Knox, Christopher; Kooima, Robert; Kuester, Falko; Leigh, Jason; Long, Lance; Otto, Peter; Petrovic, Vid; Ponto, Kevin; Prudhomme, Andrew; Rao, Ramesh; Renambot, Luc; Sandin, Daniel; Schulze, Jurgen; Smarr, Larry; Srinivasan, Madhusudhanan; Weber, Philip; Wickham, Gregory

    2011-01-01

    The CAVE, a walk-in virtual reality environment typically consisting of 4–6 3 m-by-3 m sides of a room made of rear-projected screens, was first conceived and built in 1991. In the nearly two decades since its conception, the supporting technology has improved so that current CAVEs are much brighter, at much higher resolution, and have dramatically improved graphics performance. However, rear-projection-based CAVEs typically must be housed in a 10 m-by-10 m-by-10 m room (allowing space behind the screen walls for the projectors), which limits their deployment to large spaces. The CAVE of the future will be made of tessellated panel displays, eliminating the projection distance, but the implementation of such displays is challenging. Early multi-tile, panel-based, virtual-reality displays have been designed, prototyped, and built for the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia by researchers at the University of California, San Diego, and the University of Illinois at Chicago. New means of image generation and control are considered key contributions to the future viability of the CAVE as a virtual-reality device.

  15. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

    KAUST Repository

    Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin

    2016-01-01

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

  16. DWFS: A Wrapper Feature Selection Tool Based on a Parallel Genetic Algorithm

    KAUST Repository

    Soufan, Othman; Kleftogiannis, Dimitrios A.; Kalnis, Panos; Bajic, Vladimir B.

    2015-01-01

    Many scientific problems can be formulated as classification tasks. Data that harbor relevant information are usually described by a large number of features. Frequently, many of these features are irrelevant for the class prediction. The efficient implementation of classification models requires identification of suitable combinations of features. The smaller number of features reduces the problem's dimensionality and may result in higher classification performance. We developed DWFS, a web-based tool that allows for efficient selection of features for a variety of problems. DWFS follows the wrapper paradigm and applies a search strategy based on Genetic Algorithms (GAs). A parallel GA implementation examines and evaluates simultaneously large number of candidate collections of features. DWFS also integrates various filteringmethods thatmay be applied as a pre-processing step in the feature selection process. Furthermore, weights and parameters in the fitness function of GA can be adjusted according to the application requirements. Experiments using heterogeneous datasets from different biomedical applications demonstrate that DWFS is fast and leads to a significant reduction of the number of features without sacrificing performance as compared to several widely used existing methods. DWFS can be accessed online at www.cbrc.kaust.edu.sa/dwfs.

  17. A framework for dense triangular matrix kernels on various manycore architectures

    KAUST Repository

    Charara, Ali; Keyes, David E.; Ltaief, Hatem

    2017-01-01

    We present a new high-performance framework for dense triangular Basic Linear Algebra Subroutines (BLAS) kernels, ie, triangular matrix-matrix multiplication (TRMM) and triangular solve (TRSM), on various manycore architectures. This is an extension of a previous work on a single GPU by the same authors, presented at the EuroPar'16 conference, in which we demonstrated the effectiveness of recursive formulations in enhancing the performance of these kernels. In this paper, the performance of triangular BLAS kernels on a single GPU is further enhanced by implementing customized in-place CUDA kernels for TRMM and TRSM, which are called at the bottom of the recursion. In addition, a multi-GPU implementation of TRMM and TRSM is proposed and we show an almost linear performance scaling, as the number of GPUs increases. Finally, the algorithmic recursive formulation of these triangular BLAS kernels is in fact oblivious to the targeted hardware architecture. We, therefore, port these recursive kernels to homogeneous x86 hardware architectures by relying on the vendor optimized BLAS implementations. Results reported on various hardware architectures highlight a significant performance improvement against state-of-the-art implementations. These new kernels are freely available in the KAUST BLAS (KBLAS) open-source library at https://github.com/ecrc/kblas.

  18. Open Access, Library Subscriptions, and Article Processing Charges

    KAUST Repository

    Vijayakumar, J.K.

    2016-05-01

    Hybrid journals contains articles behind a pay-wall to be subscribed, as well as papers made open access when author pays article processing charge (APC). In such cases, an Institution will end up paying twice and Publishers tend to double-dip. Discussions and pilot models are emerging on pricing options, such as “offset pricing,” [where APCs are adjusted or discounted with subscription costs as vouchers or reductions in next year subscriptions, APCs beyond the subscription costs are modestly capped etc] and thus reduce Institutions’ cost. This presentation will explain different models available and how can we attain a transparent costing structure, where the scholarly community can feel the fairness in Publishers’ pricing mechanisms. Though most of the offset systems are developed through national level or consortium level negotiations, experience of individual institutions, like KAUST that subscribe to large e-journals collections, is important in making right decisions on saving Institutes costs and support openness in scholarly communications.

  19. A novel method for improved accuracy of transcription factor binding site prediction

    KAUST Repository

    Khamis, Abdullah M.; Motwalli, Olaa Amin; Oliva, Romina; Jankovic, Boris R.; Medvedeva, Yulia; Ashoor, Haitham; Essack, Magbubah; Gao, Xin; Bajic, Vladimir B.

    2018-01-01

    Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used computational methods of TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, computational studies of transcription regulation in eukaryotes frequently require numerous PWM models of TFBSs due to a large number of TFs involved. To overcome these problems we developed DRAF, a novel method for TFBS prediction that requires only 14 prediction models for 232 human TFs, while at the same time significantly improves prediction accuracy. DRAF models use more features than PWM models, as they combine information from TFBS sequences and physicochemical properties of TF DNA-binding domains into machine learning models. Evaluation of DRAF on 98 human ChIP-seq datasets shows on average 1.54-, 1.96- and 5.19-fold reduction of false positives at the same sensitivities compared to models from HOCOMOCO, TRANSFAC and DeepBind, respectively. This observation suggests that one can efficiently replace the PWM models for TFBS prediction by a small number of DRAF models that significantly improve prediction accuracy. The DRAF method is implemented in a web tool and in a stand-alone software freely available at http://cbrc.kaust.edu.sa/DRAF.

  20. Simulations of incompressible Navier Stokes equations on curved surfaces using discrete exterior calculus

    Science.gov (United States)

    Samtaney, Ravi; Mohamed, Mamdouh; Hirani, Anil

    2015-11-01

    We present examples of numerical solutions of incompressible flow on 2D curved domains. The Navier-Stokes equations are first rewritten using the exterior calculus notation, replacing vector calculus differential operators by the exterior derivative, Hodge star and wedge product operators. A conservative discretization of Navier-Stokes equations on simplicial meshes is developed based on discrete exterior calculus (DEC). The discretization is then carried out by substituting the corresponding discrete operators based on the DEC framework. By construction, the method is conservative in that both the discrete divergence and circulation are conserved up to machine precision. The relative error in kinetic energy for inviscid flow test cases converges in a second order fashion with both the mesh size and the time step. Numerical examples include Taylor vortices on a sphere, Stuart vortices on a sphere, and flow past a cylinder on domains with varying curvature. Supported by the KAUST Office of Competitive Research Funds under Award No. URF/1/1401-01.

  1. 9th May 2008 - Members of Saudi government visiting ATLAS control room and cavern with Technical Coordinator M. Nessi and Adviser to the Director-General D. Blechschmidt.

    CERN Multimedia

    Mona Schweizer

    2008-01-01

    CERN-HI-0804043 05: from left to right 1st row Mrs. Ibtesam Badhrees, ATLAS Collaboration user Mr. Nadhmi Al-Nassr, Interim President, King Abdullah University of Science and Technology, KAUST H.E. Dr. Khaled S. Al-Sultan, Rector, King Fahd University for Petroleum and Minerals Mr. Abdallah S. Jum’ah, President and Chief Executive Officer, Saudi Aramco H.E. Dr. Ibrahim A. Al-Assaf, Minister of Finance H.E. Dr. Abdul Rahman Al-Tuwaijri, Chairman of Capital Markets Authority H.E. Dr. Mohammed I. Al-Suwaiyel, President, King Abdul Aziz City for Science & Technology KACST; 2nd row Mr. Salim S. Al-Aydh, Senior Vice President – Engineering & Project Management, Saudi Aramco Mr. Khalid A. Al-Falih, Executive Vice President – Operations, Saudi Aramco Mr. A. Othman, Saudi Aramco Mr. Peter Woicke, Member of the Saudi Aramco Board of Directors Mr. Abdulaziz F. Al-Khayyal, Senior Vice President – Industrial Relations, Saudi Aramco Mr. James W. Kinnear, Retired President & Chief Executive Office...

  2. DESTAF: A database of text-mined associations for reproductive toxins potentially affecting human fertility

    KAUST Repository

    Dawe, Adam Sean; Radovanovic, Aleksandar; Kaur, Mandeep; Sagar, Sunil; Seshadri, Sundararajan Vijayaraghava; Schaefer, Ulf; Kamau, Allan; Christoffels, Alan G.; Bajic, Vladimir B.

    2012-01-01

    The Dragon Exploration System for Toxicants and Fertility (DESTAF) is a publicly available resource which enables researchers to efficiently explore both known and potentially novel information and associations in the field of reproductive toxicology. To create DESTAF we used data from the literature (including over 10. 500 PubMed abstracts), several publicly available biomedical repositories, and specialized, curated dictionaries. DESTAF has an interface designed to facilitate rapid assessment of the key associations between relevant concepts, allowing for a more in-depth exploration of information based on different gene/protein-, enzyme/metabolite-, toxin/chemical-, disease- or anatomically centric perspectives. As a special feature, DESTAF allows for the creation and initial testing of potentially new association hypotheses that suggest links between biological entities identified through the database.DESTAF, along with a PDF manual, can be found at http://cbrc.kaust.edu.sa/destaf. It is free to academic and non-commercial users and will be updated quarterly. © 2011 Elsevier Inc.

  3. Gain-Enhanced On-Chip Antenna Utilizing Artificial Magnetic Conductor Reflecting Surface at 94 GHz

    KAUST Repository

    Nafe, Mahmoud

    2015-01-01

    In this work, the use of specially patterned reflecting surfaces for improving on- chip antenna performance is investigated. By using a periodic metallic surface on top of a grounded substrate, the structure can mimic the behavior of a perfect mag- netic conductor, hence called Artificial Magnetic Conductor (AMC) surface. Unlike conventional ground plane reflecting surfaces, AMC surfaces generally enhance the radiation and impedance characteristics of close-by antennas. Based on this property, a ring-based AMC reflecting surface has been designed in the oxide layer for on-chip antennas operating at 94 GHz. Furthermore, a folded dipole antenna with its associ- ated planar feeding structures has been optimized and integrated with the developed ring-based AMC surface. The proposed design is then fabricated at KAUST clean- room facilities. Prototype characterization showed very promising results with good correlation to simulations, with the antenna exhibiting an impedance bandwidth of 10% (90-100 GHz) and peak gain of -1.4 dBi, which is the highest gain reported for on-chip antennas at this frequency band without the use of any external o↵-chip components or post-fabrication steps.

  4. Combining position weight matrices and document-term matrix for efficient extraction of associations of methylated genes and diseases from free text.

    Directory of Open Access Journals (Sweden)

    Arwa Bin Raies

    Full Text Available BACKGROUND: In a number of diseases, certain genes are reported to be strongly methylated and thus can serve as diagnostic markers in many cases. Scientific literature in digital form is an important source of information about methylated genes implicated in particular diseases. The large volume of the electronic text makes it difficult and impractical to search for this information manually. METHODOLOGY: We developed a novel text mining methodology based on a new concept of position weight matrices (PWMs for text representation and feature generation. We applied PWMs in conjunction with the document-term matrix to extract with high accuracy associations between methylated genes and diseases from free text. The performance results are based on large manually-classified data. Additionally, we developed a web-tool, DEMGD, which automates extraction of these associations from free text. DEMGD presents the extracted associations in summary tables and full reports in addition to evidence tagging of text with respect to genes, diseases and methylation words. The methodology we developed in this study can be applied to similar association extraction problems from free text. CONCLUSION: The new methodology developed in this study allows for efficient identification of associations between concepts. Our method applied to methylated genes in different diseases is implemented as a Web-tool, DEMGD, which is freely available at http://www.cbrc.kaust.edu.sa/demgd/. The data is available for online browsing and download.

  5. CloudFlame: Cyberinfrastructure for combustion research

    KAUST Repository

    Goteng, Gokop

    2013-12-01

    Combustion experiments and chemical kinetics simulations generate huge data that is computationally and data intensive. A cloud-based cyber infrastructure known as Cloud Flame is implemented to improve the computational efficiency, scalability and availability of data for combustion research. The architecture consists of an application layer, a communication layer and distributed cloud servers running in a mix environment of Windows, Macintosh and Linux systems. The application layer runs software such as CHEMKIN modeling application. The communication layer provides secure transfer/archive of kinetic, thermodynamic, transport and gas surface data using private/public keys between clients and cloud servers. A robust XML schema based on the Process Informatics Model (Prime) combined with a workflow methodology for digitizing, verifying and uploading data from scientific graphs/tables to Prime is implemented for chemical molecular structures of compounds. The outcome of using this system by combustion researchers at King Abdullah University of Science and Technology (KAUST) Clean Combustion Research Center and its collaborating partners indicated a significant improvement in efficiency in terms of speed of chemical kinetics and accuracy in searching for the right chemical kinetic data.

  6. Using print focused collections development policies (CDPs) in digitally born libraries

    KAUST Repository

    Buck, Stephen

    2016-11-03

    The King Abdullah University of Science & Technology (KAUST) library is a ‘born digital’ library. The core, and vast majority, of library resources was acquired in electronic form and a smaller print collection, which complemented the wider collection, was acquired contemporaneously. The purpose of this paper is to determine whether, in conjunction with our specific print collections development policy, we need a complementary E-Resources policy. The writing of such a policy utilizes valuable resources (both staff and time) and involves itself with the sometimes vaguely defined and complex concept of collection evaluation. Issues in e-resources are constantly changing and updates will be necessary to reflect this. How, and how often, do we update our E-Resources CDP? While Biblarz (2001) maintains that the main argument for the existence of a print CDP is to prevent the library from being driven by events or by individual enthusiasms and from purchasing a random set of resources, which may not support the mission of the library this paper explores issues in maintaining a joint print and ‘E’ CDP.

  7. A Benchmark and Simulator for UAV Tracking

    KAUST Repository

    Mueller, Matthias; Smith, Neil; Ghanem, Bernard

    2016-01-01

    In this paper, we propose a new aerial video dataset and benchmark for low altitude UAV target tracking, as well as, a photorealistic UAV simulator that can be coupled with tracking methods. Our benchmark provides the first evaluation of many state-of-the-art and popular trackers on 123 new and fully annotated HD video sequences captured from a low-altitude aerial perspective. Among the compared trackers, we determine which ones are the most suitable for UAV tracking both in terms of tracking accuracy and run-time. The simulator can be used to evaluate tracking algorithms in real-time scenarios before they are deployed on a UAV “in the field”, as well as, generate synthetic but photo-realistic tracking datasets with automatic ground truth annotations to easily extend existing real-world datasets. Both the benchmark and simulator are made publicly available to the vision community on our website to further research in the area of object tracking from UAVs. (https://ivul.kaust.edu.sa/Pages/pub-benchmark-simulator-uav.aspx.). © Springer International Publishing AG 2016.

  8. An Experimental and Numerical Study of N-Dodecane/Butanol Blends for Compression Ignition Engines

    KAUST Repository

    Wakale, Anil Bhaurao

    2018-04-03

    Alcohols are potential blending agents for diesel that can be effectively used in compression ignition engines. This work investigates the use of n-butanol as a blending component for diesel fuel using experiments and simulations. Dodecane was selected as a surrogate for diesel fuel and various concentrations of n-butanol were added to study ignition characteristics. Ignition delay times for different n-butanol/dodecane blends were measured using the ignition quality tester at KAUST (KR-IQT). The experiments were conducted at pressure of 21 and 18 bar, temperature ranging from 703-843 K and global equivalence ratio of 0.85. A skeletal mechanism for n-dodecane and n-butanol blends with 203 species was developed for numerical simulations. The mechanism was developed by combining n-dodecane skeletal mechanism containing 106 species and a detailed mechanism for all the butanol isomers. The new mixture mechanism was validated for various pressure, temperature and equivalence ratio using a 0-D homogeneous reactor model from CHEMKIN for pure base fuels (n-dodecane and butanol). Computational fluid dynamics (CFD) code, CONVERGE was used to further validate the new mechanism. The new mechanism was able to reproduce the experimental results from IQT at different pressure and temperature conditions.

  9. TSSPlant: a new tool for prediction of plant Pol II promoters

    KAUST Repository

    Shahmuradov, Ilham A.

    2017-01-13

    Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). Moreover, TSS selection depends on cell/tissue, development stage and environmental conditions. Such complex promoter structures make their computational identification notoriously difficult. Here, we present TSSPlant, a novel tool that predicts both TATA and TATA-less promoters in sequences of a wide spectrum of plant genomes. The tool was developed by using large promoter collections from ppdb and PlantProm DB. It utilizes eighteen significant compositional and signal features of plant promoter sequences selected in this study, that feed the artificial neural network-based model trained by the backpropagation algorithm. TSSPlant achieves significantly higher accuracy compared to the next best promoter prediction program for both TATA promoters (MCC≃0.84 and F1-score≃0.91 versus MCC≃0.51 and F1-score≃0.71) and TATA-less promoters (MCC≃0.80, F1-score≃0.89 versus MCC≃0.29 and F1-score≃0.50). TSSPlant is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/.

  10. HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

    2012-01-01

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

  11. TSSPlant: a new tool for prediction of plant Pol II promoters

    KAUST Repository

    Shahmuradov, Ilham A.; Umarov, Ramzan; Solovyev, Victor V.

    2017-01-01

    Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). Moreover, TSS selection depends on cell/tissue, development stage and environmental conditions. Such complex promoter structures make their computational identification notoriously difficult. Here, we present TSSPlant, a novel tool that predicts both TATA and TATA-less promoters in sequences of a wide spectrum of plant genomes. The tool was developed by using large promoter collections from ppdb and PlantProm DB. It utilizes eighteen significant compositional and signal features of plant promoter sequences selected in this study, that feed the artificial neural network-based model trained by the backpropagation algorithm. TSSPlant achieves significantly higher accuracy compared to the next best promoter prediction program for both TATA promoters (MCC≃0.84 and F1-score≃0.91 versus MCC≃0.51 and F1-score≃0.71) and TATA-less promoters (MCC≃0.80, F1-score≃0.89 versus MCC≃0.29 and F1-score≃0.50). TSSPlant is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/.

  12. A Lean Six Sigma program in higher education

    KAUST Repository

    Svensson, Carsten

    2015-01-01

    Purpose The objective of this paper is to contribute to the body of Lean Six Sigma knowledge within the field of higher education institutions. The paper will review the initial phase of an implementation and highlight future challenges of applying the Lean Six Sigma method in a complex transactional environment. Design/methodology/approach The observations presented in this paper originate from rolling out a large Lean Six Sigma implementation at a recently established university. The paper is supported with secondary data from literature. Findings The implementation of Lean Six Sigma methodology at King Abdullah University of Science and Technology (KAUST) has resulted in improvements in business processes and efficiency. This has been achieved through project execution and training programs. Approximately 350 staff members have completed awareness training, 50 yellow belts and 150 green belts have been trained, and the first round of seven black belts have completed training of which two have completed certification. Research limitations/implications This paper is based on an empirical study of a single instance and the authors’ experiences as practitioners. Originality/value This paper is the first description of what is believed to be one of the largest implementations of Lean Six Sigma in higher education.

  13. DDPC: Dragon database of genes associated with prostate cancer

    KAUST Repository

    Maqungo, Monique

    2010-09-29

    Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc .kaust.edu.sa/ddpc/. The Author(s) 2010.

  14. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  15. Proposal of an Eco-Industrial Park based on the water desalination plant located inside the King Abdullah University of Science and Technology

    KAUST Repository

    Lopez Torres, Rodrigo

    2016-12-01

    This thesis project is a proposal of a scenario of an industrial collaboration that could become the basis for the development of an Eco-Industrial Park inside the King Abdullah University of Science and Technology using the water desalination plant as the foundation of this network. It is defined why the university is a suitable place for a development of this type; what industrial networks can be formed and what environmental, economic and social benefits could be achieved if the Kingdom of Saudi Arabia implemented this project around the country. An Eco-Industrial Park is a collaboration between industries where they share resources and create an exchange network of wastes and by-products with the objective of obtaining positive environmental, economic and social impacts. In the proposed scenario, the initial collaboration is between a PV solar plant and the water desalination located inside the university. With the use of solar energy there are savings of CO2 emissions, which turn into positive impacts on the environment. The idea is that this initial collaboration could be extended in the future to provide the entire energy consumption of the KAUST community. The project also provides an insight into how an industrial symbiosis could be formed taking as a base this industrial collaboration. However, further studies and analysis are required in order to provide more solid information regarding the development of an Eco-Industrial Park.

  16. A Benchmark and Simulator for UAV Tracking

    KAUST Repository

    Mueller, Matthias

    2016-09-16

    In this paper, we propose a new aerial video dataset and benchmark for low altitude UAV target tracking, as well as, a photorealistic UAV simulator that can be coupled with tracking methods. Our benchmark provides the first evaluation of many state-of-the-art and popular trackers on 123 new and fully annotated HD video sequences captured from a low-altitude aerial perspective. Among the compared trackers, we determine which ones are the most suitable for UAV tracking both in terms of tracking accuracy and run-time. The simulator can be used to evaluate tracking algorithms in real-time scenarios before they are deployed on a UAV “in the field”, as well as, generate synthetic but photo-realistic tracking datasets with automatic ground truth annotations to easily extend existing real-world datasets. Both the benchmark and simulator are made publicly available to the vision community on our website to further research in the area of object tracking from UAVs. (https://ivul.kaust.edu.sa/Pages/pub-benchmark-simulator-uav.aspx.). © Springer International Publishing AG 2016.

  17. Open Access, Library Subscriptions, and Article Processing Charges

    KAUST Repository

    Vijayakumar, J.K.; Tamarkin, Molly

    2016-01-01

    Hybrid journals contains articles behind a pay-wall to be subscribed, as well as papers made open access when author pays article processing charge (APC). In such cases, an Institution will end up paying twice and Publishers tend to double-dip. Discussions and pilot models are emerging on pricing options, such as “offset pricing,” [where APCs are adjusted or discounted with subscription costs as vouchers or reductions in next year subscriptions, APCs beyond the subscription costs are modestly capped etc] and thus reduce Institutions’ cost. This presentation will explain different models available and how can we attain a transparent costing structure, where the scholarly community can feel the fairness in Publishers’ pricing mechanisms. Though most of the offset systems are developed through national level or consortium level negotiations, experience of individual institutions, like KAUST that subscribe to large e-journals collections, is important in making right decisions on saving Institutes costs and support openness in scholarly communications.

  18. Linear Stability Analysis of an Acoustically Vaporized Droplet

    Science.gov (United States)

    Siddiqui, Junaid; Qamar, Adnan; Samtaney, Ravi

    2015-11-01

    Acoustic droplet vaporization (ADV) is a phase transition phenomena of a superheat liquid (Dodecafluoropentane, C5F12) droplet to a gaseous bubble, instigated by a high-intensity acoustic pulse. This approach was first studied in imaging applications, and applicable in several therapeutic areas such as gas embolotherapy, thrombus dissolution, and drug delivery. High-speed imaging and theoretical modeling of ADV has elucidated several physical aspects, ranging from bubble nucleation to its subsequent growth. Surface instabilities are known to exist and considered responsible for evolving bubble shapes (non-spherical growth, bubble splitting and bubble droplet encapsulation). We present a linear stability analysis of the dynamically evolving interfaces of an acoustically vaporized micro-droplet (liquid A) in an infinite pool of a second liquid (liquid B). We propose a thermal ADV model for the base state. The linear analysis utilizes spherical harmonics (Ynm, of degree m and order n) and under various physical assumptions results in a time-dependent ODE of the perturbed interface amplitudes (one at the vapor/liquid A interface and the other at the liquid A/liquid B interface). The perturbation amplitudes are found to grow exponentially and do not depend on m. Supported by KAUST Baseline Research Funds.

  19. Direct Numerical Simulations of a Full Stationary Wind-Turbine Blade

    Science.gov (United States)

    Qamar, Adnan; Zhang, Wei; Gao, Wei; Samtaney, Ravi

    2014-11-01

    Direct numerical simulation of flow past a full stationary wind-turbine blade is carried out at Reynolds number, Re = 10,000 placed at 0 and 5 (degree) angle of attack. The study is targeted to create a DNS database for verification of solvers and turbulent models that are utilized in wind-turbine modeling applications. The full blade comprises of a circular cylinder base that is attached to a spanwise varying airfoil cross-section profile (without twist). An overlapping composite grid technique is utilized to perform these DNS computations, which permits block structure in the mapped computational space. Different flow shedding regimes are observed along the blade length. Von-Karman shedding is observed in the cylinder shaft region of the turbine blade. Along the airfoil cross-section of the blade, near body shear layer breakdown is observed. A long tip vortex originates from the blade tip region, which exits the computational plane without being perturbed. Laminar to turbulent flow transition is observed along the blade length. The turbulent fluctuations amplitude decreases along the blade length and the flow remains laminar regime in the vicinity of the blade tip. The Strouhal number is found to decrease monotonously along the blade length. Average lift and drag coefficients are also reported for the cases investigated. Supported by funding under a KAUST OCRF-CRG grant.

  20. Numerical Simulations of High Reactivity Gasoline Fuel Sprays under Vaporizing and Reactive Conditions

    KAUST Repository

    Mohan, Balaji

    2018-04-03

    Gasoline compression ignition (GCI) engines are becoming more popular alternative for conventional spark engines to harvest the advantage of high volatility. Recent experimental study demonstrated that high reactivity gasoline fuel can be operated in a conventional mixing controlled combustion mode producing lower soot emissions than that of diesel fuel under similar efficiency and NOx level [1]. Therefore, there is much interest in using gasoline-like fuels in compression ignition engines. In order to improve the fidelity of simulation-based GCI combustion system development, it is mandatory to enhance the prediction of spray combustion of gasoline-like fuels. The purpose of this study is to model the spray characteristics of high reactivity gasoline fuels and validate the models with experimental results obtained through an optically accessible constant volume vessel under vaporizing [2] and reactive conditions [3]. For reacting cases, a comparison of PRF and KAUST multi-component surrogate (KMCS) mechanism was done to obtain good agreement with the experimental ignition delay. From this study, some recommendations were proposed for GCI combustion modelling framework using gasoline like fuels.

  1. DEEPre: sequence-based enzyme EC number prediction by deep learning

    KAUST Repository

    Li, Yu; Wang, Sheng; Umarov, Ramzan; Xie, Bingqing; Fan, Ming; Li, Lihua; Gao, Xin

    2017-01-01

    Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manuallycrafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre's ability to capture the functional difference of enzyme isoforms.The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre.

  2. A novel method for improved accuracy of transcription factor binding site prediction

    KAUST Repository

    Khamis, Abdullah M.

    2018-03-20

    Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used computational methods of TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, computational studies of transcription regulation in eukaryotes frequently require numerous PWM models of TFBSs due to a large number of TFs involved. To overcome these problems we developed DRAF, a novel method for TFBS prediction that requires only 14 prediction models for 232 human TFs, while at the same time significantly improves prediction accuracy. DRAF models use more features than PWM models, as they combine information from TFBS sequences and physicochemical properties of TF DNA-binding domains into machine learning models. Evaluation of DRAF on 98 human ChIP-seq datasets shows on average 1.54-, 1.96- and 5.19-fold reduction of false positives at the same sensitivities compared to models from HOCOMOCO, TRANSFAC and DeepBind, respectively. This observation suggests that one can efficiently replace the PWM models for TFBS prediction by a small number of DRAF models that significantly improve prediction accuracy. The DRAF method is implemented in a web tool and in a stand-alone software freely available at http://cbrc.kaust.edu.sa/DRAF.

  3. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

    KAUST Repository

    Kuwahara, Hiroyuki

    2016-04-29

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

  4. Enabling High Performance Large Scale Dense Problems through KBLAS

    KAUST Repository

    Abdelfattah, Ahmad

    2014-05-04

    KBLAS (KAUST BLAS) is a small library that provides highly optimized BLAS routines on systems accelerated with GPUs. KBLAS is entirely written in CUDA C, and targets NVIDIA GPUs with compute capability 2.0 (Fermi) or higher. The current focus is on level-2 BLAS routines, namely the general matrix vector multiplication (GEMV) kernel, and the symmetric/hermitian matrix vector multiplication (SYMV/HEMV) kernel. KBLAS provides these two kernels in all four precisions (s, d, c, and z), with support to multi-GPU systems. Through advanced optimization techniques that target latency hiding and pushing memory bandwidth to the limit, KBLAS outperforms state-of-the-art kernels by 20-90% improvement. Competitors include CUBLAS-5.5, MAGMABLAS-1.4.0, and CULAR17. The SYMV/HEMV kernel from KBLAS has been adopted by NVIDIA, and should appear in CUBLAS-6.0. KBLAS has been used in large scale simulations of multi-object adaptive optics.

  5. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

    Science.gov (United States)

    Chen, Peng; Li, Jinyan; Wong, Limsoon; Kuwahara, Hiroyuki; Huang, Jianhua Z; Gao, Xin

    2013-08-01

    Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. Copyright © 2013 Wiley Periodicals, Inc.

  6. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.

    Science.gov (United States)

    Kulmanov, Maxat; Khan, Mohammed Asif; Hoehndorf, Robert; Wren, Jonathan

    2018-02-15

    A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often only done rigorously for few selected model organisms. Computational function prediction approaches have been suggested to fill this gap. The functions of proteins are classified using the Gene Ontology (GO), which contains over 40 000 classes. Additionally, proteins have multiple functions, making function prediction a large-scale, multi-class, multi-label problem. We have developed a novel method to predict protein function from sequence. We use deep learning to learn features from protein sequences as well as a cross-species protein-protein interaction network. Our approach specifically outputs information in the structure of the GO and utilizes the dependencies between GO classes as background information to construct a deep learning model. We evaluate our method using the standards established by the Computational Assessment of Function Annotation (CAFA) and demonstrate a significant improvement over baseline methods such as BLAST, in particular for predicting cellular locations. Web server: http://deepgo.bio2vec.net, Source code: https://github.com/bio-ontology-research-group/deepgo. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  7. HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.

    2012-11-21

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

  8. Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences

    KAUST Repository

    Kalkatawi, Manal M.

    2011-11-15

    Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants. The Author(s) 2011. Published by Oxford University Press. All rights reserved.

  9. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

    KAUST Repository

    Kulakovskiy, Ivan V.

    2017-10-31

    We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database. HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.

  10. High-frequency effects in antiferromagnetic Sr3Ir2O7

    Science.gov (United States)

    Williamson, Morgan; Seinige, Heidi; Shen, Shida; Wang, Cheng; Cao, Gang; Zhou, Jianshi; Goodenough, John; Tsoi, Maxim

    Antiferromagnetic (AFM) spintronics is one of many promising routes for `beyond the CMOS' technologies where unique properties of AFM materials are exploited to achieve new and improved functionalities. AFMs are especially interesting for high-speed memory applications thanks to their high natural frequencies. Here we report the effects of high-frequency (microwave) currents on transport properties of antiferromagnetic Mott insulator Sr3Ir2O7. The microwaves at 3-7 GHz were found to affect the material's current-voltage characteristic and produce resonance-like features that we tentatively associate with the dissipationless magnonics recently predicted to occur in antiferromagnetic insulators subject to ac electric fields. Our observations support the potential of antiferromagnetic materials for high-speed/high-frequency spintronic applications. This work was supported in part by C-SPIN, one of six centers of STARnet, a Semiconductor Research Corporation program, sponsored by MARCO and DARPA, by NSF Grants DMR-1207577, DMR-1265162, DMR-1600057, and DMR-1122603, and by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. OSR-2015-CRG4-2626.

  11. Redesigning Triangular Dense Matrix Computations on GPUs

    KAUST Repository

    Charara, Ali

    2016-08-09

    A new implementation of the triangular matrix-matrix multiplication (TRMM) and the triangular solve (TRSM) kernels are described on GPU hardware accelerators. Although part of the Level 3 BLAS family, these highly computationally intensive kernels fail to achieve the percentage of the theoretical peak performance on GPUs that one would expect when running kernels with similar surface-to-volume ratio on hardware accelerators, i.e., the standard matrix-matrix multiplication (GEMM). The authors propose adopting a recursive formulation, which enriches the TRMM and TRSM inner structures with GEMM calls and, therefore, reduces memory traffic while increasing the level of concurrency. The new implementation enables efficient use of the GPU memory hierarchy and mitigates the latency overhead, to run at the speed of the higher cache levels. Performance comparisons show up to eightfold and twofold speedups for large dense matrix sizes, against the existing state-of-the-art TRMM and TRSM implementations from NVIDIA cuBLAS, respectively, across various GPU generations. Once integrated into high-level Cholesky-based dense linear algebra algorithms, the performance impact on the overall applications demonstrates up to fourfold and twofold speedups, against the equivalent native implementations, linked with cuBLAS TRMM and TRSM kernels, respectively. The new TRMM/TRSM kernel implementations are part of the open-source KBLAS software library (http://ecrc.kaust.edu.sa/Pages/Res-kblas.aspx) and are lined up for integration into the NVIDIA cuBLAS library in the upcoming v8.0 release.

  12. A framework for scalable parameter estimation of gene circuit models using structural information.

    Science.gov (United States)

    Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

    2013-07-01

    Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary data are available at Bioinformatics online.

  13. Using print focused collections development policies (CDPs) in digitally born libraries

    KAUST Repository

    Buck, Stephen; Vijayakumar, J.K.

    2016-01-01

    The King Abdullah University of Science & Technology (KAUST) library is a ‘born digital’ library. The core, and vast majority, of library resources was acquired in electronic form and a smaller print collection, which complemented the wider collection, was acquired contemporaneously. The purpose of this paper is to determine whether, in conjunction with our specific print collections development policy, we need a complementary E-Resources policy. The writing of such a policy utilizes valuable resources (both staff and time) and involves itself with the sometimes vaguely defined and complex concept of collection evaluation. Issues in e-resources are constantly changing and updates will be necessary to reflect this. How, and how often, do we update our E-Resources CDP? While Biblarz (2001) maintains that the main argument for the existence of a print CDP is to prevent the library from being driven by events or by individual enthusiasms and from purchasing a random set of resources, which may not support the mission of the library this paper explores issues in maintaining a joint print and ‘E’ CDP.

  14. Severe symptoms of short tear break-up time dry eye are associated with accommodative microfluctuations

    Directory of Open Access Journals (Sweden)

    Kaido M

    2017-05-01

    Full Text Available Minako Kaido,1,2 Motoko Kawashima,1 Reiko Ishida,1,3 Kazuo Tsubota1 1Department of Ophthalmology, Keio University School of Medicine, Tokyo, 2Wada Eye Clinic, Chiba, 3Ishida Eye Clinic, Shizuoka, Japan Aim: Validating the hypothesis that accommodative microfluctuations (AMFs may be associated with severe symptoms in short tear break-up time (BUT dry eye (DE. Methods: This study included 12 subjects with short BUT DE (age: 49.6±18.3 years. Diagnoses were performed based on the presence of DE symptoms, BUT ≤5 s, Schirmer score >5 mm, and negative keratoconjunctival epithelial damage. Tear evaluation, AMF, and functional visual acuity (VA examinations were conducted before and after DE treatment. The AMF parameters evaluated were: total high-frequency component (HFC, HFC with low accommodation for the task of staring into the distance (HFC1, HFC with high accommodation for deskwork (HFC2. A subjective questionnaire of DE symptoms was also performed. Results: Mean BUT increased from 1.9±2.0 to 6.4±2.5 s after treatment (P<0.05. The mean logarithm of the minimum angle of resolution functional VA significantly improved (from 0.19±0.19 to 0.12±0.17; P<0.05. Mean power spectrum values for total HFC and HFC1 decreased (from 61.3±5.7 to 53.8±6.6 dB and from 62.9±10.5 to 52.4±6.2 dB, respectively; P<0.05, while the mean HFC2 power spectrum values did not differ before and after treatment (P>0.05. Subjective DE symptoms were reduced in nine patients. Conclusion: Along with the improvement of BUT after treatment, DE symptoms diminished and HFC1 and functional VA improved, suggesting that tear film instability is associated with deterioration of functional VA, AMF, and DE symptoms. Keywords: accommodative microfluctuation, ciliary muscle spasm, dry eye, ocular fatigue, tear break-up time, functional visual acuity 

  15. Investigations of Sooting Laminar Coflow Diffusion Flames at Elevated Pressures

    KAUST Repository

    Steinmetz, Scott A.

    2016-12-01

    sizes plateau. Particle size in the annulus is more sensitive to pressure. Next, the development of an alternative particle size measuring technique is studied. Time Resolved Laser Induced Incandescence (TiRe-LII) is a commonly used technique to measure soot concentrations and particle size at atmospheric pressure. However, Laser Induced Incandescence (LII) models suffer from an incomplete understanding of the effects of elevated pressures on the absorption, annealing, and cooling of soot. The present study focuses on what affect the laser temporal pulse shape and duration may have on particle sizing. TiRe-LII in flames at 1 and 15 bar is carried out, using laser pulses with tophat or Gaussian temporal profiles of varying duration. Mono-disperse equivalent primary particle diameters are calculated using the KAUST LII model. Little difference in particle sizing is found for different laser pulses. However, this data will be useful for validating the KAUST LII model when absorption and poly-dispersion are accounted for. In an effort to move one step closer to logistical fuel studies, the sooting tendencies of a number of liquid fuels are studied at pressures up to 10. Of parallel relevance, a sooting index for surrogate development is evaluated for elevated pressure applications. The Yield Sooting Index (YSI) methodology is applied to 11 normal, cyclic, and branched alkanes. When referencing to two n-alkane fuels, the YSI of n-alkanes determined at atmospheric pressures accurately reflects the relative sooting tendencies of these fuels at elevated pressures. The relative sooting tendencies of cyclo- and methyl-alkanes have a lower pressure sensitivity than n-alkanes.

  16. Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil

    KAUST Repository

    Essack, Magbubah

    2013-06-10

    Background:Sickle cell disease (SCD) is a fatal monogenic disorder with no effective cure and thus high rates of morbidity and sequelae. Efforts toward discovery of disease modifying drugs and curative strategies can be augmented by leveraging the plethora of information contained in available biomedical literature. To facilitate research in this direction we have developed a resource, Dragon Exploration System for Sickle Cell Disease (DESSCD) (http://cbrc.kaust.edu.sa/desscd/) that aims to promote the easy exploration of SCD-related data.Description:The Dragon Exploration System (DES), developed based on text mining and complemented by data mining, processed 419,612 MEDLINE abstracts retrieved from a PubMed query using SCD-related keywords. The processed SCD-related data has been made available via the DESSCD web query interface that enables: a/information retrieval using specified concepts, keywords and phrases, and b/the generation of inferred association networks and hypotheses. The usefulness of the system is demonstrated by: a/reproducing a known scientific fact, the "Sickle_Cell_Anemia-Hydroxyurea" association, and b/generating novel and plausible "Sickle_Cell_Anemia-Hydroxyfasudil" hypothesis. A PCT patent (PCT/US12/55042) has been filed for the latter drug repurposing for SCD treatment.Conclusion:We developed the DESSCD resource dedicated to exploration of text-mined and data-mined information about SCD. No similar SCD-related resource exists. Thus, we anticipate that DESSCD will serve as a valuable tool for physicians and researchers interested in SCD. © 2013 Essack et al.

  17. Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

    KAUST Repository

    Magana-Mora, Arturo

    2017-08-15

    BackgroundPolyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3′-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge.ResultsIn this study, we analyzed human genomic DNA sequences for the 12 most common PAS variants. Our analysis has identified a set of features that helps in the recognition of true PAS, which may be involved in the regulation of the polyadenylation process. The proposed features, in combination with a recognition model, resulted in a novel method and tool, Omni-PolyA. Omni-PolyA combines several machine learning techniques such as different classifiers in a tree-like decision structure and genetic algorithms for deriving a robust classification model. We performed a comparison between results obtained by state-of-the-art methods, deep neural networks, and Omni-PolyA. Results show that Omni-PolyA significantly reduced the average classification error rate by 35.37% in the prediction of the 12 considered PAS variants relative to the state-of-the-art results.ConclusionsThe results of our study demonstrate that Omni-PolyA is currently the most accurate model for the prediction of PAS in human and can serve as a useful complement to other PAS recognition methods. Omni-PolyA is publicly available as an online tool accessible at www.cbrc.kaust.edu.sa/omnipolya/.

  18. dPORE-miRNA: Polymorphic regulation of microRNA genes

    KAUST Repository

    Schmeier, Sebastian

    2011-02-04

    Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.

  19. Mining Chemical Activity Status from High-Throughput Screening Assays

    KAUST Repository

    Soufan, Othman

    2015-12-14

    High-throughput screening (HTS) experiments provide a valuable resource that reports biological activity of numerous chemical compounds relative to their molecular targets. Building computational models that accurately predict such activity status (active vs. inactive) in specific assays is a challenging task given the large volume of data and frequently small proportion of active compounds relative to the inactive ones. We developed a method, DRAMOTE, to predict activity status of chemical compounds in HTP activity assays. For a class of HTP assays, our method achieves considerably better results than the current state-of-the-art-solutions. We achieved this by modification of a minority oversampling technique. To demonstrate that DRAMOTE is performing better than the other methods, we performed a comprehensive comparison analysis with several other methods and evaluated them on data from 11 PubChem assays through 1,350 experiments that involved approximately 500,000 interactions between chemicals and their target proteins. As an example of potential use, we applied DRAMOTE to develop robust models for predicting FDA approved drugs that have high probability to interact with the thyroid stimulating hormone receptor (TSHR) in humans. Our findings are further partially and indirectly supported by 3D docking results and literature information. The results based on approximately 500,000 interactions suggest that DRAMOTE has performed the best and that it can be used for developing robust virtual screening models. The datasets and implementation of all solutions are available as a MATLAB toolbox online at www.cbrc.kaust.edu.sa/dramote and can be found on Figshare.

  20. Fully Printed 3D Cube Cantor Fractal Rectenna for Ambient RF Energy Harvesting Application

    KAUST Repository

    Bakytbekov, Azamat

    2017-11-01

    Internet of Things (IoT) is a new emerging paradigm which requires billions of wirelessly connected devices that communicate with each other in a complex radio-frequency (RF) environment. Considering the huge number of devices, recharging batteries or replacing them becomes impractical in real life. Therefore, harvesting ambient RF energy for powering IoT devices can be a practical solution to achieve self-charging operation. The antenna for the RF energy harvesting application must work on multiple frequency bands (multiband or wideband) to capture as much power as possible from ambient; it should be compact and small in size so that it can be integrated with IoT devices; and it should be low cost, considering the huge number of devices. This thesis presents a fully printed 3D cube Cantor fractal RF energy harvesting unit, which meets the above-mentioned criteria. The multiband Cantor fractal antenna has been designed and implemented on a package of rectifying circuits using additive manufacturing (combination of 3D inkjet printing of plastic substrate and 2D metallic screen printing of silver paste) for the first time for RF energy harvesting application. The antenna, which is in a Cantor fractal shape, is folded on five faces of a 3D cube where the bottom face accommodates rectifying circuit with matching network. The rectenna (rectifying antenna) harvests RF power from GSM900, GSM1800, and 3G at 2100 MHz frequency. Indoor and outdoor field tests of the RF energy harvester have been conducted in the IMPACT lab and the King Abdullah University of Science and Technology (KAUST) campus territory, and 252.4 mV of maximum output voltage is harvested.

  1. ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

    KAUST Repository

    Hungler, Arnaud; Momin, Afaque Ahmad Imtiyaz; Diederichs, Kay; Arold, Stefan T.

    2016-01-01

    Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. A web server, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. © Arnaud Hungler et al. 2016.

  2. INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

    Science.gov (United States)

    Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B.

    2013-01-01

    Background The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. Results We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. Conclusions We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo. PMID

  3. SECOM: A novel hash seed and community detection based-approach for genome-scale protein domain identification

    KAUST Repository

    Fan, Ming

    2012-06-28

    With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2012 Fan et al.

  4. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining

    KAUST Repository

    Salhi, Adil

    2017-04-07

    Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer\\'s disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.

  5. BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

    Science.gov (United States)

    Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

    2015-08-18

    Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  6. An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

    KAUST Repository

    Abbas, Ahmed

    2014-04-19

    Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on \\'slices\\', which are one-dimensional vectors in three-dimensional spectra that correspond to certain (N, H) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2014 Springer Science+Business Media.

  7. Experimental and Kinetic Modeling Study of Ethyl Levulinate Oxidation in a Jet-Stirred Reactor

    KAUST Repository

    Wang, Jui-Yang

    2017-06-01

    A jet-stirred reactor was designed and constructed in the Clean Combustion Research Center (CCRC) at King Abdullah University of Science and Technology (KAUST); was validated with n-heptane, iso-octane oxidation and cyclohexene pyrolysis. Different configurations of the setup have been tested to achieve good agreement with results from the literature. Test results of the reactor indicated that installation of a pumping system at the downstream side in the experimental apparatus was necessary to avoid the reoccurrence of reactions in the sampling probe. Experiments in ethyl levulinate oxidation were conducted in the reactor under several equivalence ratios, from 600 to 1000 K, 1 bar and 2 s residence time. Oxygenated species detected included methyl vinyl ketone, levulinic acid and ethyl acrylate. Ethylene, methane, carbon monoxide, hydrogen, oxygen and carbon dioxide were further quantified with a gas chromatography, coupled with a flame ionization detector and a thermal conductivity detector. The ethyl levulinate chemical kinetic model was first developed by Dr. Stephen Dooley, Trinity College Dublin, and simulated under the same conditions, using the Perfect-Stirred Reactor code in Chemkin software. In comparing the simulation results with experimental data, some discrepancies were noted; predictions of ethylene production were not well matched. The kinetic model was improved by updating several classes of reactions: unimolecular decomposition, H-abstraction, C-C and C-O beta-scissions of fuel radicals. The updated model was then compared again with experimental results and good agreement was achieved, proving that the concerted eliminated reaction is crucial for the kinetic mechanism formulation of ethyl levulinate. In addition, primary reaction pathways and sensitivity analysis were performed to describe the role of molecular structure in combustion (800 and 1000 K for ethyl levulinate oxidation in the jet-stirred reactor).

  8. Supplementary Material for: BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.

    2015-01-01

    Abstract Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACONâ s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  9. A computational study of ethylene–air sooting flames: Effects of large polycyclic aromatic hydrocarbons

    KAUST Repository

    Selvaraj, Prabhu

    2015-11-05

    An updated reduced gas-phase kinetic mechanism was developed and integrated with aerosol models to predict soot formation characteristics in ethylene nonpremixed and premixed flames. A primary objective is to investigate the sensitivity of the soot formation to various chemical pathways for large polycyclic aromatic hydrocarbons (PAH). The gas-phase chemical mechanism adopted the KAUST-Aramco PAH Mech 1.0, which utilized the AramcoMech 1.3 for gas-phase reactions validated for up to C2 fuels. In addition, PAH species up to coronene (C24H12 or A7) were included to describe the detailed formation pathways of soot precursors. In this study, the detailed chemical mechanism was reduced from 397 to 99 species using directed relation graph with expert knowledge (DRG-X) and sensitivity analysis. The method of moments with interpolative closure (MOMIC) was employed for the soot aerosol model. Counterflow nonpremixed flames at low strain rate sooting conditions were considered, for which the sensitivity of soot formation characteristics to different nucleation pathways were investigated. Premixed flame experiment data at different equivalence ratios were also used for validation. The findings show that higher PAH concentrations result in a higher soot nucleation rate, and that the total soot volume and average size of the particles are predicted in good agreement with experimental results. Subsequently, the effects of different pathways, with respect to pyrene- or coronene-based nucleation models, on the net soot formation rate were analyzed. It was found that the nucleation processes (i.e., soot inception) are sensitive to the choice of PAH precursors, and consideration of higher PAH species beyond pyrene is critical for accurate prediction of the overall soot formation.

  10. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  11. dPORE-miRNA: Polymorphic regulation of microRNA genes

    KAUST Repository

    Schmeier, Sebastian; Schaefer, Ulf; MacPherson, Cameron R.; Bajic, Vladimir B.

    2011-01-01

    Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.

  12. DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail

    2016-03-16

    can be accessed online at: http://​www.​cbrc.​kaust.​edu.​sa/​daspfind.

  13. Automatic Peak Selection by a Benjamini-Hochberg-Based Algorithm

    KAUST Repository

    Abbas, Ahmed; Kong, Xin-Bing; Liu, Zhi; Jing, Bing-Yi; Gao, Xin

    2013-01-01

    A common issue in bioinformatics is that computational methods often generate a large number of predictions sorted according to certain confidence scores. A key problem is then determining how many predictions must be selected to include most of the true predictions while maintaining reasonably high precision. In nuclear magnetic resonance (NMR)-based protein structure determination, for instance, computational peak picking methods are becoming more and more common, although expert-knowledge remains the method of choice to determine how many peaks among thousands of candidate peaks should be taken into consideration to capture the true peaks. Here, we propose a Benjamini-Hochberg (B-H)-based approach that automatically selects the number of peaks. We formulate the peak selection problem as a multiple testing problem. Given a candidate peak list sorted by either volumes or intensities, we first convert the peaks into p-values and then apply the B-H-based algorithm to automatically select the number of peaks. The proposed approach is tested on the state-of-the-art peak picking methods, including WaVPeak [1] and PICKY [2]. Compared with the traditional fixed number-based approach, our approach returns significantly more true peaks. For instance, by combining WaVPeak or PICKY with the proposed method, the missing peak rates are on average reduced by 20% and 26%, respectively, in a benchmark set of 32 spectra extracted from eight proteins. The consensus of the B-H-selected peaks from both WaVPeak and PICKY achieves 88% recall and 83% precision, which significantly outperforms each individual method and the consensus method without using the B-H algorithm. The proposed method can be used as a standard procedure for any peak picking method and straightforwardly applied to some other prediction selection problems in bioinformatics. The source code, documentation and example data of the proposed method is available at http://sfb.kaust.edu.sa/pages/software.aspx. © 2013

  14. Analysis and Modeling of Social In uence in High Performance Computing Workloads

    KAUST Repository

    Zheng, Shuai

    2011-06-01

    High Performance Computing (HPC) is becoming a common tool in many research areas. Social influence (e.g., project collaboration) among increasing users of HPC systems creates bursty behavior in underlying workloads. This bursty behavior is increasingly common with the advent of grid computing and cloud computing. Mining the user bursty behavior is important for HPC workloads prediction and scheduling, which has direct impact on overall HPC computing performance. A representative work in this area is the Mixed User Group Model (MUGM), which clusters users according to the resource demand features of their submissions, such as duration time and parallelism. However, MUGM has some difficulties when implemented in real-world system. First, representing user behaviors by the features of their resource demand is usually difficult. Second, these features are not always available. Third, measuring the similarities among users is not a well-defined problem. In this work, we propose a Social Influence Model (SIM) to identify, analyze, and quantify the level of social influence across HPC users. The advantage of the SIM model is that it finds HPC communities by analyzing user job submission time, thereby avoiding the difficulties of MUGM. An offline algorithm and a fast-converging, computationally-efficient online learning algorithm for identifying social groups are proposed. Both offline and online algorithms are applied on several HPC and grid workloads, including Grid 5000, EGEE 2005 and 2007, and KAUST Supercomputing Lab (KSL) BGP data. From the experimental results, we show the existence of a social graph, which is characterized by a pattern of dominant users and followers. In order to evaluate the effectiveness of identified user groups, we show the pattern discovered by the offline algorithm follows a power-law distribution, which is consistent with those observed in mainstream social networks. We finally conclude the thesis and discuss future directions of our work.

  15. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining

    KAUST Repository

    Salhi, Adil; Essack, Magbubah; Alam, Tanvir; Bajic, Vladan P.; Ma, Lina; Radovanovic, Aleksandar; Marchand, Benoit; Schmeier, Sebastian; Zhang, Zhang; Bajic, Vladimir B.

    2017-01-01

    Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer's disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.

  16. TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins

    KAUST Repository

    Schaefer, Ulf

    2010-10-21

    The initiation and regulation of transcription in eukaryotes is complex and involves a large number of transcription factors (TFs), which are known to bind to the regulatory regions of eukaryotic DNA. Apart from TF-DNA binding, protein-protein interaction involving TFs is an essential component of the machinery facilitating transcriptional regulation. Proteins that interact with TFs in the context of transcription regulation but do not bind to the DNA themselves, we consider transcription co-factors (TcoFs). The influence of TcoFs on transcriptional regulation and initiation, although indirect, has been shown to be significant with the functionality of TFs strongly influenced by the presence of TcoFs. While the role of TFs and their interaction with regulatory DNA regions has been well-studied, the association between TFs and TcoFs has so far been given less attention. Here, we present a resource that is comprised of a collection of human TFs and the TcoFs with which they interact. Other proteins that have a proven interaction with a TF, but are not considered TcoFs are also included. Our database contains 157 high-confidence TcoFs and additionally 379 hypothetical TcoFs. These have been identified and classified according to the type of available evidence for their involvement in transcriptional regulation and their presence in the cell nucleus. We have divided TcoFs into four groups, one of which contains high-confidence TcoFs and three others contain TcoFs which are hypothetical to different extents. We have developed the Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB). A web-based interface for this resource can be freely accessed at http://cbrc.kaust.edu.sa/tcof/ and http://apps.sanbi.ac.za/tcof/. © The Author(s) 2010.

  17. Mining Chemical Activity Status from High-Throughput Screening Assays

    KAUST Repository

    Soufan, Othman; Ba Alawi, Wail; Afeef, Moataz A.; Essack, Magbubah; Rodionov, Valentin; Kalnis, Panos; Bajic, Vladimir B.

    2015-01-01

    High-throughput screening (HTS) experiments provide a valuable resource that reports biological activity of numerous chemical compounds relative to their molecular targets. Building computational models that accurately predict such activity status (active vs. inactive) in specific assays is a challenging task given the large volume of data and frequently small proportion of active compounds relative to the inactive ones. We developed a method, DRAMOTE, to predict activity status of chemical compounds in HTP activity assays. For a class of HTP assays, our method achieves considerably better results than the current state-of-the-art-solutions. We achieved this by modification of a minority oversampling technique. To demonstrate that DRAMOTE is performing better than the other methods, we performed a comprehensive comparison analysis with several other methods and evaluated them on data from 11 PubChem assays through 1,350 experiments that involved approximately 500,000 interactions between chemicals and their target proteins. As an example of potential use, we applied DRAMOTE to develop robust models for predicting FDA approved drugs that have high probability to interact with the thyroid stimulating hormone receptor (TSHR) in humans. Our findings are further partially and indirectly supported by 3D docking results and literature information. The results based on approximately 500,000 interactions suggest that DRAMOTE has performed the best and that it can be used for developing robust virtual screening models. The datasets and implementation of all solutions are available as a MATLAB toolbox online at www.cbrc.kaust.edu.sa/dramote and can be found on Figshare.

  18. High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur

    KAUST Repository

    Schaefer, Ulf

    2013-10-10

    available at http://cbrc.kaust.edu.sa/ddm/

  19. Dragon exploratory system on Hepatitis C Virus (DESHCV)

    KAUST Repository

    Kwofie, Samuel K.

    2011-06-01

    Even though Hepatitis C Virus (HCV) cDNA was characterized about 20 years ago, there is insufficient understanding of the molecular etiology underlying HCV infections. Current global rates of infection and its increasingly chronic character are causes of concern for health policy experts. Vast amount of data accumulated from biochemical, genomic, proteomic, and other biological analyses allows for novel insights into the HCV viral structure, life cycle and functions of its proteins. Biomedical text-mining is a useful approach for analyzing the increasing corpus of published scientific literature on HCV. We report here the first comprehensive HCV customized biomedical text-mining based online web resource, dragon exploratory system on Hepatitis C Virus (DESHCV), a biomedical text-mining and relationship exploring knowledgebase was developed by exploring literature on HCV. The pre-compiled dictionaries existing in the dragon exploratory system (DES) were enriched with biomedical concepts pertaining to HCV proteins, their name variants and symbols to make it suitable for targeted information exploration and knowledge extraction as focused on HCV. A list of 32,895 abstracts retrieved via PubMed database using specific keywords searches related to HCV were processed based on concept recognition of terms from several dictionaries. The web query interface enables retrieval of information using specified concepts, keywords and phrases, generating text-derived association networks and hypotheses, which could be tested to identify potentially novel relationship between different concepts. Such an approach could also augment efforts in the search for diagnostic or even therapeutic targets. DESHCV thus represents online literature-based discovery resource freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/DESHCV/ and its mirror site http://cbrc.kaust.edu.sa/deshcv/. © 2010 Elsevier B.V.

  20. Automatic Peak Selection by a Benjamini-Hochberg-Based Algorithm

    KAUST Repository

    Abbas, Ahmed

    2013-01-07

    A common issue in bioinformatics is that computational methods often generate a large number of predictions sorted according to certain confidence scores. A key problem is then determining how many predictions must be selected to include most of the true predictions while maintaining reasonably high precision. In nuclear magnetic resonance (NMR)-based protein structure determination, for instance, computational peak picking methods are becoming more and more common, although expert-knowledge remains the method of choice to determine how many peaks among thousands of candidate peaks should be taken into consideration to capture the true peaks. Here, we propose a Benjamini-Hochberg (B-H)-based approach that automatically selects the number of peaks. We formulate the peak selection problem as a multiple testing problem. Given a candidate peak list sorted by either volumes or intensities, we first convert the peaks into p-values and then apply the B-H-based algorithm to automatically select the number of peaks. The proposed approach is tested on the state-of-the-art peak picking methods, including WaVPeak [1] and PICKY [2]. Compared with the traditional fixed number-based approach, our approach returns significantly more true peaks. For instance, by combining WaVPeak or PICKY with the proposed method, the missing peak rates are on average reduced by 20% and 26%, respectively, in a benchmark set of 32 spectra extracted from eight proteins. The consensus of the B-H-selected peaks from both WaVPeak and PICKY achieves 88% recall and 83% precision, which significantly outperforms each individual method and the consensus method without using the B-H algorithm. The proposed method can be used as a standard procedure for any peak picking method and straightforwardly applied to some other prediction selection problems in bioinformatics. The source code, documentation and example data of the proposed method is available at http://sfb.kaust.edu.sa/pages/software.aspx. © 2013

  1. DEEP: a general computational framework for predicting enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2014-11-05

    Transcription regulation in multicellular eukaryotes is orchestrated by a number of DNA functional elements located at gene regulatory regions. Some regulatory regions (e.g. enhancers) are located far away from the gene they affect. Identification of distal regulatory elements is a challenge for the bioinformatics research. Although existing methodologies increased the number of computationally predicted enhancers, performance inconsistency of computational models across different cell-lines, class imbalance within the learning sets and ad hoc rules for selecting enhancer candidates for supervised learning, are some key questions that require further examination. In this study we developed DEEP, a novel ensemble prediction framework. DEEP integrates three components with diverse characteristics that streamline the analysis of enhancer\\'s properties in a great variety of cellular conditions. In our method we train many individual classification models that we combine to classify DNA regions as enhancers or non-enhancers. DEEP uses features derived from histone modification marks or attributes coming from sequence characteristics. Experimental results indicate that DEEP performs better than four state-of-the-art methods on the ENCODE data. We report the first computational enhancer prediction results on FANTOM5 data where DEEP achieves 90.2% accuracy and 90% geometric mean (GM) of specificity and sensitivity across 36 different tissues. We further present results derived using in vivo-derived enhancer data from VISTA database. DEEP-VISTA, when tested on an independent test set, achieved GM of 80.1% and accuracy of 89.64%. DEEP framework is publicly available at http://cbrc.kaust.edu.sa/deep/.

  2. TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins

    KAUST Repository

    Schaefer, Ulf; Schmeier, Sebastian; Bajic, Vladimir B.

    2010-01-01

    The initiation and regulation of transcription in eukaryotes is complex and involves a large number of transcription factors (TFs), which are known to bind to the regulatory regions of eukaryotic DNA. Apart from TF-DNA binding, protein-protein interaction involving TFs is an essential component of the machinery facilitating transcriptional regulation. Proteins that interact with TFs in the context of transcription regulation but do not bind to the DNA themselves, we consider transcription co-factors (TcoFs). The influence of TcoFs on transcriptional regulation and initiation, although indirect, has been shown to be significant with the functionality of TFs strongly influenced by the presence of TcoFs. While the role of TFs and their interaction with regulatory DNA regions has been well-studied, the association between TFs and TcoFs has so far been given less attention. Here, we present a resource that is comprised of a collection of human TFs and the TcoFs with which they interact. Other proteins that have a proven interaction with a TF, but are not considered TcoFs are also included. Our database contains 157 high-confidence TcoFs and additionally 379 hypothetical TcoFs. These have been identified and classified according to the type of available evidence for their involvement in transcriptional regulation and their presence in the cell nucleus. We have divided TcoFs into four groups, one of which contains high-confidence TcoFs and three others contain TcoFs which are hypothetical to different extents. We have developed the Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB). A web-based interface for this resource can be freely accessed at http://cbrc.kaust.edu.sa/tcof/ and http://apps.sanbi.ac.za/tcof/. © The Author(s) 2010.

  3. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.

    Science.gov (United States)

    Salhi, Adil; Essack, Magbubah; Alam, Tanvir; Bajic, Vladan P; Ma, Lina; Radovanovic, Aleksandar; Marchand, Benoit; Schmeier, Sebastian; Zhang, Zhang; Bajic, Vladimir B

    2017-07-03

    Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.

  4. The Red Sea Modeling and Forecasting System

    KAUST Repository

    Hoteit, Ibrahim

    2015-04-01

    Despite its importance for a variety of socio-economical and political reasons and the presence of extensive coral reef gardens along its shores, the Red Sea remains one of the most under-studied large marine physical and biological systems in the global ocean. This contribution will present our efforts to build advanced modeling and forecasting capabilities for the Red Sea, which is part of the newly established Saudi ARAMCO Marine Environmental Research Center at KAUST (SAMERCK). Our Red Sea modeling system compromises both regional and nested costal MIT general circulation models (MITgcm) with resolutions varying between 8 km and 250 m to simulate the general circulation and mesoscale dynamics at various spatial scales, a 10-km resolution Weather Research Forecasting (WRF) model to simulate the atmospheric conditions, a 4-km resolution European Regional Seas Ecosystem Model (ERSEM) to simulate the Red Sea ecosystem, and a 1-km resolution WAVEWATCH-III model to simulate the wind driven surface waves conditions. We have also implemented an oil spill model, and a probabilistic dispersion and larval connectivity modeling system (CMS) based on a stochastic Lagrangian framework and incorporating biological attributes. We are using the models outputs together with available observational data to study all aspects of the Red Sea circulations. Advanced monitoring capabilities are being deployed in the Red Sea as part of the SAMERCK, comprising multiple gliders equipped with hydrographical and biological sensors, high frequency (HF) surface current/wave mapping, buoys/ moorings, etc, complementing the available satellite ocean and atmospheric observations and Automatic Weather Stations (AWS). The Red Sea models have also been equipped with advanced data assimilation capabilities. Fully parallel ensemble-based Kalman filtering (EnKF) algorithms have been implemented with the MITgcm and ERSEM for assimilating all available multivariate satellite and in-situ data sets. We

  5. SECOM: A novel hash seed and community detection based-approach for genome-scale protein domain identification

    KAUST Repository

    Fan, Ming; Wong, Ka-Chun; Ryu, Tae Woo; Ravasi, Timothy; Gao, Xin

    2012-01-01

    With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2012 Fan et al.

  6. Synthesis, Characterization, and Application of Superhydrophobic Sands in Desert Agriculture

    KAUST Repository

    Reihmer, Joel W.

    2017-04-01

    A sustainable supply of fresh water for the human population is a global concern. Intriguingly, about 70% of the total fresh water consumed in the world annually is claimed by agriculture alone; this fraction is even higher in the Middle East and North Africa (MENA) region, where natural regeneration of groundwater is the slowest. Thus, there is a serious need for innovative materials and technologies to enhance the efficiency water usage in agriculture. To this end, plastic mulches have been employed across the developed world to minimize evaporative loss of water from top-soils. While plastic mulches are inexpensive, they do require specialized farm machinery for installation and long processing times. On one hand, plastic mulches have proven to increase crop yields, but on the other their non-biodegradability poses serious environmental concerns. In response, development of low-cost bio-/photo-degradable artificial mulches remains an area of intense research. In this thesis, we report on a novel superhydrophobic material exploiting inexpensive simple components to reduce the amount of water required for irrigation in agriculture by suppressing evaporative losses from the top-soil. Our material consists of ordinary beach sand coated with < 20 nm thick layer of paraffin wax. We synthesized and extensively characterized our material and applied them as mulches for tomato and barley plants at the KAUST greenhouse. We found that when a ~5 mm thick layer of superhydrophobic sand was placed onto the top-soil in pots, it dramatically suppressed evaporative losses and significantly enhanced the yields. Our preliminary field-scale experiments with tomatoes and barley crops at the Hada Al Sham site corroborate these results. Our approach might find applications in desert agriculture and other fields and alleviate water stress in the MENA region.

  7. Effect of Temperature, Pressure and Equivalence Ratio on Ignition Delay in Ignition Quality Tester (IQT): Diesel,n-Heptane, andiso-Octane Fuels under Low Temperature Conditions

    KAUST Repository

    Yang, Seung Yeon

    2015-11-02

    Effects of temperature, pressure and global equivalence ratio on total ignition delay time in a constant volume spray combustion chamber were investigated for diesel fuel along with the primary reference fuels (PRFs) of n-heptane and iso-octane in relatively low temperature conditions to simulate unsteady spray ignition behavior. A KAUST Research ignition quality tester (KR-IQT) was utilized, which has a feature of varying temperature, pressure and equivalence ratio using a variable displacement fuel pump. A gradient method was adopted in determining the start of ignition in order to compensate pressure increase induced by low temperature heat release. Comparison of this method with other existing methods was discussed. Ignition delay times were measured at various equivalence ratios (0.5-1.7) with the temperatures of initial charge air in the range from 698 to 860 K and the pressures in the range of 1.5 to 2.1 MPa, pertinent to low temperature combustion (LTC) conditions. An attempt to scale the effect of pressure on total ignition delay was undertaken and the equivalence ratio exponent and activation energy in the Arrhenius expression of total ignition delay were determined. Ignition delay results indicated that there were strong correlations of pressure, temperature, and equivalence ratio under most conditions studied except at relatively low pressures. Diesel (DCN 52.5) and n-heptane (DCN 54) fuels exhibited reasonably similar ignition delay characteristics, while iso-octane showed a distinct behavior under low temperature regime having a two-stage ignition, which substantiate the adoption of the gradient method in determining ignition delay.

  8. Is Attribute-Based Zero-Shot Learning an Ill-Posed Strategy?

    KAUST Repository

    Alabdulmohsin, Ibrahim; Cisse, Moustapha; Zhang, Xiangliang

    2016-01-01

    One transfer learning approach that has gained a wide popularity lately is attribute-based zero-shot learning. Its goal is to learn novel classes that were never seen during the training stage. The classical route towards realizing this goal is to incorporate a prior knowledge, in the form of a semantic embedding of classes, and to learn to predict classes indirectly via their semantic attributes. Despite the amount of research devoted to this subject lately, no known algorithm has yet reported a predictive accuracy that could exceed the accuracy of supervised learning with very few training examples. For instance, the direct attribute prediction (DAP) algorithm, which forms a standard baseline for the task, is known to be as accurate as supervised learning when as few as two examples from each hidden class are used for training on some popular benchmark datasets! In this paper, we argue that this lack of significant results in the literature is not a coincidence; attribute-based zero-shot learning is fundamentally an ill-posed strategy. The key insight is the observation that the mechanical task of predicting an attribute is, in fact, quite different from the epistemological task of learning the “correct meaning” of the attribute itself. This renders attribute-based zero-shot learning fundamentally ill-posed. In more precise mathematical terms, attribute-based zero-shot learning is equivalent to the mirage goal of learning with respect to one distribution of instances, with the hope of being able to predict with respect to any arbitrary distribution. We demonstrate this overlooked fact on some synthetic and real datasets. The data and software related to this paper are available at https://mine. kaust.edu.sa/Pages/zero-shot-learning.aspx. © Springer International Publishing AG 2016.

  9. Is Attribute-Based Zero-Shot Learning an Ill-Posed Strategy?

    KAUST Repository

    Alabdulmohsin, Ibrahim

    2016-09-03

    One transfer learning approach that has gained a wide popularity lately is attribute-based zero-shot learning. Its goal is to learn novel classes that were never seen during the training stage. The classical route towards realizing this goal is to incorporate a prior knowledge, in the form of a semantic embedding of classes, and to learn to predict classes indirectly via their semantic attributes. Despite the amount of research devoted to this subject lately, no known algorithm has yet reported a predictive accuracy that could exceed the accuracy of supervised learning with very few training examples. For instance, the direct attribute prediction (DAP) algorithm, which forms a standard baseline for the task, is known to be as accurate as supervised learning when as few as two examples from each hidden class are used for training on some popular benchmark datasets! In this paper, we argue that this lack of significant results in the literature is not a coincidence; attribute-based zero-shot learning is fundamentally an ill-posed strategy. The key insight is the observation that the mechanical task of predicting an attribute is, in fact, quite different from the epistemological task of learning the “correct meaning” of the attribute itself. This renders attribute-based zero-shot learning fundamentally ill-posed. In more precise mathematical terms, attribute-based zero-shot learning is equivalent to the mirage goal of learning with respect to one distribution of instances, with the hope of being able to predict with respect to any arbitrary distribution. We demonstrate this overlooked fact on some synthetic and real datasets. The data and software related to this paper are available at https://mine. kaust.edu.sa/Pages/zero-shot-learning.aspx. © Springer International Publishing AG 2016.

  10. Design and Implementation of a Campus-Wide Online Plagiarism Tutorial: Role played by the Library in an emerging research institution in Saudi Arabia

    KAUST Repository

    Han, Lee-Yen

    2017-06-20

    Academic dishonesty and plagiarism are serious issues in institutes of higher education especially in this Internet age with academic literature and information readily available on the web. Some research studies point to the students’ lack of understanding of the concept of plagiarism and how to cite sources as reasons why they plagiarize (Volkov, Volkov, & Tedford, 2011). Academic librarians have an important role to play in providing instruction in the ethical use of information and helping students develop abilities to attribute and cite sources in their academic writing (Mages & Garson, 2010; Maxymuk, 2006). Recognizing this important role played by librarians, the University Library at King Abdullah University of Science and Technology (KAUST) started offering face-to-face workshops on the topic in the spring of 2015. While the workshops were positively received by the participants, informal feedback from students points to a need for an online course which would provide asynchronous just-in-time training for students. In this way, students who are not able to attend the face-to-face workshops would be able to access the tutorial in their own time and at their own pace. This paper reports on the process the University Library took to create and embed an online plagiarism tutorial in Blackboard, the Learning Management System (LMS) used by the university. Drawing on and expanding on materials covered in the face-to-face workshop, the online tutorial included original multimedia material, and a summative evaluation quiz. Improvements were made based on feedback gathered from students, library staff, and other university departments, such as the Office of Writing Services, Graduate Affairs, and ESP Instructors from the Writing Center. The online tutorial was initially planned as an optional course for students, but with the support of Academic Affairs and Graduate Affairs, it has been mandated as a compulsory course for all new in-coming students.

  11. Big Data Analysis of Human Genome Variations

    KAUST Repository

    Gojobori, Takashi

    2016-01-25

    Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these three data sets by use of information on the reference human genome sequence, and we conducted the big data analysis. In particular, we constructed a phylogenetic tree of about 5,000 human individuals at the genome level. As a result, we were able to identify clusters of ethnic groups, with detectable admixture, that were not possible by an analysis of each of the three data sets. Here, we report the outcome of this kind of big data analyses and discuss evolutionary significance of human genomic variations. Note that the present study was conducted in collaboration with Katsuhiko Mineta and Kosuke Goto at KAUST.

  12. ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

    KAUST Repository

    Hungler, Arnaud

    2016-11-02

    Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for \\'crystallization and preliminary X-ray analysis\\' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. A web server, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for \\'crystallization and preliminary X-ray analysis\\' publications. © Arnaud Hungler et al. 2016.

  13. Auto-Ignition and Spray Characteristics of n-Heptane and iso-Octane Fuels in Ignition Quality Tester

    KAUST Repository

    Jaasim, Mohammed

    2018-04-04

    Numerical simulations were conducted to systematically assess the effects of different spray models on the ignition delay predictions and compared with experimental measurements obtained at the KAUST ignition quality tester (IQT) facility. The influence of physical properties and chemical kinetics over the ignition delay time is also investigated. The IQT experiments provided the pressure traces as the main observables, which are not sufficient to obtain a detailed understanding of physical (breakup, evaporation) and chemical (reactivity) processes associated with auto-ignition. A three-dimensional computational fluid dynamics (CFD) code, CONVERGE™, was used to capture the detailed fluid/spray dynamics and chemical characteristics within the IQT configuration. The Reynolds-averaged Navier-Stokes (RANS) turbulence with multi-zone chemistry sub-models was adopted with a reduced chemical kinetic mechanism for n-heptane and iso-octane. The emphasis was on the assessment of two common spray breakup models, namely the Kelvin-Helmholtz/Rayleigh-Taylor (KH-RT) and linearized instability sheet atomization (LISA) models, in terms of their influence on auto-ignition predictions. Two spray models resulted in different local mixing, and their influence in the prediction of auto-ignition was investigated. The relative importance of physical ignition delay, characterized by spray evaporation and mixing processes, in the overall ignition behavior for the two different fuels were examined. The results provided an improved understanding of the essential contribution of physical and chemical processes that are critical in describing the IQT auto-ignition event at different pressure and temperature conditions, and allowed a systematic way to distinguish between the physical and chemical ignition delay times.

  14. The Red Sea Modeling and Forecasting System

    KAUST Repository

    Hoteit, Ibrahim; Gopalakrishnan, Ganesh; Latif, Hatem; Toye, Habib; Zhan, Peng; Kartadikaria, Aditya R.; Viswanadhapalli, Yesubabu; Yao, Fengchao; Triantafyllou, George; Langodan, Sabique; Cavaleri, Luigi; Guo, Daquan; Johns, Burt

    2015-01-01

    Despite its importance for a variety of socio-economical and political reasons and the presence of extensive coral reef gardens along its shores, the Red Sea remains one of the most under-studied large marine physical and biological systems in the global ocean. This contribution will present our efforts to build advanced modeling and forecasting capabilities for the Red Sea, which is part of the newly established Saudi ARAMCO Marine Environmental Research Center at KAUST (SAMERCK). Our Red Sea modeling system compromises both regional and nested costal MIT general circulation models (MITgcm) with resolutions varying between 8 km and 250 m to simulate the general circulation and mesoscale dynamics at various spatial scales, a 10-km resolution Weather Research Forecasting (WRF) model to simulate the atmospheric conditions, a 4-km resolution European Regional Seas Ecosystem Model (ERSEM) to simulate the Red Sea ecosystem, and a 1-km resolution WAVEWATCH-III model to simulate the wind driven surface waves conditions. We have also implemented an oil spill model, and a probabilistic dispersion and larval connectivity modeling system (CMS) based on a stochastic Lagrangian framework and incorporating biological attributes. We are using the models outputs together with available observational data to study all aspects of the Red Sea circulations. Advanced monitoring capabilities are being deployed in the Red Sea as part of the SAMERCK, comprising multiple gliders equipped with hydrographical and biological sensors, high frequency (HF) surface current/wave mapping, buoys/ moorings, etc, complementing the available satellite ocean and atmospheric observations and Automatic Weather Stations (AWS). The Red Sea models have also been equipped with advanced data assimilation capabilities. Fully parallel ensemble-based Kalman filtering (EnKF) algorithms have been implemented with the MITgcm and ERSEM for assimilating all available multivariate satellite and in-situ data sets. We

  15. DEEP: a general computational framework for predicting enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios A.; Kalnis, Panos; Bajic, Vladimir B.

    2014-01-01

    Transcription regulation in multicellular eukaryotes is orchestrated by a number of DNA functional elements located at gene regulatory regions. Some regulatory regions (e.g. enhancers) are located far away from the gene they affect. Identification of distal regulatory elements is a challenge for the bioinformatics research. Although existing methodologies increased the number of computationally predicted enhancers, performance inconsistency of computational models across different cell-lines, class imbalance within the learning sets and ad hoc rules for selecting enhancer candidates for supervised learning, are some key questions that require further examination. In this study we developed DEEP, a novel ensemble prediction framework. DEEP integrates three components with diverse characteristics that streamline the analysis of enhancer's properties in a great variety of cellular conditions. In our method we train many individual classification models that we combine to classify DNA regions as enhancers or non-enhancers. DEEP uses features derived from histone modification marks or attributes coming from sequence characteristics. Experimental results indicate that DEEP performs better than four state-of-the-art methods on the ENCODE data. We report the first computational enhancer prediction results on FANTOM5 data where DEEP achieves 90.2% accuracy and 90% geometric mean (GM) of specificity and sensitivity across 36 different tissues. We further present results derived using in vivo-derived enhancer data from VISTA database. DEEP-VISTA, when tested on an independent test set, achieved GM of 80.1% and accuracy of 89.64%. DEEP framework is publicly available at http://cbrc.kaust.edu.sa/deep/.

  16. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    Science.gov (United States)

    Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

    2013-01-01

    The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

  17. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    Directory of Open Access Journals (Sweden)

    Intikhab Alam

    Full Text Available The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.We developed a data warehouse system (INDIGO that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

  18. Genome-wide Studies of Mycolic Acid Bacteria: Computational Identification and Analysis of a Minimal Genome

    KAUST Repository

    Kamanu, Frederick Kinyua

    2012-12-01

    The mycolic acid bacteria are a distinct suprageneric group of asporogenous Grampositive, high GC-content bacteria, distinguished by the presence of mycolic acids in their cell envelope. They exhibit great diversity in their cell and morphology; although primarily non-pathogens, this group contains three major pathogens Mycobacterium leprae, Mycobacterium tuberculosis complex, and Corynebacterium diphtheria. Although the mycolic acid bacteria are a clearly defined group of bacteria, the taxonomic relationships between its constituent genera and species are less well defined. Two approaches were tested for their suitability in describing the taxonomy of the group. First, a Multilocus Sequence Typing (MLST) experiment was assessed and found to be superior to monophyletic (16S small ribosomal subunit) in delineating a total of 52 mycolic acid bacterial species. Phylogenetic inference was performed using the neighbor-joining method. To further refine phylogenetic analysis and to take advantage of the widespread availability of bacterial genome data, a computational framework that simulates DNA-DNA hybridisation was developed and validated using multiscale bootstrap resampling. The tool classifies microbial genomes based on whole genome DNA, and was deployed as a web-application using PHP and Javascript. It is accessible online at http://cbrc.kaust.edu.sa/dna_hybridization/ A third study was a computational and statistical methods in the identification and analysis of a putative minimal mycolic acid bacterial genome so as to better understand (1) the genomic requirements to encode a mycolic acid bacterial cell and (2) the role and type of genes and genetic elements that lead to the massive increase in genome size in environmental mycolic acid bacteria. Using a reciprocal comparison approach, a total of 690 orthologous gene clusters forming a putative minimal genome were identified across 24 mycolic acid bacterial species. In order to identify new potential drug

  19. Two-stage Lagrangian modeling of ignition processes in ignition quality tester and constant volume combustion chambers

    KAUST Repository

    Alfazazi, Adamu

    2016-08-10

    The ignition characteristics of isooctane and n-heptane in an ignition quality tester (IQT) were simulated using a two-stage Lagrangian (TSL) model, which is a zero-dimensional (0-D) reactor network method. The TSL model was also used to simulate the ignition delay of n-dodecane and n-heptane in a constant volume combustion chamber (CVCC), which is archived in the engine combustion network (ECN) library (http://www.ca.sandia.gov/ecn). A detailed chemical kinetic model for gasoline surrogates from the Lawrence Livermore National Laboratory (LLNL) was utilized for the simulation of n-heptane and isooctane. Additional simulations were performed using an optimized gasoline surrogate mechanism from RWTH Aachen University. Validations of the simulated data were also performed with experimental results from an IQT at KAUST. For simulation of n-dodecane in the CVCC, two n-dodecane kinetic models from the literature were utilized. The primary aim of this study is to test the ability of TSL to replicate ignition timings in the IQT and the CVCC. The agreement between the model and the experiment is acceptable except for isooctane in the IQT and n-heptane and n-dodecane in the CVCC. The ability of the simulations to replicate observable trends in ignition delay times with regard to changes in ambient temperature and pressure allows the model to provide insights into the reactions contributing towards ignition. Thus, the TSL model was further employed to investigate the physical and chemical processes responsible for controlling the overall ignition under various conditions. The effects of exothermicity, ambient pressure, and ambient oxygen concentration on first stage ignition were also studied. Increasing ambient pressure and oxygen concentration was found to shorten the overall ignition delay time, but does not affect the timing of the first stage ignition. Additionally, the temperature at the end of the first stage ignition was found to increase at higher ambient pressure

  20. PetClaw: Parallelization and Performance Optimization of a Python-Based Nonlinear Wave Propagation Solver Using PETSc

    KAUST Repository

    Alghamdi, Amal Mohammed

    2012-04-01

    Clawpack, a conservation laws package implemented in Fortran, and its Python-based version, PyClaw, are existing tools providing nonlinear wave propagation solvers that use state of the art finite volume methods. Simulations using those tools can have extensive computational requirements to provide accurate results. Therefore, a number of tools, such as BearClaw and MPIClaw, have been developed based on Clawpack to achieve significant speedup by exploiting parallel architectures. However, none of them has been shown to scale on a large number of cores. Furthermore, these tools, implemented in Fortran, achieve parallelization by inserting parallelization logic and MPI standard routines throughout the serial code in a non modular manner. Our contribution in this thesis research is three-fold. First, we demonstrate an advantageous use case of Python in implementing easy-to-use modular extensible scalable scientific software tools by developing an implementation of a parallelization framework, PetClaw, for PyClaw using the well-known Portable Extensible Toolkit for Scientific Computation, PETSc, through its Python wrapper petsc4py. Second, we demonstrate the possibility of getting acceptable Python code performance when compared to Fortran performance after introducing a number of serial optimizations to the Python code including integrating Clawpack Fortran kernels into PyClaw for low-level computationally intensive parts of the code. As a result of those optimizations, the Python overhead in PetClaw for a shallow water application is only 12 percent when compared to the corresponding Fortran Clawpack application. Third, we provide a demonstration of PetClaw scalability on up to the entirety of Shaheen; a 16-rack Blue Gene/P IBM supercomputer that comprises 65,536 cores and located at King Abdullah University of Science and Technology (KAUST). The PetClaw solver achieved above 0.98 weak scaling efficiency for an Euler application on the whole machine excluding the

  1. High Performance Simulation of Large-Scale Red Sea Ocean Bottom Seismic Data on the Supercomputer Shaheen II

    KAUST Repository

    Tonellot, Thierry; Etienne, Vincent; Gashawbeza, Ewenet; Curiel, Emesto Sandoval; Khan, Azizur; Feki, Saber; Kortas, Samuel

    2017-01-01

    A combination of both shallow and deepwater, plus islands and coral reefs, are some of the main features contributing to the complexity of subsalt seismic exploration in the Red Sea transition zone. These features often result in degrading effects on seismic images. State-of-the-art ocean bottom acquisition technologies are therefore required to record seismic data with optimal fold and offset, as well as advanced processing and imaging techniques. Numerical simulations of such complex seismic data can help improve acquisition design and also help in customizing, validating and benchmarking the processing and imaging workflows that will be applied on the field data. Subsequently, realistic simulation of wave propagation is a computationally intensive process requiring a realistic model and an efficient 3D wave equation solver. Large-scale computing resources are also required to meet turnaround time compatible with a production time frame. In this work, we present the numerical simulation of an ocean bottom seismic survey to be acquired in the Red Sea transition zone starting in summer 2016. The survey's acquisition geometry comprises nearly 300,000 unique shot locations and 21,000 unique receiver locations, covering about 760 km2. Using well log measurements and legacy 2D seismic lines in this area, a 3D P-wave velocity model was built, with a maximum depth of 7 km. The model was sampled at 10 m in each direction, resulting in more than 5 billion cells. Wave propagation in this model was performed using a 3D finite difference solver in the time domain based on a staggered grid velocity-pressure formulation of acoustodynamics. To ensure that the resulting data could be generated sufficiently fast, the King Abdullah University of Science and Technology (KAUST) supercomputer Shaheen II Cray XC40 was used. A total of 21,000 three-component (pressure and vertical and horizontal velocity) common receiver gathers with a 50 Hz maximum frequency were computed in less than

  2. Soot modeling of counterflow diffusion flames of ethylene-based binary mixture fuels

    KAUST Repository

    Wang, Yu

    2015-03-01

    A soot model was developed based on the recently proposed PAH growth mechanism for C1-C4 gaseous fuels (KAUST PAH Mechanism 2, KM2) that included molecular growth up to coronene (A7) to simulate soot formation in counterflow diffusion flames of ethylene and its binary mixtures with methane, ethane and propane based on the method of moments. The soot model has 36 soot nucleation reactions from 8 PAH molecules including pyrene and larger PAHs. Soot surface growth reactions were based on a modified hydrogen-abstraction-acetylene-addition (HACA) mechanism in which CH3, C3H3 and C2H radicals were included in the hydrogen abstraction reactions in addition to H atoms. PAH condensation on soot particles was also considered. The experimentally measured profiles of soot volume fraction, number density, and particle size were well captured by the model for the baseline case of ethylene along with the cases involving mixtures of fuels. The simulation results, which were in qualitative agreement with the experimental data in the effects of binary fuel mixing on the sooting structures of the measured flames, showed in particular that 5% addition of propane (ethane) led to an increase in the soot volume fraction of the ethylene flame by 32% (6%), despite the fact that propane and ethane are less sooting fuels than is ethylene, which is in reasonable agreement with experiments of 37% (14%). The model revealed that with 5% addition of methane, there was an increase of 6% in the soot volume fraction. The average soot particle sizes were only minimally influenced while the soot number densities were increased by the fuel mixing. Further analysis of the numerical data indicated that the chemical cross-linking effect between ethylene and the dopant fuels resulted in an increase in PAH formation, which led to higher soot nucleation rates and therefore higher soot number densities. On the other hand, the rates of soot surface growth per unit surface area through the HACA mechanism were

  3. Computational Enhancements for Direct Numerical Simulations of Statistically Stationary Turbulent Premixed Flames

    KAUST Repository

    Mukhadiyev, Nurzhan

    2017-05-01

    Combustion at extreme conditions, such as a turbulent flame at high Karlovitz and Reynolds numbers, is still a vast and an uncertain field for researchers. Direct numerical simulation of a turbulent flame is a superior tool to unravel detailed information that is not accessible to most sophisticated state-of-the-art experiments. However, the computational cost of such simulations remains a challenge even for modern supercomputers, as the physical size, the level of turbulence intensity, and chemical complexities of the problems continue to increase. As a result, there is a strong demand for computational cost reduction methods as well as in acceleration of existing methods. The main scope of this work was the development of computational and numerical tools for high-fidelity direct numerical simulations of premixed planar flames interacting with turbulence. The first part of this work was KAUST Adaptive Reacting Flow Solver (KARFS) development. KARFS is a high order compressible reacting flow solver using detailed chemical kinetics mechanism; it is capable to run on various types of heterogeneous computational architectures. In this work, it was shown that KARFS is capable of running efficiently on both CPU and GPU. The second part of this work was numerical tools for direct numerical simulations of planar premixed flames: such as linear turbulence forcing and dynamic inlet control. DNS of premixed turbulent flames conducted previously injected velocity fluctuations at an inlet. Turbulence injected at the inlet decayed significantly while reaching the flame, which created a necessity to inject higher than needed fluctuations. A solution for this issue was to maintain turbulence strength on the way to the flame using turbulence forcing. Therefore, a linear turbulence forcing was implemented into KARFS to enhance turbulence intensity. Linear turbulence forcing developed previously by other groups was corrected with net added momentum removal mechanism to prevent mean

  4. Nanocomposite Membrane via Magnetite Nanoparticle Assembly

    KAUST Repository

    Xie, Yihui

    2012-07-01

    Membrane technology is one of the most promising technologies for addressing the global water crisis as well as in many other applications. One of the drawbacks of current ultra- and nanofiltration membranes is the relatively broad pore size distribution. Block copolymer membranes with ultrahigh permeability and very regular pore sizes have been recently demonstrated with pores being formed by the supramolecular assembly of core/shell micelles. Our study aimed at developing an innovative and economically efficient alternative method to fabricate isoporous membrane by self-assembly of magnetic nanoparticle with a polystyrene shell, mimicking the behavior of block copolymer micelle. Fe3O4 nanoparticles of ~13 nm diameter were prepared by co-precipitation as cores. The initiator for ATRP was covalently bonded onto the surface of magnetic nanoparticles with two strategies. Then the surface initiated ATRP of styrene was carried out to functionalize nanoparticles with polystyrene through a “grafting from” method. Finally, the nanocomposite membrane was cast from 50 wt % Fe3O4@PS brush polymer solution in DMF via non solvent phase inversion. Microscopies reveal an asymmetric membrane with a dense thin layer on top of a porous sponge-like layer. This novel class of asymmetric membrane, based on the pure assembly of functionalized nanoparticles was prepared for the first time. The nanoparticles are well distributed however with no preferential order yet in the as-cast film.I would like to thank my committee chair and advisor, Prof. Suzana Nunes, and other committee members, Prof. Klaus-Viktor Peinemann and Prof. Gary Amy, for their guidance and support throughout the course of this research. My appreciation also goes to my colleagues in our group for useful discussions and suggestions. I also want to extend my gratitude to the staff from the KAUST Core Lab for Advanced Nanofabrication, Imaging and Characterization, especially Dr. Ali Reza Behzad, Dr. Rachid Sougrat, and

  5. Nano Antenna Integrated Diode (Rectenna) For Infrared Energy Harvesting

    KAUST Repository

    Gadalla, Mena N.

    2013-01-01

    electrically tested and shown high sensitivity and rectification ability without any bias. Finally, nano antenna integrated diode is under optical testing using   a   10.6μm   2 laser at Electro-Optics Lab, Prince Sultan Advanced Technologies Research Institute (PSATRI), King Saud University due to the unavailability of the measurement setup in KAUST.

  6. Design and Fabrication of a Reconfigurable MEMS-Based Antenna

    KAUST Repository

    Martinez, Miguel Angel Galicia

    2011-06-22

    This thesis presents the design and fabrication of a customized in house Micro-Electro-Mechanical-Systems (MEMS) process based on-chip antenna that is both frequency and polarization reconfigurable. It is designed to work at both 60 GHz and 77 GHz through MEMS switches. This antenna can also work in both horizontal and vertical linear polarizations by utilizing a moveable plate. The design is intended for Wireless Personal Area Networks (WPAN) and automotive radar applications. Typical on-chip antennas are inefficient and difficult to reconfigure. Therefore, the focus of this work is to develop an efficient on-chip antenna solution, which is reconfigurable in frequency and in polarization. A fractal bowtie antenna is employed for this thesis, which achieves frequency reconfigurability through MEMS switches. The design is simulated in industry standard Electromagnetic (EM) simulator Ansoft HFSS. A novel concept for horizontal to vertical linear polarization agility is introduced which incorporates a moveable polymer plate. For this work, a microprobe is used to move the plate from the horizontal to vertical position. For testing purposes, a novel mechanism has been designed in order to feed the antenna with RF-probes in both horizontal and vertical positions. A simulated gain of approximately 0 dB is achieved at both target frequencies (60 and 77 GHz), in both horizontal and vertical positions. In all the cases mentioned above (both frequencies and positions), the antenna is well matched (< -10 dB) to the 50 Ω system impedance. Similarly, the radiation nulls are successfully shifted by changing the position of the antenna from horizontal to vertical. The complete design and fabrication of the reconfigurable MEMS antenna has been done at KAUST facilities. Some challenges have been encountered during its realization due to the immaturity of the customized MEMS fabrication process. Nonetheless, a first fabrication attempt has highlighted such shortcomings. According

  7. High Performance Simulation of Large-Scale Red Sea Ocean Bottom Seismic Data on the Supercomputer Shaheen II

    KAUST Repository

    Tonellot, Thierry

    2017-02-27

    A combination of both shallow and deepwater, plus islands and coral reefs, are some of the main features contributing to the complexity of subsalt seismic exploration in the Red Sea transition zone. These features often result in degrading effects on seismic images. State-of-the-art ocean bottom acquisition technologies are therefore required to record seismic data with optimal fold and offset, as well as advanced processing and imaging techniques. Numerical simulations of such complex seismic data can help improve acquisition design and also help in customizing, validating and benchmarking the processing and imaging workflows that will be applied on the field data. Subsequently, realistic simulation of wave propagation is a computationally intensive process requiring a realistic model and an efficient 3D wave equation solver. Large-scale computing resources are also required to meet turnaround time compatible with a production time frame. In this work, we present the numerical simulation of an ocean bottom seismic survey to be acquired in the Red Sea transition zone starting in summer 2016. The survey\\'s acquisition geometry comprises nearly 300,000 unique shot locations and 21,000 unique receiver locations, covering about 760 km2. Using well log measurements and legacy 2D seismic lines in this area, a 3D P-wave velocity model was built, with a maximum depth of 7 km. The model was sampled at 10 m in each direction, resulting in more than 5 billion cells. Wave propagation in this model was performed using a 3D finite difference solver in the time domain based on a staggered grid velocity-pressure formulation of acoustodynamics. To ensure that the resulting data could be generated sufficiently fast, the King Abdullah University of Science and Technology (KAUST) supercomputer Shaheen II Cray XC40 was used. A total of 21,000 three-component (pressure and vertical and horizontal velocity) common receiver gathers with a 50 Hz maximum frequency were computed in less

  8. Supplementary Material for: DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail

    2016-01-01

    . DASPfind can be accessed online at: http://www.cbrc.kaust.edu.sa/daspfind . Graphical abstract The conceptual workflow for predicting drug-target interactions using DASPfind

  9. Research Funding, Patent Search Training and Technology Transfer: a collaboration

    KAUST Repository

    Tyhurst, Janis

    2016-01-01

    This paper will focus on the collaboration efforts of three different university departments to create, teach and evaluate the benefits of a joint patent training series, as well as the future directions this collaboration will take. KAUST has as one of its goals the diversification of the Saudi economy. There is a strong focus at the university on developing entrepreneurial ideas and commercializing research done. The University Library supports this goal through the provision of electronic resources and introductory patent search training skills. However, the patent training class offered by the University Library is only one step in a process that faculty and students need when starting or taking their research to the next level. In the Fall of 2015, I met with representatives of the two major stakeholders in the patent arena, the office of Sponsored Research (OSR) and the Technology Transfer Office (TTO), to develop a patent training program to meet the needs of researchers. The OSR provides funding to researchers who have demonstrated that their ideas have merit with potential applications, the TTO works with researchers who are at the point of needing IP protection. The resulting discussion led us to collaborate on creating a workshop series that benefit the researcher’s information needs and each of our departments as well. In the first of the series of three 2 hour workshops, the Manager of TTO and the Lead Integrative Specialist from the OSR presented a workshop on an overview of Intellectual Property and the patenting process. These presentations focused on when and how to determine whether research is potentially patentable, why a researcher needs to protect his/her research and how to go about protecting it. The second workshop focused on introductory patent search skills and tools, how to expand a literature search to include the information found in patents, and how this kind of research will improve not only the literature search but the research

  10. PREFACE: 3rd International Symposium ''Optics and its Applications''

    Science.gov (United States)

    Calvo, M. L.; Dolganova, I. N.; Gevorgyan, N.; Guzman, A.; Papoyan, A.; Sarkisyan, H.; Yurchenko, S.

    2016-01-01

    SPIE under the Federation of Optics College and University Students (FOCUS) conference grant, as well as contributions from other organizations: the Abdus Salam International Center for Theoretical Physics (ICTP), the Optical Society (OSA), the Laboratory of Terahertz Technology of Bauman Moscow State Technical University (BMSTU), the RAU, the LT-Pyrkal, the King Abdullah University of Science and Technology (KAUST), IPR of NAS, and Ritea.

  11. PREFACE: X Meeting on Recent Advances in the Physics of Fluids and their Applications

    Science.gov (United States)

    Saita, Fernando Adolfo; Giavedoni, María Delia

    2009-07-01

    The X Meeting on Recent Advances in Physics of Fluids and Related Applications (Fluids 2008) was held in Santa Fe, Argentina, on 19-21 November 2008. It belongs to a series of meetings that started in 1989 and has continued - except for just one occasion - every other year. Thus, the first meeting took place in the city of Tandil in 1989 followed by three events in the city of La Plata (1991-93-95), Tunuyán (Mendoza) in 1997, Paraná (Entre Rios) in 1999, Buenos Aires in 2001, Tandil in 2003 and Mendoza in 2006. These meetings gather together most of the people working in Fluid Mechanics and related problems in Argentina. The objective of the meetings is to provide a forum to facilitate the interactions between participants in a friendly academic atmosphere. This goal is achieved by means of lectures and technical presentations on different subjects and from different points of view, the only constraint being the current academic/technical interest. Applications usually deal with problems of local interest. In the present meeting a variety of lecture topics were presented, among them we might mention Capillary Hydrodynamics, Wetting, Density Currents, Instabilities, Elastic-Dynamics, Flows in Porous Media, Sediment Transport, Plasma Dynamics, etc. In particular, we would like to highlight the specially invited lectures given by Dr Ramon Cerro (Chemical and Material Engineering Department University of Alabama in Huntsville, USA), Dr David Quéré (Physique et Mécanique des Milieux Hétérogènes ESPCI, FRANCE), Dr Marcelo García (College of Engineering University of Illinois at Urbana-Champaign) and Dr Víctor Calo (Earth and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST) and Institute for Computational Engineering and Sciences (ICES), University of Texas at Austin). In addition, we had 18 invited talks and more than fifty contributions that were presented in poster sessions. On behalf of both the Honorary

  12. Macroscopic Properties of Hollow Cone Spray Using an Outwardly Opening Piezoelectric Injector in GCI Engine

    KAUST Repository

    Cheng, Penghui

    2016-07-01

    Fuel mixture formation and spray characteristics are crucial for the advancement of Gasoline Compression Ignition (GCI) engine. For investigations of spray characteristics, a high-pressure high-temperature spray chamber with constant volume has been designed, tested and commissioned at CCRC, KAUST. Back light illumination technique has been applied to investigate the macroscopic spray properties of an outwardly opening piezoelec- tric injector. Three parameters including injection pressure, ambient pressure, and ambient temperature have been involved. A total of 18 combinations of experimental conditions were tested under non-reactive conditions. Through qualitative analysis of spray morphology under different operating conditions, an apparent distinction of spray morphology has been noticed. Spray morphology and propagation have shown strong dependencies on ambient pressure and ambient tempera- ture while injection pressure has a negligible effect on spray shape. Increasingly compact and bushier spray patterns were observed in the cases of high ambient pressure due to in- creasing aerodynamic drag force on spray boundary. It should also be noted that ambient temperature plays a fairly important role in fuel evaporation rate. At 200 °C, oscillating and considerably short spray shape was produced. Also, circumferential ring-like vortices and distinctive string-like structures have been identified for the fuel spray exiting this hollow cone injector. It has been observed that high ambient pressure conditions (Pamb = 4 bar and 10.5 bar) are favorable to the vortices generation, which has also been reported in previous literature. The quantitative description of macroscopic spray properties reveals that ambient pres- sure and ambient temperature are found to be the most influential parameters on liquid penetration length. The rise of ambient pressure results in considerably shorter liquid pen- etration length. Ambient temperature also appears to be a very effective

  13. MaMiCo: Transient multi-instance molecular-continuum flow simulation on supercomputers

    Science.gov (United States)

    Neumann, Philipp; Bian, Xin

    2017-11-01

    We present extensions of the macro-micro-coupling tool MaMiCo, which was designed to couple continuum fluid dynamics solvers with discrete particle dynamics. To enable local extraction of smooth flow field quantities especially on rather short time scales, sampling over an ensemble of molecular dynamics simulations is introduced. We provide details on these extensions including the transient coupling algorithm, open boundary forcing, and multi-instance sampling. Furthermore, we validate the coupling in Couette flow using different particle simulation software packages and particle models, i.e. molecular dynamics and dissipative particle dynamics. Finally, we demonstrate the parallel scalability of the molecular-continuum simulations by using up to 65 536 compute cores of the supercomputer Shaheen II located at KAUST. Program Files doi:http://dx.doi.org/10.17632/w7rgdrhb85.1 Licensing provisions: BSD 3-clause Programming language: C, C++ External routines/libraries: For compiling: SCons, MPI (optional) Subprograms used: ESPResSo, LAMMPS, ls1 mardyn, waLBerla For installation procedures of the MaMiCo interfaces, see the README files in the respective code directories located in coupling/interface/impl. Journal reference of previous version: P. Neumann, H. Flohr, R. Arora, P. Jarmatz, N. Tchipev, H.-J. Bungartz. MaMiCo: Software design for parallel molecular-continuum flow simulations, Computer Physics Communications 200: 324-335, 2016 Does the new version supersede the previous version?: Yes. The functionality of the previous version is completely retained in the new version. Nature of problem: Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics or another particle-based solver whereas large parts are covered by a mesh-based CFD solver, e.g. a lattice Boltzmann automaton. Solution method: We couple existing MD and CFD solvers via MaMiCo (macro-micro coupling tool). Data exchange and

  14. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    (PROSTA) family of pairwise structure alignment methods [1, 2] that address the fragmentation issue of pockets and interfaces, and automatically align interfaces between any types of biological complexes. Our PROSTA structure alignment methods have two critical advantages comparing to existing structure alignment methods. First, our methods are completely sequence order independent, which is critical to the success of pairwise pocket and interface structure alignments. This is achieved by introducing contact groups that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially model the topology of the global structure. Comparing to existing methods that focus on local structure or whole sequence similarities, topological similarities are more reliable to find near-optimal structure alignments in the initial alignment state. As a result, a significant number of similar pockets and interfaces are newly discovered, and literatures also support that similar functions are shared between biological complexes in our cases studies. The PROSTA web-server and source codes are publicly available at "http://www.cbrc.kaust.edu.sa/prosta/".

  15. Low cost and conformal microwave water-cut sensor for optimizing oil production process

    KAUST Repository

    Karimi, Muhammad Akram

    2015-08-01

    novel reusable 3D-printed mask based fabrication was also successfully implemented, which would resemble screen printing if it were to be implemented in 3D. In order to verify the design’s applicability for the actual scenario of oil wells, where an oil/water mixture is flowing through the pipes, a basic flow loop was constructed in the IMPACT laboratory at KAUST. The dynamic measurements in the flow loop showed that the WC sensor design is also equally applicable for flowing mixtures. The proposed design is capable of sensing the WC with a fine resolution due to its wide sensing range, in the 80 – 190 MHz frequency band. The experimental results for these low cost and conformal WC sensors are promising, and further characterization and optimization of these sensors according to oil field conditions will enable their widespread use in the oil industry.

  16. Gain-Enhanced On-Chip Antenna Utilizing Artificial Magnetic Conductor Reflecting Surface at 94 GHz

    KAUST Repository

    Nafe, Mahmoud

    2015-08-04

    . Unlike conventional ground plane reflecting surfaces, AMC surfaces generally enhance the radiation and impedance characteristics of close-by antennas. Based on this property, a ring-based AMC reflecting surface has been designed in the oxide layer for on-chip antennas operating at 94 GHz. Furthermore, a folded dipole antenna with its associ- ated planar feeding structures has been optimized and integrated with the developed ring-based AMC surface. The proposed design is then fabricated at KAUST clean- room facilities. Prototype characterization showed very promising results with good correlation to simulations, with the antenna exhibiting an impedance bandwidth of 10% (90-100 GHz) and peak gain of -1.4 dBi, which is the highest gain reported for on-chip antennas at this frequency band without the use of any external o↵-chip components or post-fabrication steps.