OpenFreezerTM: an information management system for reagent tracking and workflow automation
Sunday, July 20 - 10:45 a.m. - 11:10 a.m.
Room: 714
Presented by: Marina Olhovsky, Mount Sinai Hospital, CA
Abstract:
The importance of information integrity in biomedical research elevates the demand for a central content management system to ensure consistent data storage, easy retrieval, and user-friendly output. We present OpenFreezerTM, a web-based LIMS designed to provide support to biological laboratories by uniformly organizing reagents and experimental results and presenting them to researchers. At the core of the system is a repository of reagents available within the laboratory, their sequences, features, nomenclature and physical locations, and a GUI for searching reagents within the repository and viewing them online. OpenFreezerTM also provides computation and workflow automation tools, such as vector sequence constitution from its insert and backbone vector sequences, automated cDNA to protein translation, primer design, and mass spectrometry result tracking OpenFreezerTM implements platform- and browser-independent three-layer client-server architecture. The data layer is provided by a highly normalized (3NF) SQL database running on a MySQL server. The domain logic layer implementation employs CGI technology and OO principles. The presentation layer is a graphical user interface written in PHP and DHTML. This architecture facilitates rapid development of new modules and improvement of existing ones, better error handling, easy client- and server-side configuration and maintenance, thus achieving application robustness, portability and scalability.
In this presentation we will demonstrate to you each of the components of OpenFreezerTM, show how to search the repository, add new reagents and modify existing clones in the system, view reagent locations, design primers, create new projects, add users and laboratories.
Presentation PDF: http://www.iscb.org/uploaded/css/26/4121.pdf
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OmicsExplorer
Sunday, July 20 - 11:15 a.m. - 11:40 a.m.
Room: 714
Presented by: Pei Hao, Shanghai Center for Bioinformation Technology (SCBIT), CN
Abstract:
OmicsExplorer is designed to provide online analyses powered by workflow technology to provide rapid and modular design for the website. In the current version of the OmicsExplorer five major categories of analysis workflows, such as genomics level data analysis, sequence based evolutionary analysis, biochemical analysis, text-mining and bio-statistics, are integrated together to meet basic requirements of life science researchers in the post genome era. Such an integrated web service platform is expandable, module re-combination flexible and easy to use. OmicsExplorer is a website that is free and open to all users offering a range of multi-omics analysis services. OmicsExplorer is really a new technology of constructing research platform for integration bioinformatics data analysis.
Presentation PDF: http://www.iscb.org/uploaded/css/26/4097.pdf
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BONDplus - Challenges in Translational Medicine
Sunday, July 20 - 12:15 p.m. - 12:40 p.m.
Room: 714
Presented by: Eric Andrade and Sam Sgro, Thomson Reuters,
Abstract:
Translational medicine refers to the process of transferring insights and discoveries from the laboratory to clinical practice. Often referred to as “bench to bedside treatment”, translational medicine connects information on core molecular biology with clinical therapeutics to improve accuracy and outcomes.
Thomson Reuters (TR) provides key molecular and clinical content to over 20 million life science researchers and professionals worldwide. Increasingly, TR is being asked by researchers to provide integrated proprietary data from traditionally discrete biological domains. For example, integrating our reference protein-protein interaction databases alongside reference drug and clinical trial databases can assist researchers in assessing predicted biomarkers or accelerate drug repurposing efforts.
This presentation discusses the challenges faced by TR in trying to integrate these disparate content sources, as well as how such an integrated platform could benefit commercial and academic ventures. We will discuss a concrete example of how an integrated Translational Medicine platform could suggest alternate uses for a known pharmaceutical agent.
Presentation PDF: http://www.iscb.org/uploaded/css/26/10078.pdf
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Next Generation of Selected Bioinformatics Applications: Using Massively Parallel Supercomputers
Sunday, July 20 - 2:15 p.m. - 2:40 p.m.
Room: 714
Presented by: Carlos P. Sosa, IBM and University of Minnesota, USA
Abstract:
Next Generation of Selected Bioinformatics Applications: Using Massively Parallel Supercomputers
In bioinformatics, databases for sequence search play a key role in elucidating and annotating unknown queries, such as proteins. One of the challenges that scientists face is that these databases have been growing exponentially in size. As a result, faster sequence-search algorithms as well as more sophisticated and faster computers to search these databases continue to evolve and provide new avenues to handle very time-consuming searches. Tools such the Basic Local Alignment Search Tool (BLAST) from the National Center for Biotechnology Information and the hidden Markov model-based programs such as HMMER continue to improve; however, they cannot keep up with the rate at which the database is exponentially increasing in size. Therefore, parallel implementations have emerged to address this problem. The performance of such implementations depends on a myriad of factors including algorithmic and architectural. In this study, we describe our efforts to parallelize and optimize the performance of applications such as BLAST and HMMER.
Presentation PDF: http://www.iscb.org/uploaded/css/26/4096.pdf
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Beyond Next Gen Sequencing: Applying Bioinformatics to Obtain Biological Answers
Sunday, July 20 - 2:45 p.m. - 3:10 p.m.
Room: 714
Presented by: Arif Anwar, Synamatix Sdn Bhd, MY
Abstract:
Presentation PDF: http://www.iscb.org/uploaded/css/26/4099.pdf
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Drug Discovery
Sunday, July 20 - 3:15 p.m.- 3:40 p.m.
Room: 714
Presented by: Greg Tucker-Kellogg, Lilly Singapore Centre For Drug Discovery Pte Ltd,
Abstract:
Presentation PDF:
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