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Research Informatics Support for the Division of Intramural Research
- Chandan Sastry, PhD, Head, Unit on Computer Support Services
- Chandan Sastry, PhD, Head, Unit on Computer Support Services
- Marco Crosby, Program Engineer
- John Czapary, BS, Laboratory Technical Manager
- Michelle Duverneau, IT Specialist
- Yumiko Shepherd, BA, Intramural Research Training Award Fellow
- Melissa Sisk, BS, MS, Intramural Research Training Award Fellow
- Pawel Lubkowski, Summer Student
Our team provides informatics and research services to Intramural investigators at NIH in four key areas: clinical informatics, bioinformatics, biovisualization web services, and core IT support.
During the past year, we continued to support and develop applications related to clinical and translational medicine, including the Clinical Trials Database (CTDB) project. Such informatics tools allow researchers to design, collect, and report clinical observations related to natural history and interval-based studies. The total number of protocols and research projects supported by the CTDB team increased to approximately 300, with an expansion of research questions to over 100,000. Our software development group completed six releases that included advanced biorepository features as well as functions to support regulatory audits. We enhanced the Clinical Trial Survey System, an application for patient surveys, with two software releases, and the total enrollment rose to 70 protocols. The Clinical Datamart and wiki were upgraded to support new protocols.
Biological visualization web services
This student-led research area focuses on visualizing cellular and molecular biological processes. The bio-visualization program provides training opportunities for cross-disciple research in the areas of molecular animation, web programming, microscopy and digital imaging, and medical illustration. This year, in collaboration with Steven Suomi and Annika Paukner, the students continued to expand the animation project related to facial expressions in primates. The group also completed medical illustrations and graphics for multiple Division of Intramural Research (DIR) Investigators.
The web team also supports the DIR web services program (e.g., laboratory websites, annual report, and internet applications). Applications developed included the on-line annual report and survey modules for research and administrative questionnaires. The group continued to maintain approximately 100 DIR websites and developed graphic designs and medical illustrations for several projects: the 2011 DIR annual retreat program, the DIR Annual Spring Research Festival, and the NICHD Exchange series. The team also expanded the Science@NICHD wiki (science.nichd.nih.gov) to over 120 projects, including the NICHD Connection, a monthly newsletter for Intramural research fellows. The Science wiki allows principal investigators to create blogs and share documents/data in a secure manner. As part of this project, the group collaborated with the NIH Library, the NLM, the NINDS, and the NIH Office of the Director.
During the past year, the bioinformatics team assisted the new Molecular Genetics Laboratory with data collection and analysis for high-throughput sequencing. The scientific informatics group also develops research tools to assist investigators with genomic data management and analysis. The GermSAGE application was created as a web tool to automate access to a collection of male germ-cell transcriptome information derived from Serial Analysis of Gene Expression (SAGE). The application includes the three key germ cell stages in spermatogenesis: mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries, making them by far the most comprehensive resource available. TileMapper was developed as a comprehensive web-based tool for mapping various genomic annotation features to the tiling microarray data derived from transcriptome, ChIP-chip, or MeDIP studies. The data are visualized in a tabulated format, which permits flexible processing, and further analyzed by downstream pipelines to relate the data and perform interactions analysis. TileMapper accepts transcribed-fragments (transfrag) information in Browser Extensible Display (BED) format generated from Affymetrix Integrated Genome Browser (IGB) or downloaded from the UCSC server. The SageWorks application was maintained and transitioned to a new server to leverage the robust public databases available in combination with the SAGE data to accelerate gene and pathway discovery. This workspace accommodates any SAGE data and provides storage of large datasets. With built-in navigation/search toolsets and automated updates, SAGEWorks enables the scientific community to minimize the redundancy of manual manipulation.
Core IT services
The Unit continued to expanded its services to our DIR research community in core IT areas.
Network and Desktop Services
We serve as a key component of the NICHD IT services group to ensure that all DIR investigators and staff have reliable, secure, and efficient information technology solutions. This includes acquisition, maintenance and support for licensed software used by our DIR research community e.g., EndNote, Bookends, GraphPad Prism, PyMol, network services (e-mail, data backups, VPN, helix, PDAs, wireless configurations); and cross-platform desktop, server and application hosting in the Rockledge Data Center. We host software licenses for computation, 3D imaging and sequencing e.g., Amira, ArrayStar and QSeq, Autodesk Maya, DNASTAR Lasergene Core Suite, MathWorks MATLAB, MolSoft and SeqMan NGen. This year, MATLAB Distributed Computing Server, software and hardware (128GB, 16 Worker), has been added. Hosting these licenses permits users to leverage their research with additional tools available on Helix and Biowulf. We also assist users in specifying and purchasing custom hardware configurations to match research instrument requirements.
Data Recovery Services
We have invested in a suite of data recovery tools for all media—hard drive, SSD, and flash etc., including RAID 0 and 5 recovery tools. Since 2005, the Unit has recovered hundreds of gigabytes of research data from failed drives and media, at a substantial savings to the DIR research budget.
Custom Software Development
We develop custom software applications for DIR services. For example, we continued to enhance the Manuscript Tracking System (MTrac), a web-based application that automates the clearance and approval process for manuscripts in the DIR. The system now includes a web service feature to connect to NLM PubMed and File Transfer Process (FTP) connections to PubMed Central to allow PIs to comply with NIH's Public Access policies. The team completed four major production releases, including user support for all DIR programs. The Unit also began the requirements process for an automated travel log system to streamline travel requests. The core IT services team currently supports the DIR Administrative Management Branch (AMB) with custom reports and spreadsheets for DIR budget program planning sessions.
- The Clinical Trials Database (CTDB) project receives funding from other Intramural IC programs, including NINR, NIMH, NIDCR, NIEHS, NIAMS, and NIDDK.
- Pawel Lubkowski, Michael Curry, Jeremy Swan, Evren Ozarslan, Michal Komlosh, Mustafa Irfanoglu, Peter Basser, Chandan Sastry. Biovisualization: Elucidating Diffusion Tensor MRI and Other Medical Imaging Data Using a Video Game Engine. NIH Summer Research Festival 2012;(Poster).
- Jeremy Swan, Asma Idriss, Donna Peterson, Janek Claus, Sumeeta Singh, Marco Crosby, Matt Breymaier, Sean Ivusic, Nichole Jonas, Tim Mrozek, Ken Arceri, Loc Vu, Michelle Duverneau, John Czapary, Chandan Sastry. Research Informatics Support for the Division of Intramural Research. DIR Annual Retreat 2010;51.
- Lee TL, Cheung HH, Claus J, Sastry C, Singh S, Vu L, Rennert O, Chan WY. GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development. Nucleic Acids Res 2009;37:D891-897.
- Peter Basser, PhD, Program on Pediatric Imaging and Tissue Sciences, NICHD, Bethesda, MD
- Gabor Illei, MD, PhD, MHS, Molecular Physiology and Therapeutics Branch, NIDCR, Bethesda, MD
- Lynnette Nieman, MD, Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
- Karel Pacak, MD, PhD, DSc, Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
- Annika Paukner, PhD, Section on Comparative Behavioral Genetics, NICHD, Poolesville, MD
- Forbes D. Porter, MD, PhD, Clinical Director, NICHD, Bethesda, MD
- Owen Rennert, MD, Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
- Leorey Saligan, PhD, RN, CRNP, Deputy Clinical Director, NINR, Bethesda, MD
- Peter Schmidt, MD, Section on Behavioral Endocrinology, NIMH, Bethesda, MD
- Monica Skarulis, MD, Clinical Endocrine Section, NIDDK, Bethesda, MD
- Constantine Stratakis, MD D(med)Sci, Program in Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
- Stephen Suomi, PhD, Section on Comparative Behavioral Genetics, NICHD, Bethesda, MD
- Susan Swedo, MD, Pediatrics & Developmental Neuroscience Branch, NIMH, Bethesda, MD
- Jack Yanovski, MD, PhD, Program in Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
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