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Research Informatics Support for the Division of Intramural Research

Chandan Sastry, PhD
  • Chandan Sastry, PhD, Head, Unit on Computer Support Services
  • Marco Crosby, Program Engineer
  • John Czapary, BS, Laboratory Technical Manager
  • Michelle Duverneau, IT Specialist
  • Erin Fincher, BA, 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.

Clinical informatics

During the past year, the Unit on Computer Support Services (UCSS) 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 320, with an expansion of research questions to over 150,000. Our software development group completed five releases that included features for quality assurance, clinical monitoring, and reporting. We enhanced the Clinical Trial Survey System, an application for patient surveys, with two software releases, and the total enrollment rose to 105 protocols. The Clinical Datamart and wiki were upgraded to support new protocols.

Biological visualization web services

The UCSS team provides DIR laboratories with scientific communications and media services, including publication support, website support, audio visuals, medical arts, and print media.  A student training program provides opportunities for cross-disciple research in the areas of molecular animation, web programming, microscopy and digital imaging, and medical illustration. In collaboration with NIAID and NLM, the group was selected this year by the HHS Secretary to join the HHSignite program to develop the NIH 3D Printing Exchange. This virtual collection of biomedical 3-D printing files and tutorials will become a public resource for biomedical scientists.

The web activities of the DIR web services program include, e.g., laboratory websites, annual report, and internet applications. One of the applications developed was the on-line annual report and survey modules for research and administrative questionnaires. The UCSS continued to maintain approximately 50 public DIR websites and developed graphic designs and medical illustrations for several projects: the DIR Annual Fellows and PI (principal investigator) Retreats, the NIH Research Festival, USA Science and Engineering Festival, STEM Career Festival, NICHD 50th Anniversary, and the NICHD Exchange series. The team also expanded the Science@NICHD wiki (http://science.nichd.nih.gov) to over 168 projects, including the NICHD Connection, a monthly newsletter for Intramural research fellows. The Science wiki allows PIs 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.

Bioinformatics

During the past year, the bioinformatics team assisted the 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.

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.

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 University of California Santa Cruz (UCSC) server.

Core IT services

The Unit continued to expand 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, 3-D 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 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 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.

Additional Funding

  • The Clinical Trials Database (CTDB) project receives funding from other Intramural IC programs, including NINR, NIMH, NIDCR, NIEHS, NIAMS, NINDS, and NIDDK.

Publications

  1. Sastry C, Breymaier M, Ivusic S, Idriss A, Caruso T, Annechiarico R. Government-developed software for clinical research - open-season on open-source: the NICHD Clinical Trials Database (CTDB) and Toolkit (CTK) development and adoption Strategy. J Am Med Inform Assoc 2013;submitted.
  2. Lubkowski P, Curry M, Swan J, Ozarslan E, Komlosh M, Irfanoglu M, Basser P, Sastry C. Biovisualization: elucidating diffusion tensor MRI and other medical imaging data using a video game engine. NIH Summer Research Festival 2012 (Poster).
  3. Swan J, Idriss A, Peterson D, Claus J, Singh S, Crosby M, Breymaier M, Ivusic S, Jonas N, Mrozek T, Arceri K, Vu L, Duverneau M, Czapary J, Sastry C. Research informatics support for the Division of Intramural Research. DIR Annual Retreat 2010;51.
  4. 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.

Collaborators

  • Peter Basser, PhD, Program on Pediatric Imaging and Tissue Sciences, NICHD, Bethesda, MD
  • Darrell Hurt, PhD, Bioinformatics and Computational Biosciences Branch, NIAID, 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
  • Steven Stanhope, PhD, University of Delaware, Newark, DE
  • 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 and Developmental Neuroscience Branch, NIMH, Bethesda, MD
  • Jack Yanovski, MD, PhD, Program in Developmental Endocrinology and Genetics, NICHD, Bethesda, MD

Contact

For more information, email sastrych@mail.nih.gov

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