Skip to main content

Home > Unit on Computer Support Services

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, Technical Laboratory Manager
  • Michelle Duverneau, IT Specialist
  • Timothy Mrozek, BA, IRTA
  • Ken Arceri, BS, IRTA

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). This web-based tool allows 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 170, with an expansion of research questions to 50,000. Our software development group completed eight releases that included the following application features: a virtual biorepository module for specimen tracking, an enhanced security feature for login/password management, and a data collection feature that does not involve patient data. The group also improved the Java-based barcode applet to allow PIs to print labels using the CTDB biorepository module completed for clinical sample tracking. The Clinical Trial Survey System, an application for patient surveys, was enhanced with two software releases, and the total enrollment rose to 26 protocols. The team deployed the Patient Recruitment and Enrollment Portal (PREP) to allow investigators to dynamically create and manage recruitment websites for their studies. The Clinical Datamart and Wiki were enhanced to support new protocols.

Biological visualization web services

A 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. The student projects completed included the animation of facial expressions in primates in collaboration with Steven Suomi and Annika Paukner.

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 a survey module used for research and administrative questionnaires. The group updated and maintained approximately 90 DIR websites, and developed graphic designs and medical illustrations for multiple projects: the 2010 DIR annual retreat program, the DIR Annual Spring Research Festival, and the NICHD Exchange on stem cells. The team also expanded the Science@NICHD wiki (science.nichd.nih.gov) to over 80 projects. This includes 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 new Molecular Genetics Laboratory with high-throughput sequencing data collection and analysis. 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 their SAGE data to assist in the acceleration of gene and pathway discovery. This workspace accommodates any SAGE data and provides storage of large data sets. With built-in navigation/search toolsets and automated updates, SAGEWorks allows the scientific community to minimize the redundancy of manual manipulation.

Core IT services

The Unit continued its services to the DIR staff members in key core IT areas.

Network and Desktop Services: The Unit serves 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 support for site licenses (e.g., EndNote, GenoMatix, QUOSA), desktop (PC, Mac), server and application hosting in the Rockledge Data Center, and network services (e-mail, data backups, VPN, helix, PDAs, wireless configurations).

Data Recovery Services: The UCSS invested and expanded its data recovery capabilities for all media — hard drive, SSD, flash and magnetic media (including DLT). This year RAID 0 and 5 recovery tools were added, resulting in two successful RAID recoveries. Over the past several years, the UCSS has recovered hundreds of gigabytes of research data from failed drives and media, at a substantial savings to the DIR budget.

Custom Software Development: The UCSS team develops custom software applications for DIR services. For example, the Unit 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, and NIDDK.

Publications

  • 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.

Collaborators

  • Raymond Dionne, DDS, PhD, Scientific Director, NINR, Bethesda, MD
  • Jane Fall-Dickson, PhD, RN, Laboratory of Symptom Management, NINR, Bethesda, MD
  • Gabor Illei, MD, PhD, MHS, Molecular Physiology and Therapeutics Branch, NIDCR, Bethesda, MD
  • Lynnette Nieman, MD, Program on Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
  • Annika Paukner, PhD, Section on Comparative Behavioral Genetics, Poolesville, MD
  • Owen Rennert, MD, Program on Reproductive and Adult Endocrinology, NICHD, 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 on Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
  • Pamela Stratton, MD, Gynecology Consult Service, NICHD, Bethesda, MD
  • Stephen Suomi, PhD, Section on Comparative Behavioral Genetics, NICHD, Bethesda, MD
  • Susan Swedo, MD, Pediatrics & Developmental Neuroscience Branch, NIMH, Bethesda, MD
  • Marian Tanofsky-Kraff, PhD, Program on Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
  • Jack Yanovski, MD, PhD, Program on Developmental Endocrinology and Genetics, NICHD, Bethesda, MD

Contact

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

Top of Page