The Computer Support Services Core provides informatics and research services to NICHD investigators in four key areas: clinical informatics, bioinformatics, biovisualization web services, and core IT support.
The team supports and develops 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 210, with an expansion of research questions to 70,000. Our software development group completed five releases that included the following application features: an advanced biospecimen management feature for barcode printing, the eRegulatory binder, and a third-party validation module. We enhanced the Clinical Trial Survey System, an application for patient surveys, with two software releases, and the total enrollment rose to 26 protocols. We enhanced the Clinical Datamart and wiki to support new protocols.
Biological Visualization Web Services
This area focuses on visualizing cellular and molecular biological processes. The bio-visualization program provides training opportunities for cross-disciplinary research in the areas of molecular animation, web programming, microscopy and digital imaging, and medical illustration.
The web team also supports the DIR web services program (e.g., laboratory websites, annual report, and internet applications). Applications developed included the online annual report and survey modules for research and administrative questionnaires. The group updates and maintains approximately 100 DIR websites and develops graphic designs and medical illustrations for several projects. The team also expanded the Science@NICHD wiki (science.nichd.nih.gov) to over 90 projects, including
The NICHD Connection, a monthly newsletter for intramural research fellows. The wiki enables principal investigators to create blogs and share documents/data in a secure manner.
The bioinformatics team assists the NICHD Molecular Genetics Core with high-throughput sequencing data collection and analysis. The group also develops research tools to assist investigators with genomic data management and analysis. For example, the GermSAGE application was created as a web tool to automate access to a collection of male germ-cell transcriptome data 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). 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
Network and Desktop Services: The team serves as a key component of the NICHD IT services group to ensure that all DIR investigators and staff have reliable, secure, and efficient IT solutions. This includes acquisition, maintenance, and support for site licenses e.g., EndNote, QUOSA; network services (e-mail, data backups, VPN, helix, PDAs, wireless configurations); and cross-platform desktop, server and application hosting.
Data Recovery Services: We have invested in and expanded data recovery capabilities for all media—hard drive, SSD, and flash and magnetic media (including DLT).
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 investigators to comply with NIH's Public Access policies. The team completed four major production releases, including user support for all DIR programs.