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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 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 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 included the animation of facial expressions in primates in collaboration with Steven Suomi and Annika Paukner. The group also completed medical illustrations for Paraganglioma and Pheochromocytoma in collaboration with Stephanie Fliedner and Karel Pacak.
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 updated and maintained 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 90 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 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 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 and expanded its services to our DIR 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 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 in the Rockledge Data Center. This year, license hosts were added for Amira, ArrayStar and QSeq, Autodesk Maya, DNASTAR Lasergene Core Suite, MathWorks MATLAB and SeqMan NGen. Hosting these titles permits users to leverage their research with additional tools available on Helix and Biowulf.
Data Recovery Services: We invested in and expanded data recovery capabilities for all media—hard drive, SSD, and flash and magnetic media (including DLT). In addition to the RAID 0 and 5 recovery tools added last year, Forencis Lab tools were added. Since 2005, the Unit has recovered hundreds of gigabytes of research data from failed drives and media, at a substantial savings to the DIR 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.