This project is a core service for the Division of Intramural Research. It focuses on the development of informatics tools to support multiple investigators and a variety of disease areas. The project supports four key areas: clinical informatics, bioinformatics, biovisualization web services, and scientific 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 280, with an expansion of research questions to 70,000. Our software development group completed eight releases that included the following application features: QA/QC module, electronic regulatory binder, features for the biorepository module, and electronic signatures. The project obtained 21CFR Part 11 compliance. 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 50 protocols. The Clinical Datamart and Wiki were enhanced to support clinical data integration. 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 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 2012 DIR annual retreat program, the DIR Annual Spring Research Festival, and the NICHD Exchange on stem cells. The team also expanded the ScienceNICHD wiki (science.nichd.nih.gov) to over 150 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. Bioinformatics - During the past year, the bioinformatics team continued to assist the core 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. Scientific Informatics and Management - This area provides network and desktop services to ensure investigators and staff have reliable, secure, and efficient information technology solutions. Custom data recovery methods are developed for all media (hard drive, SSD, flash and magnetic media, DLT) associated with scientific instrumentation. This project area also develops custom software applications for scientific management. 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 two major production releases, including user support for all DIR programs.
|Huser, Vojtech; Sastry, Chandan; Breymaier, Matthew et al. (2015) Standardizing data exchange for clinical research protocols and case report forms: An assessment of the suitability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM). J Biomed Inform 57:88-99|
|Cheung, Hoi-Hung; Claus, Janek; Singh, Sumeeta et al. (2013) Mapping Genomic Features of Tiling Microarray Data by TileMapper. Methods Mol Biol 1067:225-33|
|Lee, Tin-Lap; Li, Yunmin; Cheung, Hoi-Hung et al. (2010) GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development. Bioinformatics 26:585-6|
|Lee, Tin-Lap; Cheung, Hoi-Hung; Claus, Janek et al. (2009) GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development. Nucleic Acids Res 37:D891-7|