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 informatics systems and services support NICHD researchers and investigators from other programs at NIDCR, NINR, NIDCR, NIMH, NIAMS, and NIDDK. The Unit supports four key areas: clinical informatics, bioinformatics, biovisualization web services, and core IT support. CLINICAL INFORMATICS During the last 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 supported by the CTDB support team increased to approximately 110, with an expansion of research questions to 35,000. Our software development group completed four major releases that included the following application features: a data-coordinating center module for multi-site studies, a Java-based web service to connect to the NLM Unified Medical Language System (UMLS) to obtain medical codes (SNOMED and LOINC), and software integration (Oracle 10g, Solaris 10, Java, Tomcat, and Apache). The group also completed a Java-based barcode applet to allow PIs to print labels using the CTDB biorepository module completed for clinical sample tracking. Together with several PIs at NICHD and the NIDCR, the support team initiated a pilot phase for the Sample Tracking Module. The Clinical Trial Survey System, an application for patient surveys, was enhanced with three software releases, adding features for skip rules and PDA usage. The total enrollment was increased to 19 protocols. The Clinical Datamart star schema and reporting structure was enhanced to support research and hospital data integration. This design accomomdates clinical and genomic family history data, and biospecimens. The total number of protocol reports designed increased to 220. The team developed an integration with a Cognos engine for additional reporting functionality and expanded the existing CTDB Datamart with additional FACT tables. The Clinical Wiki was also advanced to improve communications for clinical research. Collaborative web portals were created for the OB/GYN services, pediatric endocrinology, biomedical education, and other laboratories within the Division of Intramural Research (DIR). BIOLOGICAL VISUALIZATION AND WEB SERVICES This student-led research area focuses on visualizing cellular and molecular biological processes. The biovisualization 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 the Golgi project in collaboration with J. Lippincott-Schwartz, who presented the work at the Golgi conference in Italy. A Golgi rapid prototype three-dimensional model was created and accepted into the Golgi Museum in Pavia, Italy. The group redesigned and architected a new DIR Website based on the revised organizational structure of program areas. The team also supports the DIR web services program (e.g., laboratory websites, annual report, and internet applications). The group updated and maintained approximately 90 DIR websites, and developed graphic designs and medical illustrations for multiple projects: DIR annual retreat program, the Graduate Partnerships Program brochure for the Office of Education, DIR Annual Spring Research Festival, ClinicalTrial Tool Kit (CTK) brochure, and NICHD Summer Program t-shirt. The team also expanded the ScienceNICHD wiki (science.nichd.nih.gov) to over 30 projects. This tool 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 to conduct a wiki workshop for NIH Intramural Investigator BIOINFORMATICS The scientific informatics group continued development of 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 with 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 enables 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 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 (email, data backups, VPN, helix, PDAs, wireless configurations). 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 six major production releases, including user training for all DIR programs. The Unit also began the requirements process for an administrative datamart. This business intelligence tool will enable PIs to query and analyze data from Personnel, Budget, MTrac, and other admininstrative systems. The core IT services team currently supports the DIR Administrative Management Branch (AMB) with custom reports and spreadsheets for DIR budget program planning sessions.
