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 is approximately 412 across 14 NIH institutes, addressing more than 180,000 research questions. The Clinical Trial Survey System is an application for patient surveys. The Clinical Datamart includes vitals, medications, and ECG/EKG datamarts and supports new protocols.
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. 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 SageWorks application leverages the robust public databases available in combination with the SAGE data to accelerate gene and pathway discovery. A high performance computing (HPC) cluster assists with genomics computational requirements. The Genomics workbench Galaxy on the HPC makes use of parallel processing capabilities. The team also manages dozens of Terabytes of storage to support genomic research.
Biological Visualization Web Services
This area provides DIR laboratories with visualization and web services, including publication support, website support, audiovisual production, medical arts, print media, and 3D printing. For example, staff create medical illustrations for publications by NICHD scientists, provide photography, web, and audiovisual support for NICHD retreats and the NIH Research Festival, and provide web support for the DIR annual report. The team also provides input and support to the NIH Library’s Technology Sandbox in an effort to provide direct 3D printing capabilities to all NIH staff.
Core IT Services
Network and Desktop Services: The team supports reliable, secure, and efficient information technology solutions. This includes acquisition, maintenance, and support for licensed software used by our research community, such as EndNote/Reference Manager, Bookends, GraphPad Prism, PyMol, network services, and cross-platform desktop, server, and application hosting. The following software licenses for computation, 3D imaging, and sequencing are available: Amira, ArrayStar, QSeq, Autodesk Maya, DNASTAR Lasergene Core Suite, MathWorks MATLAB, MolSoft, and SeqMan NGen. The MATLAB Distributed Computing Server, software and hardware (128GB, 16 Worker) was added. Hosting these licenses allows users to leverage their research with additional tools available on Helix and Biowulf. Furthermore, the team helps identify, research, and purchase custom hardware configurations to match research instrument requirements.
Data Recovery Services: We have invested in and expanded data recovery capabilities for all media—hard drive, SSD, and flash, including RAID 0 and 5 recovery tools.
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 also is working to streamline travel requests using an automated travel log system and to develop a model that compares protocol cost and effectiveness.