Research Informatics Support for the Division of Intramural Research
- David Songco, Head, Unit on Computer Support Services
- Marco Crosby, Program Engineer
- John Czapary, BS, Laboratory Technical Manager
- Michelle Duverneau, IT Specialist
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.
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) 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 410 for 14 NIH institutes, with an expansion of research questions to over 180,000. Our software development group completed three releases that included features for the electronic regulatory binder, machine data upload, and bio-repository improvement. We supported the Clinical Trial Survey System (CTSS), an application for patient surveys, used for 136 protocols. The Clinical Datamart was expanded to include vitals, medications, and ECG/EKG datamarts and upgraded to support new protocols.
Biological visualization web services
The UCSS team provides DIR laboratories with scientific communications and media services, including publication support, website support, audio visuals production, medical arts, and print media. We participated in the Science in 3D meeting hosted by NIAID and helped launch the NIH 3D Printing Exchange and their participation in the White House Maker Fair. We continued contributing to the virtual collection of biomedical 3D printing files by producing 34 videos and video tutorials, which serve as a public resource for biomedical scientists and educators. UCSS presented on 3D printing and graphics to the Graduate Partnership Program, the “3 Blind Mice” (the NIH visually impaired user group), and visiting students. We designed and produced 3D representations of Cajal Illustrations for an exhibit in the Porter Neuroscience building and provided input and support to the NIH Library’s Technology Sandbox in their effort to provide direct 3D printing capabilities to all NIH staff.
The web activities of the DIR web services program include: laboratory websites, annual report, and internet applications. A recent feature was added to collect and submit data to the Intramural Research Program website, building on the annual report on-line data collection system. The application was also enhanced to include the Fellows' Annual Progress Report, a unified means of tracking and mentoring intramural trainees along with easing the re-appointment process. The UCSS continued to maintain approximately 50 public DIR websites and began developing graphics for a redesign effort. We created medical illustrations for several publications by NICHD scientists. In addition, we provided photography and graphic, web, and media production for the DIR Annual Fellows and PI (principal investigator) Retreats, the NIH Research Festival, Science in 3D, and the NICHD Exchange series. The team continued support for the NICHD Connection, a monthly newsletter for Intramural research fellows and also expanded the Science NICHD wiki (http://science.nichd.nih.gov) to over 168 projects. The Science wiki allows PIs to create blogs and share documents/data in a secure manner. It played an integral part in intramural reorganization and was a platform for conducting the scientific review by the Board of Scientific Counselors. As part of this project, the group collaborated with the NIH Library, the NLM, the NINDS, and the NIH Office of the Director.
Bioinformatics
The bioinformatics team assisted the Molecular Genomics Laboratory with data collection and analysis for highthroughput sequencing. The scientific informatics 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, ChIPchip, 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 transcribedfragments (transfrag) information in Browser Extensible Display (BED) format generated from Affymetrix Integrated Genome Browser (IGB) or downloaded from the UCSC (University of California Santa Cruz) server. The SAGEWorks application was maintained and transitioned to a new server to leverage the robust public databases available in combination with the SAGE (Serial Analysis of Gene Expression) 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 permits the scientific community to minimize the redundancy of manual manipulation. A high-performance computing (HPC) cluster was set up to assist with genomics computational requirements. The Genomics workbench Galaxy was installed and configured on the HPC to take advantage of the parallel processing capabilities. The UCSS also continues to provide and manage dozens of Terabytes of storage to support genomic research.
Core IT services
The Unit continued to expand its services to the Division of Intramural Research (DIR) community in core IT areas.
Network and desktop services
The unit supports reliable, secure, and efficient information technology solutions. This includes acquisition, maintenance, and support for licensed software used by the DIR research community e.g., EndNote/Reference Manager, Bookends, GraphPad Prism, PyMol, network services (e-mail, data backups, VPN, helix, PDAs, wireless configurations); and crossplatform desktop, server, and application hosting in the Rockledge Data Center. We host software licenses for computation, 3D imaging, and sequencing e.g., Amira, ArrayStar and QSeq, Autodesk Maya, DNASTAR Lasergene Core Suite, MathWorks MATLAB, MolSoft, and SeqMan NGen. This year, MATLAB Distributed Computing Server, software and hardware (128GB, 16 Worker), was added. Hosting these licenses permits users to leverage their research with additional tools available on Helix and Biowulf. We also assist users in identifying, researching, and purchasing custom hardware configurations to match research instrument requirements.
Data-recovery services
Core data-recovery tools were implemented for all media, hard drive, SSD, and flash etc., including RAID 0 and 5 recovery tools. Since 2005, the Unit has recovered over a Terabyte of research data from failed drives and media, at a minimum of $2500 savings per instance to the DIR research budget.
Custom software development for scientific and administrative support
This aspect of support includes 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 three production releases, including users' support for all DIR programs. UCSS also continued the requirements process for an automated travel log system to streamline travel requests. The UCSS deployed the Cost Tracker module for the DIR, enabling the capture, organization, and reporting of various expenses on a per-protocol basis. The UCSS worked closely with the Office of the Clinical Director to develop a model for protocol cost vs. effectiveness.
Additional Funding
- The Clinical Trials Database (CTDB) project receives funding from other Intramural IC programs, including NINR, NIMH, NIDCR, NIEHS, NIAMS, NINDS, CC, NHLBI, NIAAA, NIA and NIDDK.
Publications
- Huser V, Sastry C, Breymaier M, Idriss A, Cimino JJ. 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 2015; 57:88–99.
Collaborators
- Forbes D. Porter, MD, PhD, Clinical Director, NICHD, Bethesda, MD
- Lynnette Nieman, MD, Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
- Karel Pacak, MD, PhD, DSc, Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
- Owen Rennert, MD, Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, MD
- Leorey Saligan, PhD, RN, CRNP, Deputy Clinical Director, NINR, Bethesda, MD
- Peter Schmidt, MD, Behavioral Endocrinology Branch, NIMH, Bethesda, MD
- Monica Skarulis, MD, CDR, USPHS, Clinical Endocrinology Branch, NIDDK, Bethesda, MD
- Steven Stanhope, PhD, University of Delaware, Newark, DE
- Constantine Stratakis, MD, D(med)Sci, Program in Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
- Stephen Suomi, PhD, Section on Comparative Behavioral Genetics, NICHD, Bethesda, MD
- Susan Swedo, MD, Pediatrics and Developmental Neuroscience Branch, NIMH, Bethesda, MD
- Jack Yanovski, MD, PhD, Program in Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
