Research Informatics Support for NICHD's Division of Intramural Research
- David Songco, Head, Computer Support Services Core
- Marco Crosby, Program Engineer
- John Czapary, BS, Laboratory Technical Manager
- Michelle Duverneau, IT Specialist
- Nareg Bakirci, Contractor
- Vida Bayat Mokhtari, Contractor
- Matt Breymaier, Contractor
- Nenna Emeche, Contractor
- Ayelech Gibrehiwot, Contractor
- Raquel Gray, Contractor
- Audrey Harrell, Contractor
- Asma Idriss, Contractor
- Sean Ivusic, Contractor
- Joelle Khoriaty, Contractor
- Kesa Koresko, Contractor
- Tamara Prodanov, Contractor
- Patricia Pullen, Contractor
- Jeremy Swan, Contractor
- Nichole Swan, Contractor
- George Tran, Contractor
- Loc Vu, Contractor
The Computer Support Services Core (CSSC) Facility provides informatics and research services to intramural investigators at NICHD in four key areas: clinical informatics, bioinformatics, biovisualization web services, and core IT support.
During the past year, the team initiated a new hardware upgrade of all its infrastructure by increasing storage capacity and computing resources and by providing a ‘failover’ backup operational mode.
Clinical informatics
The CSSC 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 530 for 16 NIH institutes, with an expansion of research questions to over 200,000. The software development group completed one release that included features for the repeating-questions group, auto-fill searchable textbox, questions-option upload, quality-assurance query improvement, and various performance enhancements. We also supported the Clinical Trial Survey System (CTSS), an application for patient self-reporting, now used for 158 protocols. The Clinical Datamart, which provides lab results, vitals, medications, and ECG/EKG datamarts, was upgraded to support new protocols. The Clinical Datamart now also provides reporting for audits and edited information from the CTDB. The database and migration team worked on approximately 600 reports during the year and migrated a large amount of data for NHLBI, an institute that had previously chosen MetaData Rave as a Clinical Research Tool.
Biological visualization web services
The CSSC team provides the laboratories of NICHD's Division of Intramural Research (DIR) with scientific communication and consulting and media services, including publication support, website and content management support, audio/visual production, image-processing services and consulting, bio-medical graphics, 3D printing, Virtual Reality support, and print media pre-production. This year, we were invited to co-lead the Virtual and Augmented Reality Interest Group (VARIG).
The web activities of the DIR web services program include: DIR and Division of Intramural Population Health Research (DIPHR) laboratory websites, administrative support sites, the annual report, and internet applications. The CSSC continued to maintain approximately 139 public DIR websites, while reducing the number and footprint of web properties, as well as implementing a redesign effort by adapting 60 websites into a content-management system under a standardized design template; we also facilitated a data feed for updating IRP website.
The bioviz team created many illustrations for publications and journal covers on behalf of NICHD scientists. We provided research video support, recording audio/video for the Adult and Pediatric Endocrinology Training Programs, DIPHR’s anniversary celebration, and NICHD’s Three-Minute Talks. In addition, we provided photography, design, and printing support for the DIR Annual Fellows and PI Retreats. For the IRP Research Festival, we expanded the activities of the previous year, coordinating with the NIH Library, NINDS, NLM, and NHGRI to provide eight virtual reality (VR) headsets to demonstrate how VR is being used, or could be used around the NIH, and helping to produce and print booth materials. The team continued graphic design support for and authored several articles for The NICHD Connection, a monthly newsletter for Intramural research fellows. Continued support of the Science@NICHD wiki allows principal investigators (PIs) to maintain a customized web presence for external audiences. We also support an intranet for knowledge management, collaboration within the DIR and with other NIH labs, the sharing of lab protocols and scientific data, and the recruitment of fellows.
Bioinformatics
The CSSC works with the scientific community in NICHD’s DIR to create and manage web applications supporting research publications and the dissemination of information within the community. For example, the CSSC runs several applications that facilitate sharing and searching of genomic data from mutations to gene expression. The bioinformatics team assisted the Molecular Genomics Core in the maintenance of related applications. 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 parallel processing capabilities. The CSSC also continues to provide and manage dozens of terabytes of storage to support genomic research.
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. Improvements were also made to the Fellows Annual Progress Report for the DIR. This module helps facilitate a strong relationship between mentor and fellow while granting the Office of Education invaluable feedback on the training program. Significant changes were made to the division’s Training Tracking module to improve staff registration and safety training compliance. The team completed multiple production releases, including user support for all DIR programs. The CSSC completed a new Cost Tracker release, an application that permits capturing, organizing, and reporting of various expenses on a per-protocol basis. The CSSC continues to work closely with the Office of the Clinical Director to improve protocol cost vs. effectiveness and a protocol-cost estimator module.
Core IT Services
The CSSC continued to expand its services to the DIR community in core IT areas.
Network and desktop services
We support reliable, secure, and efficient information technology solutions, which 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, and wireless configurations); and cross-platform desktop, server, and application hosting in the Rockledge Data Center. We host software licenses for computation, 3-D 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 the high-performance computing systems Helix and Biowulf. We also assist users in identifying, researching, and purchasing custom hardware configurations to match research instrument requirements.
Data-recovery services
We implemented core data-recovery tools for all media, hard drive, solid state drive (SSD), and flash, etc., including RAID 0 and 5 recovery tools. Since 2005, the Core 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.
Additional Funding
- The Clinical Trials Database (CTDB) project receives funding from other NIH Intramural Institute or Center programs, including NINR, NIMH, NIDCR, NIEHS, NIAMS, NINDS, CC, NHLBI, NIDCD, NHGRI, NCCIH, and NIDDK.
Collaborators
- Karel Pacak, MD, PhD, DSc, Section on Medical Neuroendocrinology, NICHD, Bethesda, MD
- Forbes D. Porter, MD, PhD, Clinical Director, NICHD, Bethesda, MD
- Peter Schmidt, MD, Behavioral Endocrinology Branch, NIMH, Bethesda, MD
- Steven Stanhope, PhD, University of Delaware, Newark, DE
- Constantine Stratakis, MD, D(med)Sci, Scientific Director, Division of Intramural Research, NICHD, Bethesda, MD
- Jack Yanovski, MD, PhD, Section on Growth and Obesity, NICHD, Bethesda, MD
Contact
For more information, email songcod@mail.nih.gov.
