Network and Desktop During the past year, the CSSC has upgraded its hardware for all applications and database servers to Oracle / Sun T5. The core continued on supporting reliable, secure, and efficient information technology solutions. This includes acquisition, maintenance, and support for licensed software used by our DIR research community e.g., EndNote/Reference Manager, Bookends,GraphPad Prism, PyMol, network services (email, 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), has been 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 datarecovery tools were implemented for all mediahard drive, SSD, and flash etc., including RAID 0 and 5 recovery tools. Since 2005, the Unit has recovered over two Terabyte of research data from failed drives and media, at a minimum of $2500 savings per instance to the DIR research budget. Clinical informatics The Computer Support Services Core (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 454 for 14 NIH institutes, with an expansion of research questions to over 190,000. Our software development group completed two releases that included features for the electronic regulatory binder, data download, and bio-repository improvement. We supported the Clinical Trial Survey System (CTSS), an application for patient surveys, used for 149 protocols. The Clinical Data-mart was expanded to support new protocols. The core hardware upgrade enabled the CTDB project to operationally add more protocols and more data, while improving performance, as the prior hardware had reached its operational limits. In addition to the server upgrade, the CTDB project now uses a SAN for its data storage, this allows the project to grow into Terabyte space. The hardware and storage upgrade have given the CTDB project both performance and storage improvements and is the culmination of years of planning and testing. Biological visualization web services The CSSC team provides DIR laboratories with scientific communications and media services, including publication support, website support, audio/visual production, and print media. The core is providing support to both the Pediatric and Adult training programs by recording audio and video of presenters in the Didactic lectures and STEEP (Survival Training in Endocrinology for Enhanced Productivity) and hosting the website to distribute these assets. We continue to facilitate the use of new technologies through demos and via a booth at the Intramural Research Festival, in coordination with the Virtual and Augmented Reality Interest Group. The web activities of the DIR web services program include: laboratory websites, annual report, and internet applications. This application was also enhanced to include the Fellows Annual Progress Report; a unified means for tracking and mentoring intramural trainees along with easing the re-appointment process. Success with the Fellows APR has garnered interest from various other institutes and plans to implement a scalable and cost-effective inter-institute service are underway. The CSSC has been consolidating DIR websites under a unified design in a Content Management System known as ScienceNICHD (http://science.nichd.nih.gov). We created medical illustrations for many publications by NICHD scientists. In addition, we continue to provide photography and graphic , web, and media production for: the DIR Annual Fellows and PI (principal investigator) Retreats, the NIH Research Festival, and the NICHD Exchange series and continued support for 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. It played an integral part in intramural reorganization and was a platform for conducting 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 During the past year, the bioinformatics team assisted the new Molecular Genetics 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 webbased 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 CSSC server. The SageWorks application was maintained and transitioned to a new server to leverage the robust public databases available in combination with the SAGE 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 enables 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 make use of the 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 the project included 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 multiple production releases, including addressing data sharing policies and upgrading the NLM web service interface, as well as providing user support for all DIR groups. The CSSC deployed the Cost Tracker module for the DIR, enabling the capture, organization, and reporting of various disparate expenses on a per-protocol basis. The CSSC worked closely with the Office of the Clinical Director to develop a model for protocol cost vs. effectiveness.
