On March 19, 2009 the National Center for Research Resources (NCCR) issued a request for Administrative Supplements to institutions and organizations with active NIH Research Grants. This request was based on the American Recovery and Reinvestment Act of 2009 (ARRA), which was signed into law on February 17, 2009 with the goal of promoting job creation and economic development, along with accelerating the pace and achievement of scientific research. Supplements could be submitted under an NIH CTSA parent award. The goal of each supplement was to advance either the NCRR Pilot Project Mechanism, the CTSA Consortium Strategic Goals, Collaborative Community Engagement Research, Science Education and Dissemination, Collaborative and Basic and Translational Research, or Research Workforce Development and Dissemination. Of the Supplements submitted by the Rockefeller University Center for Clinical and Translational Science (CCTS), four were recommended for funding on July 15, 2009. If awarded at the requested budgets, they will result in $2,234,770 in additional total funding over two years.  Five new staff members will be hired to conduct the studies. A brief description of the supplements to conduct the studies recommended for funding are provided below.

1. Administrative Supplement for Enhancing NCRR Pilot Project Mechanism, Knut Wittkowski, secondary PI. This Pilot Project aims at using the NCBI CASP database of Genotypes and Phenotypes (dbGAP): (1) to empirically validate a methodology by comparing its results to those from traditional approaches; (2) to conduct a proof of principle analysis to explore a recent finding from ongoing research under the parent CTSA award which suggests that genetic factors may determine why psoriasis affects primarily the skin in some patients, while others develop psoriatic arthritis; and (3) to accelerate sharing of technology through rapid dissemination of the results, Web-based documentation of the analyses as case studies for the use of the novel technology, and development of training material in collaboration with neighboring CTSA institutions in the New York City area.

2. Administrative Supplement to Advance Translational (T1 & T2) Research, Agata Smogorzewksa, secondary PI. Using the Bleeding History Phenotyping System as a prototype of a comprehensive patient phenotyping instrument, this submission proposed the creation of a comprehensive, ontology-driven phenotyping system and database for Fanconi anemia (FA). Work stemming from this proposal will create a uniform phenotyping ontology based on a comprehensive Fanconi Anemia Phenotyping Questionnaire (FAPQ) that will be designed and peer-reviewed by experts in the field. Information will be used to generate a Fanconi anemia phenotyping database (FAPD), which will be accessible to physicians and researchers worldwide through a secure Web-based interface.

3. Administrative Supplement to Advance Translational (T1 & T2) Research, Knut Wittkowski, secondary PI. To Advance Translational (T1 & T2) Research by increasing accuracy and accelerating analyses and dissemination of results, two critical enhancements with long-term implications for the use of the Rockefeller-developed programs µStat and WISDOM as resources for clinical and translational research will be made. (1) CCTS will partner with industry to move WISDOM another step towards becoming a comprehensive support system for clinical and translational scientists by making the meta database already used for the REDCap link a resource shared with a graphical user interface to assist and provide help with specifying statistical analyses to be performed on the µStat Web server. (2) A full time software engineer will be hired to provide technical assistance to clinical and translational researchers while enhancing the capacity, stability, and functionality of the grid, in general, and automating the iterative resubmission of interim results as the number of factors analyzed increases. After the 2-year period, WISDOM will facilitate clinical and translational research as a coherent user interface with intelligent, knowledge-based help for both REDCap as a data entry system and µ-stat as an innovative statistics server. To accelerate further development, it will have been ported to the industry standard Java and have an innovative and easily expandable help system to facilitate training and dissemination.

4. Administrative Supplement for Research Workforce Development and Dissemination, Edward Barbour, secondary PI. This supplement proposes to create a comprehensive course in the area of Applied Bioinformatics for the further education of clinical researchers. The field of bioinformatics, which applies information technology to molecular biology data, is being elevated to a prominent role as newer equipment for DNA, RNA, and protein sequencing is generating vast amounts of data from scientific experiments. Therefore, it is of great value to the researchers responsible for such experiments to understand the tools and techniques that are available to analyze this vital data. As in many areas of rapidly advancing technology, many educational programs are not able to keep up with the advanced pace of this educational need. This submission will fill that gap by creating a Web-based course that will contain numerous examples and exercises, giving the researcher the full advantage of knowing what it takes to draw valid scientific conclusions from such data. This course will look at the subcategories of bioinformatics including genomics, protein structure and interaction networks, metabolomics, natural language processing, and simulation using complex systems. The course will also expose the researcher to currently available bioinformatics tools including open source and leading third party tools, as well as the low level components used to build such tools.