J D R F S P E C I AL R E Q U E S T F O R AP P L I C AT I O N S : JDRF MICROBIOME CONSORTIUM DATA COORDINATING CENTER
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1 J D R F S P E C I AL R E Q U E S T F O R AP P L I C AT I O N S : MICROBIOME CONSORTIUM DATA COORDINATING CENTER PURPOSE is soliciting applications to establish an innovative, efficient, cost-effective solution to creating a Data Coordinating Center (DCC) for the Microbiome Consortium. Microbiome Consortium members generate multiple types of data, including, but not limited to, 16S rrna Sequencing data, genetics, clinical meta-data, immunological and metabolic data and various omics data, thus requiring responses to this call for proposals to offer a solution that allows the management and integration of disparate, heterogeneous data sources. BACKGROUND The incidence of type 1 diabetes (T1D) has been increasing worldwide, indicating the presence of one or more major environmental factors affecting the pathogenesis of the disease. This increased incidence is most marked in children ages one to five years suggesting that immunoregulation in childhood has been altered. Early data from the Microbiome Consortium and elsewhere suggests a role for the intestinal microbiome in T1D development. Currently, the data is associative and definitive studies are lacking. believes that a truly collaborative consortium approach is needed to advance the field forward to definitely answer the question of the role of the microbiome in T1D. In 2011, established the Microbiome Consortium and was founded on these goals: 1. Establish a collaborative network of funded investigators that will both individually, as well as collectively, address key questions related to the role for the microbiome in T1D pathogenesis and therapy. 2. Work with staff and an external advisory group to define key knowledge gaps, and identify opportunities, for key discoveries related to the importance of the microbiome for T1D. 3. Define what microbial communities are positively or negatively associated with T1D in both humans and mouse models of the disease. 4. Identify a biomarker (immune, metabolomic, mucosal, etc.) of a positive or negative microbiome association with T1D. This Consortium is actively collecting data, with each group using their own data system, techniques and analysis tools. Moving forward, aims to create a common platform for deposition of data, sharing of protocols, and facilitation of data sharing. OBJECTIVES The Microbiome Consortium Data Coordinating Center (DCC) must: 1. Define a model of data elements, working collaboratively with the Microbiome Consortium groups a. Work interactively with Microbiome Consortium investigators to understand scientific questions to be addressed and prepare an appropriate data model b. Develop a corresponding data dictionary c. Develop the data ontology appropriate for controlled language descriptions of these data elements (multiple mapped ontologies) d. Create an organizational schema appropriate to this model Page 1
2 e. Facilitate consensus among the Microbiome Consortium for the data model before implementation 2. Create and/or implement tools to unify storage, retrieval, monitoring, and translation of the data from each of the Consortium sites. The goal is returning one homogeneous, integrated data set to a single interface in response to a request for data. a. Create and/or implement web-based interfaces to enable data deposition or its equivalent. b. Create and/or implement technology to facilitate efficient, effective query and retrieval of data sets in a uniform manner for analysis from each of the seven Microbiome Consortium groups c. Implement role-based access to specific functions within the system (data deposition, user management, queries, and bulk download). d. Create and/or implement data reporting and provenance tracking formats e. Document the usage of the Consortium portal for critical tasks including data deposition, access and user account control, query-based data retrieval, and bulk data download f. Facilitate consensus among the Microbiome Consortium for the operational model before implementation g. Promote, moderate and facilitate sharing of data within the timeframe of the policies of the Microbiome Consortium 3. Support the Bioinformatics efforts of the Microbiome Consortium a. Collaboratively support existing local Bioinformatics efforts (acting not as the primary informatics resource but in a collaborative role with center technical staff) b. Work with Microbiome Consortium to bring any data that is part of the Microbiome Consortium into a well-structured, searchable form, as necessary c. Work with Microbiome Consortium to map group data to the common data model 4. Work with each Microbiome Consortium technical and operational staff to resolve institutional data sharing challenges and successfully operate within guidelines a. Assist in preparing documentation for IRB approval of data sharing strategies b. Ensure that all data sharing operates within HIPAA guidelines 5. Create a system that is scalable to accommodate current and future needs a. Ensure flexibility to add groups, users, and permissions to the Microbiome Consortium repository and portal b. Ensure the potential to modify and expand the data being collected by the Microbiome Consortium c. Ensure sustainable interconnectivity among the Microbiome Consortium d. Ensure future maintenance at reasonable cost e. Ensure sufficient documentation for simple, effective future user training ELIGIBILITY Applicants must hold an M.D., D.M.D., D.V.M., Ph.D., or equivalent academic degree and a faculty position or equivalent at a college, university, medical school, for-profit research based organization or other comparable institution. Applications may be submitted by domestic or foreign public or private non-profit organizations, such as colleges, universities, hospitals, laboratories, units of state or local governments or eligible agencies of the federal government. Please note that applications from for-profit entities or industry collaborations with academia may be submitted to this RFA, however, additional information will be requested from forprofit entities if a full application is invited. There are no citizenship requirements. MECHANISM RFAs in response to this announcement can be submitted to the following mechanism: Page 2
3 Strategic Research Agreements for up to 3 years of funding (including 10% indirect costs). Budgets should be determined by the applicant(s) and be relative to scope of work. Cost-effectiveness will be one consideration for choosing the awardee, so applicants are encouraged to be thorough in their assessment of costs, but reasonable. DEADLINES o Release Date:... February 23, 2015 o Letter of Intent... April 10, 2015 (5:00pm, Eastern Time) o LOI Notification... April 20, 2015 o Application Due Date:... May 21, 2015 (5:00pm, Eastern Time) o Response to Applicants Date:... August 2015 o Earliest Anticipated Start Date:... September 2015 SUMBISSION INSTRUCTIONS Applicants must register as an applicant and submit their letter of intent and application in response to this RFA using s on-line research management system RMS360 ( LOI COMPONENTS Prospective applicants should submit an expression of interest on-line via RMS360 at The LOI template located under the LOI Research Plan tab must be used to submit. LOI submissions will undergo expedited review. Applicants will be notified if they have been approved to submit a full application. Letters of Intent should be no more than 3 pages in length including the following information: An overview of the applicant institution s or company s capabilities and experience with projects similar to that outlined in this RFA Ability to interact well with Consortium investigators and adherence to the goals outlined A cost-effective budget References (no page limit) PROPOSAL Applicants must have developed system(s) with similar capabilities to those described in this RFA, have experience in integrating multiple web-based systems into a cohesive data platform, and have the capability to design, develop, host and manage a registry that will be used for clinical research in T1D. The qualified applicant will have cross-disciplinary experience in clinical disease, epidemiology, and bioinformatics. The proposal will demonstrate extensive, successful experience implementing HIPAAcompliant systems that dynamically retrieve and integrate biomedical and clinical data maintained in heterogeneous, disparate repositories. Applications should be no more than 12 pages in length including the following information: An overview of the applicant institution s or company s capabilities and experience with projects similar to that outlined in this RFA A point by point outline of the proposed broad approach to developing a platform that can be used for this particular consortium (in response to the aforementioned objectives) Ability to interact well with Consortium investigators and adherence to the goals outlined A cost-effective budget Proposal section templates in MS Word should be type-written, single-spaced and in typeface no smaller than 10-point font and have no more than six vertical lines per vertical inch. Margins, in all directions, must be at least ½ inch. Complete information should be included to permit review of each application without reference to previous applications. The Research Plan must be organized as follows: 1) Background and Significance of this work to the goals of the RFA 2) Proposed Approach to Platform Development 3) Details of Platform Page 3
4 4) Advantages over alternative approaches that would address the same goal 5) Intellectual Property or commercial efforts associated with the current application 6) References (no page limit) 7) Principal Investigator Assurance For SRAs, all information in items 1-5 must be incorporated in the 12-page limit without exception. Note that applications with research plans exceeding the page limit will not be reviewed. PROPOSAL COMPONENTS o Applicant and Institutional Demographics (including Financial and Administrative Officer) o Institutional Letter of Support o Key Personnel o Lay and Technical Abstracts o Budget o Budget Justification o Subcontract Budget (if applicable) o Subcontract Budget Justification (if applicable) o Other Support (for the PI only) o Organization Assurances (IRB and/or IACUC) o Biosketches (for all Key Personnel) o Research Plan o Human Subject Research plan (if applicable) o Resources o Supporting Documents (i.e. Letter(s) of Collaboration, etc.) REVIEW CRITERIA Applications will be evaluated based on s standard confidential award policy and according to the following criteria: Significance Relevance Approach Innovation Investigator Experience Environment Significance: Does this study address an important problem? What will be the expected effect of the DCC to furthering the mission of the Microbiome Consortium? Relevance: Is the proposed platform relevant to the objectives of this RFA? What will be the expected impact of these studies on the s mission? Approach: Is the proposed platform adequately developed, well integrated and appropriate to the aims of the Consortium? Does the applicant acknowledge potential problem areas and consider alternative tactics? Is the proposed platform feasible within the term of the award? Are resources and knowledge based on prior experience and know-how? Innovation: Does the platform employ novel concepts, approaches or methods? Are the aims original and innovative? Does the project challenge existing paradigms or develop new methodologies or technologies? Investigator Experience: Is the investigator appropriately trained and well suited to carry out the planned platform? Is the work proposed appropriate to the experience level of the principal investigator? Does the PI have working relationships with members of the Microbiome Consortium? Is the project well led and coordinated? Environment: Does the scientific environment in which the work will be performed contribute to the probability of success? Does the platform take advantage of unique features of the scientific environment or employ useful collaborative arrangements? Is there evidence of institutional support? Page 4
5 SCIENTIFIC CONTACTS Jessica Dunne, Ph.D Andrew Rakeman, Ph.D ADMINISTRATIVE CONTACTS Jami Goodman Research Coordinator If you have any grant-specific questions as you work within RMS360, please contact the administrative contact listed above. For any non-grant-specific inquiries or issues, please contact SmartSimple Support Services via or phone (866) Support hours are Monday through Friday between 5:00am and 9:00pm US Eastern Standard Time. Page 5
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