SOURCES SOUGHT
A -- Bioinformatics Resource Centers for Infectious Diseases
- Notice Date
- 4/20/2016
- Notice Type
- Sources Sought
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Office of Acquisitions, 5601 Fishers Lane, 3rd Floor, MSC 9821, Bethesda, Maryland, 20892, United States
- ZIP Code
- 20892
- Solicitation Number
- HHS-NIH-NIAID-RDSS-16-NIHAI2016BRC
- Archive Date
- 5/25/2016
- Point of Contact
- Miranda S. Adams, Phone: 240-669-5344, Stanley Knight, Phone: 240-669-5181
- E-Mail Address
-
miranda.adams@nih.gov, knights@niaid.nih.gov
(miranda.adams@nih.gov, knights@niaid.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- RESEARCH AND DEVELOPMENT SOURCES SOUGHT 1. Agency/Office Department of Health and Human Services, National Institutes of Health, NIAID 2. Contracting Office Location Office of Acquisitions Division of Extramural Activities, NIAID 5601 Fishers Lane Rockville, MD 20852 3. Description INTRODUCTION/SYNOPSIS This is a Research and Development (R & D) Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. This Sources Sought Notice (SS) is for information and planning purposes only and shall not be construed as a solicitation or as anobligation on the part of the NIAID. The purpose of this notice is to obtain information regarding the availability and capability of all qualified sources including small and small disadvantaged businesses to perform a potential R & D requirement. BACKGROUND This National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) project is for work related to the contract below: - Bioinformatics Resource Centers for Infectious Diseases, "Bacterial Species Organisms," University of Chicago (Contract HHSN272201400027C) This contract was awarded on a competitive basis for a one-year base period in 2014 with four (4) one-year option periods. In addition, the contract contains option quantities for the base year and each subsequent term option year. The period of performance, if all options are exercised, is September 15, 2014 to September 14, 2019. The value of the contract, if all options are exercised, is $22,037,546. The objective of the contract is for maintenance, expansion, enhancement, and provision of NIAID's Bioinformatics Resource Center database systems, analysis tools and algorithms; user friendly web interfaces for data query, retrieval, and display; provision of bioinformatics services to the scientific community; provision of community outreach activities; interaction with NIAID funded programs; and support of bioinformatics infrastructure and data services for the bacterial species. During the course of this contract, comprehensive and robust capture, integration, analysis and release of data, and metadata for bacterial species in category A-C pathogens have been conducted. In addition, development and deployment of web-based services and tools critical to advancing research and studies of the global infectious disease research community and NIAID- supported projects and center have been undertaken. The Pathosystems Resource Integration Center (PATRIC) web resource has exponentially scaled data services with the number of public genomes and datasets available to the community while simultaneously building a comprehensive user workspace that supports processing and analysis of user submitted data and virtual integration of private data with public data to support comparative analysis. Key features provided include fully integrated, consistent, accurate and up-to-date genome assembly, annotation, and metabolic modeling capabilities as well as integration of tools for differential expression analysis and visualization. The PATRIC system annotation engine produces high quality genome annotations derived from manually curated databases that represent common molecular pathways, organism-specific subsystems, and custom databases for genes associated with virulence and antibiotic resistance. The PATRIC annotation system supports all bacterial and archaeal domains. The PATRIC database integrates data sets and data types generated in the NIAID supported Functional Genomics Centers, Genomic Centers for Infectious Diseases, Structural Genomics Centers for Infectious Diseases, and Systems Biology Centers including but not limited to genomes, transcriptomes, proteomes, transposon data, phenotypes, antimicrobial resistance (AMR) screens, fitness data and models. PURPOSE AND OBJECTIVES The purpose of this Research and Development Sources Sought Notice is to discern whether or not there are other contractors, including small or small disadvantaged businesses, capable of and interested in performing the work described herein. The NIAID does not intend to award a contract on the basis of responses received nor otherwise pay for the preparation of any information submitted. As a result of this R & D Sources Sought Notice, the NIAID may issue a Request for Proposal (RFP) if it deems this necessary and appropriate. THERE IS NO SOLICITATION AVAILABLE AT THIS TIME. However, should such a requirement materialize, no basis for claims against NIAID shall arise as a result of a response to this Sources Sought Notice or the NIAID's use of such information as either part of our evaluation process or in developing specifications of any subsequent requirement. The objective of this acquisition is to increase the effort available to continue development of and support for antimicrobial resistance related data and computational services. Antibiotic resistant bacterial pathogens are a serious global public health threat and have major implications for treatment strategies with available antibiotics. The United States Centers for Disease Control (CDC) estimates antibiotic resistant bacteria cause at least two million illnesses and 23,000 deaths each year in the U.S. Unnecessary use of antibiotics in healthcaresettings and animals continues to be a driver of the emergence of antibiotic resistance, and bacterial resistance to antibiotics is increasing. Bioinformatics platforms enabling easy access to comprehensive data and computational tools that support antimicrobial resistance studies are not currently available. New and improved means for rapid and accurate diagnostics are urgently needed for informed clinical treatment decisions and to reduce antibiotic misuse in point of care and hospital settings. PROJECT REQUIREMENTS The NIAID intends to modify the existing University of Chicago contract HHSN272201400027C to increase the Level of Effort by 5 Full Time Equivalents, or 10,400 direct labor hours for option year 2. This project aims to developcomprehensive antimicrobial resistance (AMR) analyses, models, and tools to enable AMR investigation at the systems level, and for clinical applications by expanding the infrastructure and systems established in the PATRIC BRC. Specifically it will extend the PATRIC subsystem-based curation and annotation system to support DNA sequence level variants associated with AMR phenotypes, to enable encoding of known protein variants associated with AMR pathways, and extend the annotation framework to support variant tags and variant annotations. Additionally, this modification will extend the PATRIC data model including the AMR database to include AMR associated loci and increase the coverage of organisms, antibiotics and screen results associated with specific antibiotic resistance profiles, and integrate datasets from various high throughput omics technologies applied in AMR studies using the systems biology approach. Finally, this modification will enhance the PATRIC predictive and analytical capabilities to enable the construction and visualization of phylogenetic trees based on AMR variants, phenotypes and associated genomic markers, provide access to the AMR classifiers as free services for the scientific community, and develop applications of AMR prediction in clinical settings for diagnostics and therapeutics. This work will build upon 1) PATRIC web resource internal data model and the large body of genomic, transcriptomic, protein-protein interaction and related metadata amassed in the current PATRIC BRC; 2) software and hardware architecture, design and implementations in place that support the PATRIC web resource; 3) PATRIC web resource workflow development pipelines; 4) PATRIC manual curation efforts; 5) crucial comparative analysis assets in place such as domain and genus level protein families, subsystem and functional role identification, k-mer (a nucleotide or peptide sequence of length k) databases and highly performant search methods; and 6) current PATRIC work in developing machine learning classifiers for AMR. ANTICIPATED PERIOD OF PERFORMANCE The increase in Labor Hours is anticipated to be applied to Option Period 2 (September 15, 2016- September 14, 2017) of the current contract. OTHER IMPORTANT CONSIDERATIONS CAPABILITY STATEMENT/INFORMATION SOUGHT Tailored Capability Statements submitted as a result of this announcement should demonstrate the offerors' facilities, qualifications and experience, specifically providingevidence as to their capability to perform this requirement, with particular attention to the following areas: 1. Ready access to PATRIC related subsystem annotation and curation capabilities. These subsystem annotation and curation capabilities must be compatible with those currently used to drive the PATRIC annotation engine. 2. Extensive knowledge of the RAST (Rapid Annotation using Subsystem Technology) annotation system architecture and design sufficient to extend the system to support specific sequence level annotations. 3. Deep understanding of the PATRIC protein families including FigFam (protein families that are used for annotation in RAST) and PATyFAM (protein families that are used for comparative analysis in PATRIC). Understanding of the methodology for construction and modification. Understanding of use of these protein families in the PATRIC data ingest process and web based comparative analysis tools. 4. Ready access to and understanding of the PATRIC data models sufficient to add new data types while preserving data model coherence. 5. Established and extensive knowledge of the PATRIC application service architecture and design sufficient to extend it for new services and applications. 6. Established and extensive knowledge of the PATRIC user workspace architecture and design. 7. Extensive knowledge of the PATRIC graphical user interface design and implementation. 8. Access to comparable hardware systems and backend servers that currently support PATRIC software systems. Access requires training that is up-to-date. 9. Domain expertise in AMR studies in basic research and clinical settings. Established multi- disciplinary team with expertise in microbiology, clinical studies, infection diseases, IT systems architecture, bioinformatics, and computational analysis software applications and development. 10. Access to equipment, expertise and facilities for performing the work required above. 11. Knowledge of both the PATRIC internal infrastructure and web resource needed to train scientific researchers both domestically and internationally in the analysis capabilities, tools, and services. Sources are expected to have the necessary skills, experience, and infrastructures to meet the requirements of this project. Capability statements must include the following: 1. Respondents' DUNS number, organization name, address, and point of contact. 2. Respondents' opinions about the difficulty and/or feasibility of the potential proposed acquisition, - possible solutions and approaches that may currently exist in the marketplace, and information regarding innovative ideas or concepts. 3. Information regarding respondents' a. Staff expertise, including their availability, experience, and formal or other training b. Current in-house capability and capacity to perform the work c. Prior completed projects of similar nature 4. Any other information that may be helpful in developing or finalizing the acquisition requirements. SUBMISSION INSTRUCTIONS This sources sought notice requires interested parties to submit a capability statement via the NIAID electronic Contract Proposal Submission (eCPS) website at https://ecps.nih.gov/NIAID. For directions on using eCPS, go to https://ecps.nih.gov/NIAID/home/howto. Submissions should be in PDF format, no smaller than 10 pt. font and 10 pages or less. DISCLAIMER AND IMPORTANT NOTES This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. CONFIDENTIALITY No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NIAID/HHS-NIH-NIAID-RDSS-16-NIHAI2016BRC/listing.html)
- Place of Performance
- Address: N/A, United States
- Record
- SN04090273-W 20160422/160420234640-12747d7fa0400923358f462f71f8109c (fbodaily.com)
- Source
-
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