Software Development and Data Analysis in Support of the Practical Haplotype Graph (PHG) and TASSEL

Sources Sought Notice Software Maintenance/Development Sources Sought #1096493-SS This is a Sources Sought notice Only. This is NOT a solicitation for proposals, proposal abstracts, or quotations. This Sources Sought is issued for information and planning purposes only as part of USDA ARS market research and does not itself constitute an RFQ. The United States Department of Agriculture (USDA), Agricultural Research Service (ARS) is searching for firms who can provide Soft ware Development and Data Analysis inSupport of Trait analysis by Association, Evolution, and Linkage (TASSEL) andthe Practical Haplotype Graph (PHG) to develop genomic databases. The work involves supporting the maintenance and development of software developedby the project - Improving Crop Eff iciency Using Genomic Diversity andComputational Modeling (8062-21000-043-000-D) and providing analytical support for genetic and bioinformatic analysis. Background: The United States Department of Agriculture (USDA) Agriculture Research Service (ARS) Office of the Chief Information Officer (OCIO) requires contractor assistance. The solution shall include: - Optimize and deploy the PHG's Kmer based read mapping approach so that it uses one-fifth the memory of the current pipeline that relies on MiniMap2. - Optimize and deploy the Diploid and Haploid Path finding algorithms in the PHG specifically targeting sorghum, cassava, rice and cowpea. Code and algorithms will need to be generalized to account for a wide range of recombination and heterozygosity patterns found in these species. By the end of the contract, path finding will be done for each species PHGs. - Integrate these and any additional improvements with the Genomics Breeding Hub for data and analysis as applicable. This will include developing new User Interfaces, TASSEL Plugins, sample Jupyter notebooks and APIs to allow for seamless access and use of these algorithms and tools by users of the Genomics Breeding Hub. - Implement haplotype based genome wide association algorithm in TASSEL6 and associated rTASSEL. - All software and related documentation will be delivered to the project's Bitbucket repository. Commits to the repository will provide sufficient documentation of the contractor's deliverables. Bitbucket is a secure, commercial concurrent versioning system for tracking software and document changes. Submitted software must be reviewed and approved by the project's programming team. In addition, tasks are to be tracked in the project Trello board. Trello is a project tracking system. Full Statement of Work is attached. The Contractor Shall: perform all work described in the attached Statement of Work in accordance with all applicable Federal, State, and local laws, regulations, codes, technical specifications, manufacturers guidelines, USDA, REE, and the ARS mission. This Sources Sought is only for the purpose of identifying potential sources as part of USDA ARS market research. The Government does not intend to make an award based on responses to this inquiry. This notice does not constitute a commitment by the Government. Responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. The purpose of this notice is to obtain information regarding the availability and capability of qualified sources; Small Businesses; HUBZone small business; service-disabled, veteran-owned small business; 8(a) small business; veteran-owned small business; woman-owned small business; or small disadvantaged businesses; All information submitted in response to this announcement is voluntary, and the Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the Government. Any organization responding to this notice should ensure that its response defines how it can specifically meet the specifications for the items requested. 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 review of the responses received, a Combined Synopsis solicitation notice may be published on Sam.gov. Original Point of Contact: All responses to this Sources Sought Notice must be received by April 28, 2023 by 9:00 am. PST the specified due date and time to be considered. Email responses to Elizabeth Wilson at contact@example.gov. Responses will not be returned. Responders are solely responsible for all expenses associated with responding to this Inquiry. Do not submit pricing information in response to this Request.