Software Development and Data Analysis in Support Tender - 81839537

Procurement Summary

Country: USA

Summary: Software Development and Data Analysis in Support of the Practical Haplotype Graph (Phg) and Tassel

Deadline: 28 Apr 2023

Posting Date: 19 Apr 2023

Other Information

Notice Type: Tender

TOT Ref.No.: 81839537

Document Ref. No.: 1096493-SS

Competition: ICB

Financier: Self Financed

Purchaser Ownership: Public

Tender Value: Refer Document

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Tender Details

Description
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...
Active Contract Opportunity

Notice ID : 1096493-SS

Related Notice

Department/Ind. Agency : AGRICULTURE, DEPARTMENT OF

Sub-tier : AGRICULTURAL RESEARCH SERVICE

Office : USDA ARS NEA AAO ACQ/PER PROP

General Information

Contract Opportunity Type: Sources Sought (Original)

All Dates/Times are: (UTC-07:00) PACIFIC STANDARD TIME, LOS ANGELES, USA

Original Published Date: Apr 17, 2023 01:05 pm PDT

Original Response Date: Apr 28, 2023 09:00 am PDT

Inactive Policy: 15 days after response date

Original Inactive Date:

Initiative: None
Classification

Original Set Aside:

Product Service Code:

NAICS Code: 541511 - Custom Computer Programming Services
Place of Performance: Ithaca, NY 14853 USA

Documents

 Tender Notice

Statement-of-Work.docx