Workbench Software

Active

Contract Opportunity

Request for Information (RFI)

Walter Reed Army Institute of Research (WRAIR)

Workbench Software

General Information:

This is an RFI as defined in FAR 15.201(e) to ascertain whether a commercial item exists that provides the capabilities described herein.

This RFI is issued solely for information and planning purposes and does not constitute a solicitation. All information received in response to this RFI will be treated as business confidential information. Nonetheless, submitters should properly mark their responses if the information is confidential. Responses to the RFI will not be returned. Responses to this notice are not offers and cannot be accepted by the Government to form a binding contract. Responders are solely responsible for all expense associated with responding to this RFI.

RFI Response and due date: 14 April 2025 10:59 AM ET

NAICS – 518210

PCS – 7A21

Instructions to Responders:

Responses from all capable and qualified sources are encouraged to respond to this request.

White papers should adhere to the following formatting and outline instructions:

1. All submissions shall be made electronically and be in one of the following formats: Microsoft Word or Adobe PDF.

2. Cover Page (1page)

• Title


• Organization


• Responders technical and administrative points of contact (names, addresses, phone, fax number and email addresses)


• Topic area(s) addressed


• NAICS Code

3. Interested parties are asked to respond to this RFI and submit a capabilities statement that supports the focus of this RFI as detailed below. Please review the place of performance requirements. Please submit written responses via email in Microsoft Office 2000 or 2007 format. All responses should be complete: in 12-point font; and not to exceed 3 pages total, including graphics, tables, and appendices.

No hardcopies shall be accepted. No written solicitation document is available at this time. Telephone requests will not be honored, and no bidders list shall be maintained. No inquiries regarding any potential future acquisition activities shall be entertained.

Potential offerors are requested to direct all questions via email to the Point of Contact listed below. Responses are due to the Point of Contact, Mr. Keith C. Crum at email: keith.c.crum.civ@health.mil no later than 10:59 AM ET, 14 April 2025.

The purpose of this requirement is to provide Workbench bioinformatics software solution for DNA or RNA analysis providing next-generations sequencing (NGS) workflows, interpretations and visualization for WRAIR’s Medical Readiness Systems Biology Branch (MRSB). The term of the license subscription is one base period plus four (4) option periods. One license is required.

WRAIR’s requirement for Workbench Software:

1. Requirement Description

The Walter Reed Army Institute of Research (WRAIR), Medical Readiness Systems Biology Branch (MRSB) requires a web-based research platform for deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) analysis. Term of license subscription is 12 months, one license required.

2. Background

The WRAIR's MRSB branch aims to apply robust and precise molecular-based solutions for military-relevant health performance, resilience and readiness. MRSB is a disease-agnostic program that utilizes high-throughput, multi-omics platforms supported by a suite of cutting edge, targeted assay tools and AI-driven analytical capabilities to identify diagnostic and prognostic biomarkers and generate a knowledge base about biological mechanisms and personalized care. MRSB is committed to developing a seamless, integrative module enabling to interrogate genome-to-phenome landscape to inform medical interventions and develop products to improve Warfighter health, performance, resilience, and readiness.

Specific Product Requirements:

• Product description:
  
  
  
  • Web-based bioinformatics software solution for DNA or RNA analysis. Provides next-generation sequencing (NGS) workflows, interpretation, and visualization.
  
  
  
  


• Quantity required:
  
  
  
  • One - 12 month license, renewed annually via option year contract
  
  
  
  


• Product capability requirements:
  
  
  
  • Sanger sequencing data analysis - Import Sanger sequencing data (.SCF, .ABI, .PHD) and map them to a reference sequence or assemble them into contigs. Identify and inspect called variants and inconsistencies, and visualize traces, trimmed ends, coverage and more for each contig.
  
  
  • Primer design - Design oligonucleotides (primers) with adjustable criteria and dynamically updating calculations.
  
  
  • Cloning - Vector design and analysis tools for different types of cloning, including in silico, in silico homology-based (Gibson), restriction and Gateway (single- and multi-site).
  
  
  • Expression analysis - Analyze expression data produced on microarray platforms and perform quality control, transformation, normalization and statistical analyses to measure differential expression.
  
  
  • Phylogenies - Create phylogenetic trees and add associated metadata with K-mer-based tree construction. Test models to find the best statistical approaches and visualize imported metadata on tree topology.
  
  
  • Workflows – Capability to build custom workflows, moving data through any sequence of tools and standardizing sample analysis. Workflows can be used locally, on servers, or sent to colleagues.
  
  
  • 3D protein structure viewer - View annotations and variants in their structural context with synchronized views for proteins and nucleic acids.
  
  
  • Alignment - Workbenches shall include pairwise and multiple sequence alignments of DNA, RNA and protein sequences, including ClustalW and Muscle. Whole Genome Alignment, to allow user to investigate dot plots, multiple genome alignments, and average nucleotide identities.
  
  
  • Provenance - Export the timestamped history of every data element as a PDF or txt/JSON file. Metadata shall include data origin, author, workflow and algorithm version names, parameters and other values set.
  
  
  
  

• Product component details required:
  
  
  
  • Genome analysis – De-novo assembly, including trimming tools to remove low-quality data, and support for Sanger sequencing, short and long read NGS data and hybrid assemblies.
    
    
    
    • De-novo assembly and genome finishing
    
    
    • Whole genome alignment
    
    
    • Gene finding and annotation
    
    
    • Bisulfite sequencing
    
    
    • ChIP-seq analysis for transcription factors and histones
    
    
    
    
  
  
  • Transcriptomics - Workflows that cover the entire analysis process and accommodate any experimental design. All tools account for sequencing depth differences, removing the need to normalize input data.
    
    
    
    • RNA-seq analysis
    
    
    • Differential expression analysis
    
    
    • Transcript discovery
    
    
    • Single-cell analysis
    
    
    
    
  
  
  • Resequencing - Start detecting and comparing genetic variants, including low-frequency, single- and multi-nucleotide, copy number and other large structural variants, insertions, deletions and replacements.
    
    
    
    • Ultra-fast read mapping and comprehensive variant detection
    
    
    • Support for targeted amplicon panels, hybrid capture and WGS
    
    
    • Consensus sequence creation
    
    
    • Oncology scoring tools for TMB, MSI and HRD
    
    
    • Viral integration site detection
    
    
    
    
  
  
  • Microbiome metagenomics and meta transcriptomics – Ability to investigate outbreaks and antimicrobial resistance.
    
    
    
    • Microbiome analysis (OTU and ASV)
    
    
    • Taxonomic profiling
    
    
    • Metagenomic binning and assembly tools
    
    
    • Functional annotation and pathway analysis
    
    
    • Microbial outbreak analysis, including AMR and virulence typing, MLST support and SNP, k-mer and minimum spanning trees
    
    
    
    
  
  
  
  

• Website shall include the following security features:
  
  
  
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    • Hosted on servers owned by the vendor and located in SSAE 18 SOC 2 Type II certified data centers
    
    
    • Support of two factor authentication
    
    
    • Support of IP whitelist access restriction
    
    
    • Performance of annual penetration testing
    
    
    • Project level data access control
    
    
    
    
  
  
  
  

The Periods of Performance for this contract are as follows:

Base Period - 30 May 2025 - 29 May 2026

Option Period 1 - 30 May 2026 - 29 May 2027

Option Period 2 - 30 May 2027 - 29 May 2028

Option Period 3 - 30 May 2028 - 29 May 2029

Option Period 4 - 30 May 2029 - 29 May 2030

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