Primary Contract Specialist
Secondary Contracting Officer
Baltimore, MD 21201
This notice of proposed acquisition is posted as an intent to award a FFP contract on a non-competitive basis to C M Cherry Consulting LLC to purchase Bioinformatics analysis of single cell RNA-sequencing data from developing and mature B cell populations of RelA, Rel deletion and wild type mouse models.
This acquisition is being conducted under Federal Acquisition Regulation (FAR) Part 13 - Simplified Acquisition Procedures, and FAR Part 12- Acquisition of Commercial Items, and the resultant contract award will include all applicable provisions and clauses in effect through Federal Acquisition Circular 2023-04 dated June 2, 2023.
The National Institute on Aging (NIA), Laboratory of Molecular Biology and Immunology (LMBI) research Intronic enhancer deletion models that have been studied in the LMBI’s lab to identify its role in B cell development, variable repertoire of B cells. It has previously found to grossly impair B cell development and only a few B cells escape to become mature B cells. However, these mice are apparently not immune compromised. So, it is important to know how limited BCR repertoire can compensate the immune response in these animals. B cells are a specialized type of immune cells that are involved in diverse function like antibody production, antigen presentation, T cell activation, memory response and many more. Hence, studying the individual B cell genomics is imperative to fully understand the varied outcomes and functional fates. Sc-RNA sequencing will help the lab to investigate the transcriptome at a single cell level in mouse B cells in presence and absence of the different transcription factors. However, bioinformatic analysis and interpretation of sc-RNA-seq data involves s high skill and expertise.
The Contractor shall perform the following tasks:
Complete data analysis of the combined single B cell RNA sequencing data set including all steps from alignment through finalized report generation. The contractor will also be responsible for explaining the results and working with the client to generate new analyses to follow up on interesting biological findings as they come up through the project. The contractor will be responsible for assisting the client in preparing the data in a coherent story for publication, preparing appropriate plots for preparation of figures, and detailing specific pitfalls that are common in submission of single cell data sets.
If not already run, the contractor will use Cellranger to run alignment on samples and verify good quality alignment. The results of Cellranger alignment and QC HTML documents will be explained and provided.
Filtering and QC:
The contractor will filter samples based on total UMI count, feature count, and percentage of mitochondrial genes and will generate an HTML report visualizing these quality control metrics by sample.
Batch effect correction and clustering:
The contractor will evaluate the presence of batch effect, and if present will correct it using Harmony.
The contractor will run appropriate clustering along with visualizations to assist in identification of clusters including marker genes requested by the client and differentially expressed genes by cluster.
All results will be compiled into an HTML report with accompanying table listing all differentially expressed genes by cluster.
The contractor will evaluate the proportion of cells from each sample and run statistics with associated covariates to identify clusters specific to covariates of interest.
The contractor will perform differential expression and gene set enrichment analysis comparing covariates of interest within clusters and among any other groups of interest.
All results will be compiled into an HTML report with accompanying tables giving numbers of cells per sample/cluster, all differential expression results, and all gene set enrichment results.
RNA velocity and pseudotime:
The contractor will perform RNA velocity and visualize changes in expression over time across cells grouped by similar phenotypes (i.e. all tumor cell).
The contractor will use pseudotime analysis to identify genes varying with time along potential differentiation trajectories.
All results will be compiled into an HTML report with accompanying tables giving all genes varying significantly with pseudotime trajectories of interest.
The government will provide all raw data to be analyzed by the contractor via Globus.
DELIVERY OR DELIVERABLES
All deliverable products shall be submitted for review, comment and approval by the client. Results may include HTML reports with PNG and PDF copies of all plots, excel-compatible tables, and individual PDF files. Edits will be made as needed based on clients’ additional needs and questions about results.
Initial QC deliverables will be given within 1 week of complete receipt of input data files and subsequent analyses will be delivered within 1 week of the receipt of request based on proceeding results.
DATA RIGHTS: The National Institute on Aging shall have unlimited rights to, and ownership of all deliverables provided under this contract including reports, recommendations, briefings, work plans and all other deliverables. This includes the deliverables provided under the basic contract and any optional task deliverables exercised by the contracting officer. In addition, it includes any additional deliverables required by contract change. The definition of “unlimited rights” is contained in Federal Acquisition Regulation (FAR) 27.401, “Definitions.” FAR clause 52.227-14, “Rights in Data-General,” is hereby incorporated by reference and made a part of this contract/order.
Contract Type: A Firm Fixed Price type order award not exceeding the Simplified Acquisition Threshold is anticipated to be awarded resulting from this requirement.
The Unique Entity Identifier (UEI), the Taxpayer Identification Number (TIN), certification of country of ownership, and the certification of business size must be included in the response.
All offerors must have an active registration in the System for Award Management (SAM) "www.sam.gov."
Quoter Terms and Conditions (To be completed by the Offeror):
1. Period of Performance OR Delivery Date After Receipt of Order:
2. Shipping Point (F.O.B. OR Destination):
3. Payment Discount Terms:
4. NIH BPA Number, if applicable:
5. SAM UEI Number:
6. Name of Company:
7. Street Address, City, State, Zip code:
8. Name of Person Authorized to Provide Quote:
9. Telephone Number and Email Address of Person Authorized to Provide Quote:
For equipment/parts/supply requirements under this requirement, if applicable, responses must include: the place of manufacturing (i.e., address if supply/equipment is a domestic end product and include country of manufacture).
ADDITIONAL TERMS AND CONDITIONS, PROVISIONS, AND REPRESENTATIONS
The FAR Clauses are incorporated by reference and are provided in full text at https://www.acquisition.gov/:
1. FAR Provision 52.212-1 Instructions to Offerors-Commercial Items (Mar 2023) is applicable to this solicitation.
2. FAR Provision 52.212.2 Evaluation-Commercial Items (Nov 2021) is applicable to this solicitation. The Government will evaluate quotations or offers in accordance with FAR 13.106-2 and award a purchase order from this solicitation to the responsible offeror whose quote conforming to the solicitation will be most advantageous to the Government, price and other factors considered. The following factors shall be used to evaluate quotes: Technical capability of the item offered to meet the Government requirement; Price; and Past performance [see FAR 13.106-2(b)(3)]
3. FAR Provision 52.212-3, Offeror Representations and Certifications Commercial Items (Dec 2022), is applicable to this solicitation.
4. FAR Clause 52.212-4, Contract Terms and Conditions-Commercial Items (Dec 2022) is applicable to this solicitation.
5. FAR clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders-Commercial Items (June 2023) is applicable to this solicitation.
6. FAR Clause 52.227-14, Rights in Data-General
In addition, the following FAR provisions and clauses are applicable to this solicitation and incorporated by reference:
1. 52.204-7 System for Award Management (Oct 2018),
2. 52.204-13 System for Award Management Maintenance (Oct 2018),
3. FAR 52.204-16, Commercial and Government Entity Code Reporting (Aug 2020),
4. 52.204-18 Commercial and Government Entity Code Maintenance (Aug 2020),
5. HHSAR 352.239-73, Electronic and Information Technology Accessibility Notice (December 18, 2015).
6. FAR 52.204-27, Prohibition on a ByteDance Covered Application (Jun 2023)
The following provisions and clauses apply to this acquisition and are available as an attachment. Offerors MUST complete the provision at 52.204-24 and 52.204-26 and submit completed copies as separate documents with their quotation.
1. FAR 52.204-24, Representation Regarding Certain Telecommunications and Video Surveillance Services or Equipment (Nov 2021)
2. FAR 52.204-25, Prohibition on Contracting for Certain Telecommunications and Video Surveillance Services or Equipment (Nov 2021)
3. FAR 52.204-26, Covered Telecommunications Equipment or Services Representation (Oct 2020) 3. NIH Invoice and Payment Provisions
4. NIH Invoice and Payment Provisions
All responses must be received by 9/18/2023, at 9AM EST and must reference announcement/solicitation number 23-011483. Responses may be submitted electronically to Randall Carter (Randall.email@example.com). Fax responses will not be accepted.
All responsible sources may submit response which, if timely received, must be considered by the agency.”
Interested parties may identify in writing their interest and capability in response to this requirement. Responses to this notice shall contain sufficient information to establish the interested parties’ bona-fide capabilities for fulfilling the requirement and include: unit price, list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov.
All responses must be received by closing date and must reference the announcement. Responses may be submitted electronically to the attention of the contract specialist. Fax responses will not be accepted.
All responsible sources may submit a bid, proposal, or quotation which shall be considered by the agency.