RFP 75N96022R00001_Attachments.pdf

RFP-75N96022R00001 Attachment 1

PACKAGING AND DELIVERY OF PROPOSAL Page 1 of 2

Packaging and Delivery of Proposals for Use with the NIH electronic Contract Proposal Submission (eCPS) Website

I. PROPOSAL SUBMISSION

A. eCPS

1. Proposals must be submitted via the electronic Contract Proposal Submission (eCPS) website at https://ecps.nih.gov.

2. Proposals submitted by facsimile or e-mail will not be accepted.

3. Follow the “How to Submit an Electronic Proposal” instructions provided on the eCPS website at: https://ecps.nih.gov/home/howto. Please note that creating an account to submit may take up to three (3) business days. Please apply for a new account early to allow enough time for the registration process.

4. Offerors are solely responsible for submitting proposals and any modifications or revisions so as to reach the Government office designated above by the date and time specified in the solicitation. If your proposal is not received by the date and time specified in the solicitation, it will be considered a “late proposal,” in accordance with HHSAR 352.215-70, Late Proposals and Revisions (December 18, 2015).

B. Creating and Naming Files:

1. Create one PDF file of your Technical Proposal, including all attachments. The Technical Proposal should be created in a PDF format that enables word searches to the maximum extent practicable. Forms and/or documents requiring signature(s) may be scanned but must be merged into the Technical Proposal PDF file.

2. Create one PDF file of your Business Proposal, including all attachments:

The Business Proposal should be created in a PDF format that enables word searches to the maximum extent practicable. Forms and/or documents requiring signature(s) may be scanned but must be merged into the Business Proposal PDF file. Additionally, the “Breakdown of Proposed Estimated Costs (plus Fee) with Excel Spreadsheet” (Breakdown of Proposed Estimated Costs (plus Fee) with Excel Spreadsheet) must be included in the Business Proposal.

3. Create your Business Document Excel. The Excel file should be the “Breakdown of Proposed Estimated Costs (plus Fee) with Excel Spreadsheet” (Breakdown of Proposed Estimated Costs (plus Fee) with Excel Spreadsheet) included in the Business Proposal in its original Excel format, not PDF. Multiple Excel files may be included, as necessary.

https://ecps.nih.gov/ https://ecps.nih.gov/home/howto http://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/spshexcl_dec2012.xlsx http://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/spshexcl_dec2012.xlsx http://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/spshexcl_dec2012.xlsx

RFP-75N96022R00001 Attachment 1

PACKAGING AND DELIVERY OF PROPOSAL Page 2 of 2

4. Each of the proposals, Technical and Business, must be separate and complete in itself.

Do not reference one proposal in another.

5. File naming convention: It is requested that the filenames for your Technical Proposal, Business Proposal, and Excel Workbook include the name of the offeror, the solicitation number, and the type of proposal (i.e., Technical, Business, or Excel Workbook).

Examples:

Technical Proposal: XYZ Company_NIHAI2012001_Technical.pdf Business Proposal: XYZ Company_NIHAI2012001_Business.pdf Excel Workbook: XYZ Company_NIHAI2012001_Business.xlsx

II. FORMATTING AND PAGE LIMITATIONS:

A. Formatting for proposals

1. Proposal page layout shall be letter size 8.5” x 11" for all pages.

2. Proposals shall not include links to internet web site addresses (URLs) or otherwise direct readers to alternate sources of information.

3. Proposals shall not include audio or video files of any type.

4. Font size must be 10 to 12 points.

5. Spacing should be no more than 15 characters per inch. Within a vertical inch, there must be no more than six lines of text.

6. Margins must be at least one-inch on all sides.

7. Failure to adhere to the formatting requirements above may impact whether your proposal is reviewed in its entirety.

B. Page limitations:

1. Each Curriculum Vitae (CV) shall not exceed 20 pages.

2. The response to the Sample Scenarios should not exceed 15 pages.

3. Pages exceeding limitations will be removed from the proposal and will not be considered.

RFP 75N96022R00001 Attachment 2

Statement of Work - SOW Page 1 of 9

STATEMENT OF WORK

Overview The National Institute of Environmental Health Sciences (NIEHS) requires bioinformatic analysis in support of research initiatives in the Division of the National Toxicology Program (DNTP) and the Division of Intramural Research (DIR). The fields of study are diverse and include, but are not limited to, toxicology, genomics, structural chemistry, high throughput screening, data and text mining, high content image analysis, and downloading and use of large public data sources. For bioinformatics needs, the Government wants to ensure: 1) delivery of consistent and reproducible bioinformatic data analysis, 2) delivery of software/program tools that meet study/government performance requirements, and 3) the Government rights to use, modify, distribute, and publish source code, data products, methods, and supporting documentation developed and/or used under this contract.

Background The NIEHS located in Research Triangle Park (RTP), North Carolina (niehs.nih.gov), is one of 27 research institutes and centers that comprise the National Institutes of Health (NIH) (nih.gov).

The mission of the NIEHS is to reduce the burden of human illness and disability by understanding how the environment influences the development and progression of human disease. In-house research at NIEHS is conducted by investigators in the DIR NIEHS DIR Research and the DNTP NIEHS DNTP Research. A goal of this research is to provide experimental and large-scale biological data that includes biological and technological advances in molecular and computational biology.

The DNTP has organized its strategic planning network around three Health Effects Innovation Programs including carcinogenicity, cardiovascular effects and developmental neurotoxicity aimed at developing disease-focused environmental toxicology as described in the url, Health Effects Innovation Programs (nih.gov). Scientific tools will be applied in an integrated fashion to provide an evidence-based approach that allows us to identify and understand potential environmental contributors to contemporary and common diseases. In addition, there are exposure-based, responsive-focused and capabilities-building research programs in the url, National Toxicology Program (NTP) Division Strategic Planning Framework (nih.gov).

Current DNTP study initiatives include examining the effects of per- and polyfluoroalkyl substances (PFAS), endocrine disruptors, botanical supplements, chemical mixtures and nanomaterials, cell phone radiation, and new approaches to advance high throughput (high speed and high quantity) screening of chemicals to reduce the number of animals used in research. High throughput in vitro screening assays are conducted both within the DNTP and in collaboration with the National Center for Advancing Translational Sciences (NCATS) and the http://www.niehs.nih.gov/index.cfm http://www.nih.gov/ https://www.niehs.nih.gov/research/atniehs/dir/index.cfm https://www.niehs.nih.gov/research/atniehs/dntp/index.cfm https://www.niehs.nih.gov/research/atniehs/dntp/strategic-plan/health/index.cfm https://www.niehs.nih.gov/research/atniehs/dntp/strategic-plan/health/index.cfm https://www.niehs.nih.gov/research/atniehs/dntp/strategic-plan/index.cfm

Statement of Work - SOW Page 2 of 9

Environmental Protection Agency (EPA). Several DNTP Offices are engaged in evaluating scientific literature on selected topics (Integrative Health Assessment Branch and Office of Policy, Review and Outreach).

The NIEHS DIR conducts research on biological and chemical processes, the role of environmental agents in human disease and dysfunction, underlying mechanisms of environmentally associated diseases, and intervention/prevention strategies to reduce the effects of exposures to environmental agents. Specific DIR research topics may be found at NIEHS DIR Research.

NIEHS requires bioinformatic analysis in support of DNTP and DIR research initiatives. The fields of study are diverse and include, but are not limited to, toxicology, genomics, structural chemistry, high throughput screening, data and text mining, high content image analysis, and downloading and use of large public data sources. For bioinformatics needs, the Government wants to ensure: 1) delivery of consistent and reproducible bioinformatic data analysis, 2) delivery of software/program tools that meet study/government performance requirements, and 3) the Government rights to modify, distribute and publish source code, data products, methods, and supporting documentation developed and/or used under this contract.

General Requirements

1. Independently, and not as an agent of the government, the contractor shall provide all the necessary services, qualified personnel, material, equipment, and facilities not otherwise provided by the Government as needed to assist in the performance of the bioinformatics, data mining and computational activities described herein.

2. The contractor shall provide support to conduct bioinformatics projects on NIEHS data as directed by the Contracting Officer’s Representative (COR). When carrying out the work described below, in consultation with the COR, the contractor shall use a variety of statistical, mathematical, and computational methods, which include, but are not limited to applications to genomics, text mining, structure activity relationships, high throughput screening, and other assessments. Deliverables may include, but are not limited to data analysis, analysis pipelines, programming, or source code, informatic products, data sets created, databases created/constructed, approaches and solutions as directed by the COR.

3. The government intends to distribute data and products generated under this contract for use by the public under the MIT license agreement (https://opensource.org/licenses/MIT) or equivalent unless otherwise specified. Accordingly, the Contractor shall provide NIEHS (DNTP http://www.niehs.nih.gov/research/atniehs/dir/index.cfm https://opensource.org/licenses/MIT

Statement of Work - SOW Page 3 of 9 and/or DIR) with a copy of the tools including binaries, code annotations, documentation, and software generated. NIEHS (DNTP and/or DIR) will have unlimited rights in the tool, which shall include object and source code, consistent with FAR 52.227-14 and shall have the right to modify the software and its documentation for government purposes. The Government shall have unlimited rights in the software, consistent with FAR 52.227-14, and shall have the right to modify, distribute, and share object and source code and data made under this contract unless stated otherwise by the COR. Publicly accessible, non-proprietary program language, as determined by the Government shall be used by the Contractor to develop all software under this contract unless the COR specifies otherwise. See FAR 27.409(b)(1) Rights in Data – General 52.227-14).

4. Code delivered to the government shall be written in such a way as to run on government servers and/or systems, adhere to government security and other standards such as compliance with section 508 of the Rehabilitation Act. Contractor shall provide updates to software to address evolving security policies and other standards. Contractor shall supply support to ensure that the code can transfer smoothly to the government network and run as expected; training for use of products shall be provided by the Contractor upon request.

Code shall be delivered according to the schedule established by the Government. Generally, code shall be delivered at the completion of an assigned project. In addition, contractor shall deliver an updated compilation of code every 6 months from the contract start date for all projects unless the COR directs otherwise. It may not be feasible to ascertain all the data/code requirements at the contract award (FAR 52.227-16 and FAR 27.406-2).

5. For new products, contractor may not incorporate any propriety-nongovernment object or source code or data in performance of the government contract unless such data, object or source code are identified. Furthermore, if directed by the COR, prior to incorporation in any product, contractor shall grant to the government a worldwide, nonexclusive, royalty-free irrevocable license to use such data, object or source code in perpetuity including, but not limited to the ability to use, copy, modify, merge, publish, and distribute the data, object, or source code. All of the above applies to any subcontractor approved under this contract.

6. Contractor shall test Code and go through a process of quality assessment to identify and remove errors, unless the Government requests otherwise (e.g., to receive interim code). The Government will review Code/deliverables and may require edits/adjustments prior to acceptance which shall be made by the Contractor in a timely manner.

7. The government may require the Contractor to provide access to tools available on the open market to conduct government work (e.g., Ingenuity Pathway Analysis, Qiagen).

Statement of Work - SOW Page 4 of 9

8. The contractor shall consult with the COR and COR-designated NIEHS staff regarding its various bioinformatics activities and shall report results of data analyses to the COR and COR-designated NIEHS staff, committees and workgroups as directed by the COR.

9. The Contractor shall access the NIEHS’s CEBS (Chemical Effects on Biological Systems) database for download and upload of raw data as directed by the COR. Data files shall be in standard scientific, or industry standard formats approved by the COR for computer compatibility. In addition, data may be provided from other sources as determined by the Government. Results of analysis shall be deposited in CEBS using a standard format or other location as directed by the COR. Standard metadata shall be provided by the Contractor. If requested, the Contractor shall deposit on a server indicated by the Government for pilot use to determine operational capability.

10. The Contractor shall understand and stay current with new trends and developments in multiple areas of bioinformatics, data/text mining and computational methods and advise the Government regarding possible utilization of these procedures. Since bioinformatics is broad and is cross-disciplinary, this may involve but not be limited to multiple areas of biology including toxicology, genomics, gene expression, stem cell biology and other scientific areas such as biocomputation to develop supportive algorithms, innovative bioinformatic pipelines and tools.

11. The Contractor shall possess and maintain the ability to participate in frequent interactions with the COR or other designated researchers during regular business hours as there are often issues of experimental design, data analysis, and understanding of nuances of data analyses that require in-depth discussion and development of solutions together in real time.

Such interactions usually occur with short notice (less than 24 hours) and must be addressed quickly to facilitate timely progress of work. In addition, the Contractor shall attend various NIEHS meetings identified by the COR, including meetings on reports or other topics (generally on a bi-monthly or more frequent basis) to provide context for information reported by the contractor. Therefore, the Contractor shall maintain the capability to participate in such meetings and provide a one-hour response time to ensure rapid, coordinated communication between the COR, NIEHS scientists and other groups to ensure efficient timing of resources for meeting the government’s schedules. Regular business hours are: Monday – Friday 9:00 am to 5:00 pm Eastern time excluding Federal holidays.

12. All work described herein shall be performed in coordination with the Government. All specifications, requests, technical direction, and changes to technical direction will be

Statement of Work - SOW Page 5 of 9 provided to the contractor by the COR. At times, the Government may revise the endpoints, types of analyses needed, source of study data, or the format required. The actual number, type and mix of studies for which analyses are required may be higher, lower, or different than the number, types and mix of studies indicated below, depending upon the needs of the government and available funding.

13. Badges (identification cards) to access NIEHS resources such as the library, NIEHS network, and government data will be required. Upon proper security clearance, the Government will provide select Contractor staff access to the NIEHS/NIH library and electronic resources (NIH Library) as well as relevant NIEHS/DNTP databases. In order to access these resources and databases, the Contractor staff must obtain NIEHS security badges and shall pay any travel costs associated with attaining badges. Contractor government badge holders shall meet annual DHHS/NIH/NIEHS security training requirements and all training indicated in contract.

The Contractor shall adhere to NIH/NIEHS requirements for connecting to the NIEHS information technology resources. The Contractor’s equipment used for access, such as computers, as well as software, shall support Internet and Intranet connections, shall be compatible with NIH computer operating systems, and shall comply with NIH security policies. The Contractor shall be responsible for providing appropriate and reliable internet connectivity to complete work. The Contractor shall have adequate internet bandwidth to conduct and participate in virtual meetings and to make virtual presentations.

Specific Technical Requirements:

1. DATA ANALYSIS SUPPORT FOR GENOMIC AND EPIGENOMIC SEQUENCING DATA.

NIEHS conducts genomics studies such as exon-captured DNA-Seq and whole genome and DNA amplicon panels of biological samples that require bioinformatics data analysis. These studies include NextGeneration Sequencing (NGS) of genomic samples by DNA-Seq from a variety of species. NIEHS also conducts various epigenomic studies (DNA and/or histone methylation) utilizing bisulfite NGS sequencing or microarray platforms. The Contractor shall be able to identify differentially methylated regions (DMRs) on DNA and histones within the genome. The contractor shall provide bioinformatics and data mining support for the analysis of data from platforms including but not limited to DNA-seq, exome-seq and epigenomic data, and shall advise on the design of experiments generating these data. It is anticipated that there may be approximately 6-8 genomic and epigenomic sequencing bioinformatics studies per year.

http://nihlibrary.nih.gov/researchtools/Pages/default.aspx http://nihlibrary.nih.gov/researchtools/Pages/default.aspx

Statement of Work - SOW Page 6 of 9

2. TRANSCRIPTOMICS AND TOXICOGENOMICS SUPPORT.

NIEHS conducts toxicogenomics studies (transcriptomics applied to toxicology) as part of short term, long term and/or in vitro exposure studies followed by use of microarray or Next Generation Sequencing (NGS) platforms. This requirement focuses on transcriptomic data including mRNA transcripts, microRNA, and non-coding transcript data. Toxicogenomic studies generate vast amounts of gene expression data that require bioinformatics data analysis such as quality control statistics, normalization, identification of differentially expressed genes and assignment of genes to pathways and networks for biological analysis/interpretation. The contractor shall provide bioinformatics and data mining support for the analysis of RNA-Seq and microarray data. Familiarity with other toxicogenomics database resources (e.g., GEO, SRA) and browsers (e.g., UCSC browser) is required. To support transcriptomic and toxicogenomics studies, the Contractor will extract data from a variety of sources including large public and private databases. For example, any Tox21 chemicals and transcript expression data may be extracted from databases; data integration and mining may be requested from documents in EPA dockets. It is anticipated that approximately 5-7 transcriptomics studies per year will need bioinformatics support.

3. HIGH THROUGHPUT TRANSCRIPTOMICS (HTT).

As NIEHS embarks upon the next phase of Tox21 program, the DNTP is conducting transcriptomics experiments using high throughput platforms to screen large numbers of chemicals (See Ramaiahgari et al 2019, ToxSci 169:553-566). For this purpose, the Contractor shall assist with selection of key genes to be included in the screening as well as selection of relevant platforms for screening experiments. The Contractor, in consultation with the COR, may participate in experimental design, gene or cell line selection and bioinformatics analysis of the resulting data. The data to be generated will depend upon the choice of platform used by NIEHS for HTT. The Contractor shall provide bioinformatics support for large scale high throughput transcriptomics studies such as the S1500+ platform (See Ramaiahgari et al (2019) Tox Sci 169:553-566). The Contractor shall provide bioinformatics support for approximately 3-5 high (and/or medium) throughput transcriptomics studies per year.

4. BIOSTATISTICAL, COMPUTATIONAL AND INFORMATIC METHODS.

Contractor shall apply computational, mathematical, and statistical methods to address bioinformatic/biological problems such as analysis of genetic/genomic, in vitro, and in vivo laboratory data, including multi-scale modeling. The contractor shall use algorithms to efficiently extract/process data. Various supervised and unsupervised machine-learning methods shall be used based on data project needs for high efficiency, interpretability, and performance. The Contractor shall provide biostatistical, computational, informatic and reporting support for approximately 6-8 studies per year.

Statement of Work - SOW Page 7 of 9

5. QSAR AND READ-ACROSS (CHEMINFORMATICS) SUPPORT FOR HTS DATA ANALYSIS AND

INTEGRATION.

DNTP conducts high throughput screening assays on hundreds to several thousand chemicals through the Tox21 program. The high throughput assays include more than one hundred different in vitro assays conducted on approximately 10,000 compounds as described in the url (tox21 - PubChem Substance - NCBI (nih.gov)). In consultation with Government, the Contractor shall provide cheminformatics support for high throughput and medium throughput screening studies. Support includes but is not limited to analysis of dose-response associations, comparing responses across assays and across chemicals, use of chemical features along with other available data to make predictive models and conduct activities for combining, visualizing, and/or comparing large volumes of data. Data integration support includes, but is not limited to, use of strategies for acquiring and combining data from various sources to make it available for constructing molecular structure-based predictive models and read-across protocols. Computational support includes, but is not limited to, implementation of data analysis pipelines for efficient data analysis. The Contractor shall provide bioinformatics and reporting support for approximately 3-4 cheminformatic studies per year.

6. IMAGE ANALYSIS AND PATTERN RECOGNITION.

The Contractor shall analyze cell culture images for morphological changes indicating subcellular structural (e.g., mitochondria, nucleus) and physiological changes (e.g., calcium signaling) related to chemical exposure. For example, machine and deep-learning based automated classification methods could be used to determine gradations of chemical-cytotoxicity from high throughput cell-based screening studies. Cell culture imaging may include different cell types (e.g., hepatocytes, neural cells, cardiomyocytes) two-dimensional (2D) cultures, 3D spheroids or complex multicellular structures and organoid in cultured or microphysiological systems as well as pathology images. The Contractor shall implement imaging algorithms to meet specific project needs. The Contractor shall provide bioinformatics support for up to approximately 2-3 image analysis projects per year.

7. INFORMATICS METHODS AND INFORMATION MINING FOR SCIENTIFIC LITERATURE-BASED

REVIEWS.

DNTP conducts literature-based evaluations that identify, capture, and assess published scientific literature, gray literature (i.e., academic, industry, or government reports available but not published in typical journals or captured in bibliographic databases), and government or publicly available research data. To assist with this process, the Contractor shall provide computational/informatics support to identify, adapt and/or develop approaches such as https://www.ncbi.nlm.nih.gov/pcsubstance/?term=tox21

Statement of Work - SOW Page 8 of 9 natural language processing, text mining, and/or machine learning, and develop/implement methods/tools for scientific literature-based reviews. The Contractor shall implement computational/informatics approaches including but not limited to literature mining, web-mining of the internet, and natural language processing/generation. These efforts shall be designed to interoperate with existing ontologies, data vocabularies and data models. The Contractor shall provide bioinformatics support for up to approximately 2-3 scientific literature-based projects per year.

8. SUPPORT FOR STUDY DESIGNS.

It is anticipated that, unique/new study designs or experiment types may be adopted by the NIEHS, which may require bioinformatics analysis methods specific to these designs.

Contractor contribution to study design shall include but is not limited to types of data reduction methods employed such as clustering analysis and/or data visualization, pathway analysis employed (such as KEGG pathways Kyoto Encyclopedia of Genes and Genomes), IPA (Ingenuity Pathway Analysis, Qiagen) analysis and/or GSEA (Gene Set Enrichment Analysis) and/or SVM (support vector machine) analysis. The Contractor shall provide a data management plan for studies as required. The Contractor shall provide bioinformatic support for up to approximately 3-4 study design or related projects per year.

9. COMPUTATIONAL SUPPORT.

The Contractor shall assist in the coding for biostatistical/computational programs including but not limited to Java, Python, C++, and R. Activities supported shall include but are not limited to bioinformatics, natural language processing, text mining, interactive data interrogation tools, machine learning, and biostatistical methods; support shall include testing and deployment of bioinformatic and software tools. The Contractor shall provide bioinformatics support for up to approximately 3-4 projects each year.

10. PUBLICATION AND MEETING PRESENTATION SUPPORT.

The Contractor shall assist in organizing data for publication/presentations, meetings, or peer-reviewed publications. Such assistance shall include but is not limited to constructing graphs, tables and figures from data; providing written text to summarize methods and results for publication or presentations; providing relevant citations and references to support analytical procedures; reviewing draft technical reports, manuscripts and related information; providing power point slides that summarize data analysis approaches; making presentations of data to study design teams in DNTP and DIR to discuss and interpret data and providing assistance in entering data files into public databases (e.g. GEO, SRA) as required for publication. The contractor shall provide bioinformatics support in publication

Statement of Work - SOW Page 9 of 9 assistance and meeting presentations for approximately 6-8 publications and presentations each year.

11. TRAVEL.

From time to time, travel may be required as determined necessary by the COR to attend scientific meetings such as the Society of Toxicology Annual Meeting for the Contractor to make oral or poster presentations that will further the interests of DNTP or DIR programs on projects related to the work as described in this SOW. Any travel shall require prior written approval of the Contracting Officer and shall be in accordance with Federal travel regulation and NIH Efficient Spending Policy.

GOVERNMENT FURNISHED PROPERTY

The following Government-furnished property will be made available to the successful offeror for use in performance of the resultant contract:

Description:

[Name, Part Number and Description, manufacturer, and National Stock Number (if needed for additional identification tracking and/or disposition).]

Quantity/ Unit of Measure

Unit Acquisition

Cost Item

Identifier

Furnished “As-Is”

* YES NO

*When property will be furnished in “as-is” condition, the Contractor will be given the opportunity to inspect such property prior to the property being provided at a time and place mutually agreed upon by the Government and the Contractor.

The following statement is applicable for competitive solicitations:

The Contractor shall be responsible for all costs related to making the property available for use, such as payment of all transportation, installation or rehabilitation costs.

Government Furnished Property Page 1 of 1 (2/2011)

RFP 75N96022R00001 ATTACHMENT 3

RFP 75N96022R00001 NIEHS Bioinformatics Support ATTACHMENT 6

ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS

These additional Technical Proposal instructions are tailored to the specific requirements of the RFP and provide specific instructions and formatting specifications for the Technical Proposal.

These instructions shall be used in conjunction with Section L of the RFP, which provides Technical Proposal instructions applicable to all National Institutes of Health (NIH) solicitations.

The information requested in these instructions shall be used, along with Sections L. and M. of the RFP, to format and prepare the Technical Proposal.

Offerors are advised to carefully consider the Statement of Work (SOW) and Attachments, Technical Evaluation Factors per Section M, and the entirety of the RFP in the development of their Technical Proposals. Offerors should not assume that the evaluation panel is aware of the offeror’s abilities, capabilities, plans, facilities, organization, or any other pertinent fact that is important to the accomplishment of required services.

Discuss any specific factors which support your technical proposal using specifically titled subparagraphs. These factors may include unique arrangements or other characteristics that may be considered advantageous for effective implementation of this project.

The Technical Proposal, including appendices, shall include a detailed table of contents, be formatted by sections, and be cross-referenced to the Technical Evaluation Criteria. It is recommended that Offerors use the following template for the development of the Technical Proposal and present information in the order specified below.

PART I: COVER PAGES AND TABLE OF CONTENTS

A. PROPOSAL TITLE PAGE.;

B. TABLE OF CONTENTS. Include a Table of Contents with indicated pages of proposal sections that at a minimum uses the Headings and Subheadings that appear below.

Additional subheadings may be entered at the Offeror’s discretion.

PART II: MANDATORY CRITERIA

Offerors shall place all information which documents or supports the mandatory qualification criteria in one clearly marked section of the technical proposal.

1. The Offeror shall demonstrate the ability to meet the required response time as described in the mandatory criteria. Provide documentation of staff availability during NIEHS normal business hours of operation, including documentation of adequate internet services/speed, availability of and use of virtual meeting software, and access to appropriate cellular connectivity when required. Staff must have the ability to obtain NIEHS badges in order to access government data via the internet. Information regarding background checks can be found at (background-checks-info).

2. The Offeror shall prepare and submit a completed Voluntary Product Accessibility Template (VPAT) (Version 2.1 or later) and an Accessibility Conformance Report (ACR) to indicate the ability to meet all required Section 508 requirements applicable to this project.

PART III: TECHNICAL EVALUATION CRITERIA

SECTION 1: APPROACH AND UNDERSTANDING OF THE PROJECT (See TEC #1)

1. Describe the approach to successfully accomplish all areas of the SOW. The approach shall demonstrate an appropriate understanding of and experience in bioinformatics/biostatistics including genomics, epigenomics, transcriptomics, cheminformatics, image analysis, text mining, and computational support.

2. Sample Scenario: Provide a technical response to the Sample Scenario and ensure it is appropriately marked and identified as such in the proposal. Offerors shall construct a strategy and describe the technical approach for addressing each of the activities in the scenario. Describe in detail the type of informatics, databases, biostatistical tools and relevant software that would be used to solve the request, including a description of deliverables and the proposed staffing mix. Identify any potential problems and articulate solutions typically encountered in work described in the Sample Scenario, including alternative strategies and benchmarks for success. The response to the Sample Scenario should not exceed 15 pages.

SECTION 2: CONTRACT MANAGEMENT AND COORDINATION (See TEC #2)

1. To demonstrate approach to contract management, the Offeror shall provide a detailed management plan which addresses the following areas:

• Provide a functional organizational chart that describes the reporting structure of the organization.

https://gogovernment.org/background-checks-and-security-clearances-for-federal-jobs/

• Provide a staffing plan which details the mix of labor and level of effort required to accomplish the work.

• Describe procedures for how work will be scheduled, a description of timeframes for deliverables, and explain how progress will be monitored to ensure deadlines are met.

• Describe procedure for managing multiple bioinformatics projects simultaneously

• Describe procedures for ensuring quality of deliverables.

• Describe the approach for managing and retaining staff and maintaining an appropriate mix of qualified staff.

• Describe the experience and ability of staff to work together as a multi-disciplinary team and interact with sponsor researchers, including the ability to communicate, coordinate, and function as a coherent team with subcontractors, consultants and in interactions with the Government. The Principal Investigator shall be the lead of the team and facilitate effective communication between the government and contract staff.

• Describe procedures for oversight of any proposed subcontractors/consultants.

Describe the subcontractor/consultant’s role and provide a letter(s) of commitment plus documentation of expertise, qualifications and prior performance, and a narrative describing how the subcontractor/consultant will be managed. Describe how to handle privity of contract issues, i.e., explain how information will flow between NIEHS, the Offeror, and any subcontractors since the prime contractor's presence is required for any discussions.

• Describe procedures to prevent and/or mitigate potential and actual conflicts of interest.

SECTION 3: PERSONNEL QUALIFICATIONS (See TEC #3)

Clearly identify personnel in a list or table showing name, highest degree, organizational affiliation (employer), role on the project and percentage of effort to be committed to the project for all personnel including any subcontract personnel. Subcontractor staff shall be labeled as such.

At the time of proposal submission, the Offeror must provide documentation for each proposed Key Personnel indicating the availability to perform the work during the period of performance.

The Offeror shall assure that Key personnel proposed shall not be committed on all combined projects for more than a total of 100% of their time. The Offeror shall submit a completed

Summary of Related Activities form for each Key personnel proposed. Offerors shall provide the following information to demonstrate qualifications and experience of the proposed person:

1. Key Personnel

a. Principal Investigator (PI)

• Describe the duties of the PI and the proposed effort and availability to the project.

• The PI shall have an advanced degree in bioinformatics, biophysical, applied sciences or closely related field.

• Document leadership in directing multidisciplinary projects requiring bioinformatics analysis of toxicology and environmental health research problems; document participation and daily management of bioinformatics projects; document supervising bioinformatics personnel in a professional setting.

• Document past scientific presentations (e.g., oral or poster) of bioinformatics work at scientific conferences.

• Document experience in genomics experimental design and analysis of genomics, epigenomics and transcript-based gene expression data.

• Document experience in toxicogenomic studies including NextGen sequencing and/or microarray-based data analysis.

• Document experience with implementation of bioinformatics methods for the application of text, information, and data mining techniques within the environmental health sciences.

b. Lead Bioinformatician

• Describe the duties of the Lead bioinformatician and the proposed effort and availability to the project.

• The Lead Bioinformatician shall have an advanced degree in bioinformatics, biophysical, applied sciences or closely related field.

• Document experience in working with support personnel to manage a variety of bioinformatics and/or text mining projects.

• Document the ability to analyze NextGen sequencing data or microarray data-based data analysis; epigenomic data analysis; and text mining in literature-based research.

• Demonstrate adequacy of programming skills, preferably with software development experience and detailed working knowledge of bioinformatics and text information mining techniques to be applied to environmental health science-based research.

c. Lead Biostatistician

• Describe the duties of the Lead Biostatistician and the proposed effort and availability to the project.

• The Lead Biostatistician shall have an advanced degree in biostatistics, bioinformatics, biophysical, applied sciences or closely related field.

• Document experience working with support personnel to manage biostatistical support for a variety of bioinformatics and/or text mining projects.

• Document the ability to provide quality control metrics and biostatistical support for NextGen sequencing data or microarray data-based data analysis;

epigenomic data analysis; and text mining in literature-based research.

• Demonstrate adequacy of programming skills preferably with R or SAS, experience with statistical analysis of longitudinal and multivariate discrete data, familiarity with high throughput screening (HTS) data, toxicology studies, machine learning and experimental design as needed for genomics studies, dose-response, and environmental health studies.

2. Technical Support Personnel

Support personnel shall include technical staff to oversee and contribute to the development of computational tools and applications that support advanced bioinformatics capabilities, including tools for processing, analysis and interpretation of biological data (e.g., genomic, epigenetic, metabolomic, toxicogenomic), text mining and other data science activities.

Provide a list of all other proposed technical support personnel for the project with a description of role, education, training, experience, expertise, qualifications, and percentage of effort.

Offerors shall provide information to demonstrate qualifications and experience of the proposed support personnel as follows:

• Describe the support personnel’s ability to provide quality control metrics and bioinformatics/biostatistics support for a variety of data, including epigenomic and microarray, as well as literature mining and use of large databases.

• Provide information to demonstrate bioinformatics/biostatistics and computational expertise with evidence of publications in peer-reviewed literature and staff’s experience working in teams on projects of a similar scope as those described in the statement of work.

• Provide information to demonstrate experience ensuring tools are developed according to best practices for engineering/testing/deployment as well as maintaining and updating as required, including to match requirements needed to operate tools within government managed infrastructure.

• Provide information to demonstrate experience overseeing tools that run on Windows and/or Linux environments and are built in a variety of languages, including C/C++, Java, Python, R, JavaScript, HTML/CSS.

• Preferably, support personnel should have an advanced degree in computer science, data science or information science (or a combination of education and experience) and demonstrate experience working in a team environment.

• Document capabilities for project coordination/management as well as bioinformatics data analysis for the genomics bioinformatics methods that include, but are not limited to, the following molecular analyses:

- DNA-Seq

- RNA-Seq

- ChIP-Seq

- Exome-Seq

- NextGen Sequencing analysis including use of Bowtie, Cufflinks, Cuffdiff, GATK

- Web mining protocol

- Text mining techniques

- Machine learning based algorithms

- Artificial Intelligence based algorithms

- Adobe Acrobat Pro XI (new version may be required as new releases become available)

- Time trend and dose-response analysis

- Benchmark Dose Analysis (BMD)

- Use of genomic data visualization browsers and applications

- qHTS analysis – quantitative high throughput screening data analysis

- Chemoinformatic dataset analysis

SECTION 4 – ORGANIZATIONAL EXPERIENCE (SEE TEC #4)

1. Discuss recent prior experience (within the last five years) in conducting bioinformatics analysis projects that are similar in scope and complexity to the requirements outlined in the Statement of Work. Provide a brief synopsis of each project and explain how it relates to the activities required by this project. Identify areas where there is no work experience.

SECTION 5 – FACILITIES, EQUIPMENT, QUALITY ASSESSMENT AND SECURITY (SEE TEC # 5)

1. Provide information that demonstrates an adequate work environment for employees, including availability of all required equipment and adequate connectivity for a project of this size and scope. The information provided shall include a list of equipment, including hardware and software, available for use in performance of the work as described in the statement of work. Discuss the ability to obtain any other equipment that is necessary to support the work to be performed under the contract.

2. Describe the proposed approach and procedures for quality assessment and quality control.

Discuss details of organizational procedures and experience of staff.

3. Describe policies and procedures relating to data security management. Describe the training, experience, and competency of the proposed IT professionals as demonstrated by biographical sketch) and support staff, including specific duties and effort on the project;

include those of any proposed subcontractors/consultants. Provide a draft IT Security Plan in accordance with NIEHS and NIH requirements.

RFP 75N96022R00001 ATTACHMENT 10

Additional Business Proposal Instructions Page 1 of 3

ADDITIONAL BUSINESS PROPOSAL INSTRUCTIONS

These additional Business Proposal instructions reflect the requirements of the Request for Proposal (RFP). While Section L. of the RFP provides general Business Proposal instructions, these instructions are tailored to the specific requirements of the RFP and provide uniform costing assumptions and business clarifications.

The business proposal shall be submitted as a separate volume from the technical proposal. The following information should be used to assist offerors in preparing the business proposal.

A. Base and Options Structure

The contract shall be proposed as a cost reimbursement plus fixed fee type contract and shall consist of one (1) base year + six (6) optional years to extend for a total performance period of seven (7) years. In addition, Option II (Optional Quantities) may be exercised to add additional level of effort to the contract period of performance. This option may be exercised multiple times as needed during each period of performance, up to 5% of the base level of effort for that particular period.

B. Uniform Cost Assumptions

In order to estimate the total effort and cost for each year of the contract, offerors are to assume a start date of September 24, 2023 and shall use the following information to develop costs for each year of the contract:

1. Yearly Analyses and Reports – Assume that the following types and numbers of analyses and reports will be required each year of the contract. The amount of time required for each project can be variable, depending on the specific requirements. The estimate for the total number of bioinformatics projects per year is 46 projects at an average of approximately 500 hours per project:

a. Bioinformatics reports summarizing data analysis and methods for Genomic or Epigenomic technologies. (6 per year)

b. Bioinformatics reports summarizing data analysis and methods for Transcriptomic or

Toxicogenomics Data. (6 per year)

c. Bioinformatics reports summarizing data analysis and methods for High Throughput

Transcriptomics. (4 per year)

d. Biostatistical, Computational and Informatics Methods reports summarizing data analysis and methods for High Throughput Transcriptomics. (4 per year)

e. Bioinformatics reports summarizing data analysis and methods for conducting

Cheminformatics support for HTS data analysis and integration. (4 per year)

Additional Business Proposal Instructions Page 2 of 3

f. Image Analysis and Pattern Recognition reports summarizing data analysis and methods for conducting Cheminformatics support for Image Analysis and pattern recognition. (3 per year)

g. Bioinformatics reports summarizing informatics and information mining for scientific document review studies. (3 per year)

h. Bioinformatics reports summarizing study design reports. (4 per year)

i. Bioinformatics reports summarizing new bioinformatics methods development projects. (4 per year)

j. Publication and meeting presentation assistance projects combined. (8 per year)

2. Travel, Meetings, and Conferences – Assume all airfare to be economy class, and hotel and per diem at US Government rates for the applicable city/location. Virtual meetings may be substituted for in-person meetings at the discretion of the Contracting Officer’s Representative (COR). For purposes of proposing, assume the following:

a. Travel to one professional scientific meeting annually for one key personnel (for example, the

Principal Investigator), as described in the SOW. For costing purposes, assume travel from Raleigh, NC to San Diego, CA.

b. Other travel and meeting costs may be proposed based on management of subcontracts and other task activities.

3. Government Furnished Equipment –

a. Software and licenses: The contractor will be responsible for obtaining and maintaining all necessary licenses and access to commercially available software. The Government will provide access and licenses to any government-specific software and/or applications that cannot otherwise be obtained commercially.

b. Equipment: The Government will provide a small number of laptops with VPN capability for the Contractor’s use, as needed. All other equipment shall be the responsibility of the Contractor.

C. Business Proposal Format

Refer to Business Proposal Instructions, Section L of this solicitation. The Instructions contain the requirements for proper submission of cost/price data which must be adhered to. This format should be used as a guideline. It may require amending to meet the specific requirements of this solicitation. This format must be used to submit the breakdown of all proposed estimated cost elements. List each cost

Additional Business Proposal Instructions Page 3 of 3 element and sub-element for direct costs, indirect costs and fee, if applicable. In addition, provide detailed calculations for all items. For example:

• For all personnel, list the name, title, rate per hour and number of hours proposed. If a pool of personnel is proposed, list the composition of the pool and how the cost proposed was calculated.

List the factor used for prorating Year One and the escalation rate applied between years.

• For all materials, supplies, and other direct costs, list all unit prices, etc., to detail how the calculations were made.

• For all indirect costs, list the rates applied and the base the rate is applied to.

• For all travel, list the specifics for each trip.

• For any subcontract proposed, submit a separate breakdown format.

• Justification for the need of some cost elements may be listed as an attachment, i.e., special equipment, above average consultant fees, etc.

• If the Government has provided "uniform pricing assumptions" for this solicitation, the offeror should identify each item. If a deviation from the uniform cost assumption is made, identify the deviation, and provide an explanation.

Costs should be presented as follows:

• Base Years Cost Estimate (Base year and each of the 6 Option years) – provide a detailed cost estimate for the base year and each successive year.

• Overall Cost Estimate (Base + 6 Option years + Option II at 5% each year) – provide a cost estimate for the base year and each successive year which also includes the exercise of Option II (Optional Quantities). Assume Option II is exercised at the full 5% level of effort each year.

• Summary Cost Estimate (Base + 6 Option years + Option II at 5% each year) - include an overall total summary cost estimate for all years and options.

• Option for a 6-month extension - If…