updated_Technical_Proposal_Instructions_Amendment_1.pdf

Additional Technical Proposal instructions March 2016

Additional Technical Proposal instructions

These Technical Proposal instructions reflect the requirement of the RFP and provide additional instructions for the preparation of the Technical Proposal. While Section L of the RFP provides a generic set of Technical Proposal instructions, these additional instructions are tailored to the specific requirements of the RFP.

Offerors are advised to give careful consideration to all aspects of the Statement of Work (SOW), the Mandatory Qualification Criteria, the Technical Evaluation Criteria, and the RFP as a whole in the development of their proposal. The offeror may include additional pertinent information within the guidelines listed below. The offeror shall refer to all referenced documents in the RFP and attachments.

The proposal, including appendices, shall include a detailed table of contents, be formatted by sections, and be cross-referenced to the Technical Evaluation Criteria. In addition to FIVE full paper copies of the proposal, the offeror shall submit TWO discs containing electronic copies (password protected; use Password: BIOINFO2016) of the Technical Proposal including appendices in a PDF searchable format.

Proposals should NOT include links to Internet website addresses or otherwise direct readers/reviewers to alternate sources of information.

The offeror shall submit a detailed plan indicating how each aspect of the SOW is to be accomplished.

• The Technical Proposal shall include information on how the project is to be organized, staffed, and managed.

• Information should be provided to demonstrate the understanding of management of time frames for planning and accomplishing the work.

• The Technical Proposal shall be in as much detail as necessary to explain the proposed methods and rationale, and should reflect a clear understanding of the nature of the work being undertaken.

• The Technical Proposal shall include unique arrangements, facilities, equipment, or other factors that the offeror deems advantageous to the project.

• The offeror shall include all information and supporting documentation addressing the mandatory qualification criteria in one clearly marked section of the Technical Proposal.

In order to facilitate efficient preparation and review of proposals and reduce paperwork burden, the following page limits shall apply to the technical proposal. Additionally, the total proposal including appendices shall not exceed 25 MB.

Aspect Page limit* Mandatory Qualification Criteria #1 5 Pages Mandatory Qualification Criteria #2

20 Pages

Technical Evaluation Criteria

1. Personnel Personnel Description o 2 pages for Key Personnel o 1 page for additional technical

Aspect Page limit* personnel by job function (e.g.

bioinformatics analyst)

Summary Table--NOT LIMITED (summarizing personnel and years of experience)

2. Technical Approach 25 pages

3. Sample Assignments 25 pages per dataset (100 pages total)

4. Project Management and

Coordination 20 pages

5. Environment – Facilities, Equipment, and Security

No page limit

Appendices

A. Biographical sketches** 5 pages/person B. Data Management Plan 50 pages C. DRAFT Information

Technology Security Plan 50 pages

*The total proposal including appendices shall not exceed 25 MB.

**Required for all personnel with a Master’s or Doctorate degree, or the equivalent in experience and/or responsibility.

Specific Technical Proposal Evaluation Criteria Instructions

Each individual criterion of the Technical Evaluation Criteria is provided below followed by a list of information that offerors shall submit as part of their Technical Proposal in response to the Technical Evaluation Criteria.

1) Technical Evaluation Criteria 1—Personnel

Provide the following:

i) Summary Table—Provide a table of personnel that will work on the project, including major roles/disciplines on the project, highest degree, years of experience, proposed effort on (percent time), and availability to the project. List additional technical personnel and total effort to the project by job function (e.g. bioinformatics analyst). If subcontractors/consultants are proposed, they shall be included and designated as such. The Principal Investigator, Lead Bioinformatician and Lead Biostatistician shall be considered key personnel.

ii) Personnel Position Descriptions-Provide a position description of all personnel along with a description of their proposed duties. This description shall be limited to 2 pages for each key personnel/critical staff and 1 page for other professional personnel and should be included in the proposal body. If key personnel/critical staff are committed to other government-supported projects, include their time commitment to these projects.

iii) Biographical Sketches-Provide a biographical sketch for all key personnel and all other personnel (in an appendix) with a Master’s or Doctorate degree, or the equivalent in experience and/or responsibility. Use the biographical sketch form in Attachment #7 of the RFP. Include information to document relevant training, experience, scientific expertise (professional staff only), and competencies relevant to the bioinformatics requirements outlined in the Statement of Work. Include selected references for publications relevant to the scope of the project (limited to 5 pages; see RFP), necessary for the successful completion of all contract requirements.

Principal Investigator-The biographical sketch for the PI shall include evidence of an advanced degree in bioinformatics, biophysical computation, applied sciences or a closely related field. The biographical sketch shall also include a summary description of: prior bioinformatics projects, leadership positions, peer-reviewed publications, past scientific presentations (e.g. oral or poster) of bioinformatics work at scientific conferences and a description of experience with the specifications outlined in the Statement of Work (SOW).

Lead Bioinformatician-The biographical sketch for the Lead Bioinformatician shall include a summary description of: prior bioinformatics projects, previous positions relevant to bioinformatics, programming skills, peer-reviewed publications, past scientific presentations (e.g.

oral or poster) of bioinformatics work at scientific conferences and a description of experience with the specifications outlined in the Statement of Work (SOW).

Lead Biostatistician-The biographical sketch for the Lead Biostatistician shall include a summary description of: prior bioinformatics projects, previous positions, programming skills and experience with statistical analysis relevant to bioinformatics, peer-reviewed publications, past scientific presentations (e.g. oral or poster) of bioinformatics work at scientific conferences and a description of experience with specifications outlined in the Statement of Work (SOW).

Technical Support Personnel-Provide documentation of capabilities for the genomics bioinformatics methods outlined in the SOW included, but not limited to:

- DNA-Seq

- RNA-Seq

- ChIP-Seq

- FAIRE-Seq

- Exome-Seq

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

- Web mining protocol

- Text mining techniques

- Machine learning

- Adobe Acrobat Pro XI (the COR may require new version as new releases become available)

- Time trend and dose response analysis

- Use of genomic data visualization browsers and applications

- qHTS analysis – quantitative high throughput screening data analysis

- Chemoinformatic dataset analysis

NOTE - The Principal Investigator, Lead Bioinformatician and Lead Biostatistician are designated as key personnel. Key personnel are considered essential to the contract and shall be an employee of the contractor. The Principal Investigator shall be available to supervise and consult with each bioinformatics support staff and NIEHS scientists.

Experience in bioinformatic analysis of various types of NextGen sequencing data in genomics, epigenomics and transcriptomics is highly desirable since NIEHS staff require support in these diverse areas of biomedical science. The offeror should be able to contribute to the experimental design, analysis and data visualization on appropriate genome browsers.

Experience in toxicogenomics analysis (e.g. the study of chemical exposure on gene expression) is highly desirable since the use of microarray, RNAseq and other analysis are critical to the NIEHS mission. Use and familiarity with downloading and analyzing expression data from public databases is desired by NIEHS. Experience with access and analysis of hight throughput screening data from Tox21 activities is highly desirable. Experience in computationally assisted text mining and impact research are highly desirable to meet scientific and program needs.

2) Technical Evaluation Factor #2—Technical Approach

Provide the following:

a) Provide documentation to demonstrate the approach that will be used to accomplish the project requirements outlined in the Statement of Work, including overall strategy, methodologies, analyses, technologies, and services, including those that are novel or innovative. Provide a list of Standard Operating Procedures to be used in the management and technical conduct of these studies.

b) Provide documentation to demonstrate the offeror’s understanding of how all aspects of the project will be achieved.

c) Identify potential problems that may be encountered during performance of work under the project and solutions to these problems; identify alternative strategies to accomplish the goals of the project; identify benchmarks for success under the project.

3) Technical Evaluation Criteria #3-Sample Assignments

The sample assignments consists of a collection of datasets. Accessibility of datasets is at the url:

http://ntp.niehs.nih.gov/go/biodatasets . This website contains a 1) a Cover Sheet document; 2) a README document, describing the nature of the data files in each Dataset 1-4; and 3) a Bioinformatics Datasets document that requests specific outputs and how analysis was performed for each dataset. Each dataset (Dataset 1-4) contains raw data files (e.g. .CEL files; .bw files) explained in the README document that are to be used by Offerors in responding to questions posed in the Bioinformatics Dataset document for each dataset. Note that the data files can be opened using specialized software that could be a commercial product or an ‘open source’, meaning public, algorithm according to the Offerors choice. Offerors can open individual data files if desired and examine the data (e.g. numerical data, sequencing data, text data) but the objective is for Offerors to computationally process raw data in these data files using software or specific algorithms to deliver an output that addresses the posed questions for each dataset. A brief description is requested for the software or algorithms used and how they were used to obtain the outputs in each dataset.

http://ntp.niehs.nih.gov/go/biodatasets

a) The offeror shall carry out detailed analyses of four datasets which are provided at http://ntp.niehs.nih.gov/go/biodatasets. The datasets are typical of what might be encountered in the contract with DNTP and DIR scientists. Offerors will be given instructions on analysis objectives for each dataset as outlined above. Offerors shall fully describe analysis methods, carry out analyses of datasets, and report results of analysis. Analysis and documentation related to these 4 sample datasets shall be addressed in a clearly marked section of the proposal.

b) Describe the technical approach to the Sample Assignments. Provide a brief overview to demonstrate an understanding of the sample assignment. Include detail on how the sample work assignment is to be organized (i.e. staffed and managed) and conducted. Also, include dates for critical events, and details for the submission of all reports/deliverables. Include detail on all aspects of the work to be performed by contractor staff and any proposed subcontractors/consultants. Finally, identify potential problems or issues with the conduct of these assignments and proposed solutions to these problems or issues.

4) Technical Evaluation Criteria #4—Project Management and Coordination

a) For subcriteria a:

i) Provide a discussion of proposed approach to how data will be evaluated for quality and statistical significance. Provide details on assessing quality and statistical significance of NextGen sequencing data; of microarray data; of chemoinformatics data; of high throughput screening data; of text mining data; of impact research data.

ii) Provide a functional organization chart, including lines of reporting.

iii) Provide documentation of proposed project staff working together as a team. The daily interaction and constant coordination of efforts needed amongst these discipline areas throughout the performance of work makes it critical that they be physically and organizationally together.

iv) Provide the proposed approach for communication among project staff and with Government staff.

v) Provide details on the scope of the project, how work will be scheduled, and how progress will be monitored.

vi) Provide a summary of Corporate experience in the conduct and management of bioinformatics analysis projects of similar size, scope, and complexity to those described in the SOW.(This includes projects of any proposed subcontractors)

vii) Provide documentation of offeror’s flexibility to perform multidisciplinary assignments and manage multiple bioinformatics projects. Note that these assignments may occur simultaneously on occasion. Describe how staffing will be handled during periods of peak activity (e.g., close to deadline) to ensure continued progress on all ongoing assignments.

http://ntp.niehs.nih.gov/go/biodatasets

viii) Provide an explanation for use of any proposed subcontractors and documentation of procedures for acquisition and oversight of any proposed subcontractors/consultants. If any subcontractors/consultants are proposed, the offeror must clearly define how any proposed subcontract/consultant arrangements would meet program needs. A letter of commitment from each subcontractor/consultant must be provided. If subcontracting is proposed, details must be given as to how this would be structured, organized, managed, and monitored.

b) For subcriteria b:

NOTE: The Principal Investigator is designated as key personnel. As key personnel, the PI is considered essential to the contract and shall be an employee of the contractor. The Principal Investigator must be knowledgeable in all aspects of the Program/contract, including the status of bioinformatics studies, record keeping, reporting, and detailed analysis of cost for any or all functions which make up the total contract operation.

i) Provide detail on the PI’s experience in the leadership, management, and coordination of multidisciplinary projects requiring bioinformatics analysis similar to those described in the SOW and evidence of managing contractual activities. Include experience supervising bioinformatics personnel.

ii) Provide a summary outlining how the PI will provide daily management of the contract and serve as the point of contact for communication with Government officials. Include any evidence of the PI’s experience in managing and/or supervising large-scale bioinformatics programs across all disciplines described in the SOW.

5) Technical Evaluation Criteria #5 - Environment – Facilities, Equipment and Security

a) For subcriteria a:

Provide detailed facility floor plans that exhibits work space for employees and equipment relevant to technical conduct of work on the project. Include all disciplines relevant to the contract with clear labels as to the location of equipment and function/use of all rooms. Describe available space for the performance of work. Document compliance with all applicable Federal and state regulations and guidelines for all aspects of the contract. Include the above for any proposed subcontractors/consultants.

b) For subcriteria b:

i) Describe equipment and physical resources proposed for use on all aspects of the contact, including descriptions and locations of the equipment. Demonstrate the ability to obtain any other necessary equipment in support of the work identified herein.; include procedures for handling/disposal of biohazards; include those of any proposed subcontractors/consultants.

c) For subcriteria c:

i) Provide information to document policies and procedures surrounding data collection, management, and security.

ii) Provide a draft IT Security Plan for ensuring integrity and security of information.