Amendment_2_RFP_NIHES2015048_20Apr2016.pdf

RFP Number : NIHES2015048 Amendment 2

- 1 -

OFFICE OF ACQUISITIONS

NATIONAL CANCER INSTITUTE

REQUEST FOR PROPOSAL NUMBER: NIHES2015048

Amendment No.: 2

Date of Issuance: April 20, 2016

The above numbered Request For Proposal (RFP) is amended as set forth below. The hour and date specified for receipt of Offerors changed to 3:30 p.m. E.S.T. on May 9, 2016.

Offerors MUST acknowledge receipt of the amendment prior to the hour and the date specified in the solicitation or as amended, by separate Electronic Mail which includes a reference to the RFP and Amendment numbers. For your convenience, the Proposal Intent Response Form is provided in SECTION J - List of Attachments of this RFP, for this purpose. This acknowledgement must also be included on NIH Form 2043 if a proposal is submitted.

FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERORS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN REJECTION OF YOUR OFFER.

This Amendment revises the RFP as stated below:

NOTE--Submission requirements have been updated. Please see response to Question #6.

Additional Questions and Responses

The Government's response to questions submitted regarding this solicitation are provided as follows:

RFP Questions

1. The RFP (Article B.2, on Page 4) requests pricing for a Base year, Option I (4 years), Option II (additional hours for the 5 years), and Options III to extend the contract for an additional 6 months. However the document "Technical Proposal Cost Summary Information" requests hours and direct cost information for Years 1-7. May we assume the following regarding the Technical Proposal Cost Summary Information:

• Base Year data is to be provided in Year 1,

• Option I data is to be provided in Years 2-5,

• Option II data is to be provided in Year 6, and

• Option III data is to be provided in Year 7

RESPONSE-The offeror's assumptions above are incorrect. The performance periods and quantities for the base contract and options are outlined throughout the RFP and in Attachment 11-Additional Business Proposal Instructions. Offerors are to use these specifications to prepare the Technical Proposal Cost Summary table referenced on page 49 of the RFP. Please note that the document entitled "Technical Proposal Cost Summary Information" is provided as a sample format and offerors should tailor this document to the specifics of this requirement.

2. The RFP (1_RFP_NIHES2015048.pdf) states on Page 27 in Article H.9, Section E.4 Vulnerability Scanning Requirements, that "This acquisition requires the Contractor to host an NIH webpage or database." However, there is no additional or supporting information regarding this requirement in the RFP or SOW documents. Please provide additional details regarding this requirement.

RESPONSE-The Vulnerability Scanning Requirements outlined on page 27 under Article H.9. are hereby deleted. Likewise, the Vulnerability Scanning Reports referenced on page 9, item "h" are also deleted.

3. With the exception of the requirement referenced in Question 19 (Article H.9, Section E.4, Vulnerability Scanning Requirements), specific information system requirements are not provided in the RFP or SOW documents. Please confirm that the only information system requirement for this contract is to support general purpose file storage for

- 2 -reports, plans, and other miscellaneous documents that may be created and maintained during the execution of the contract.

RESPONSE-The information security requirements are outlined in the RFP under Article H.9.-Information and Physical Access Security, which begins on page 20 and continues through page 27. Additional details regarding information security requirements are also provided on pages 7 through 9 and again on pages 52 through 62 of the RFP.

4. The RFP (Section L.1.d., Page 46) states that "2080 hours are to be assumed as a person year." Is the contractor's full-time equivalent an acceptable alternative if the annual number of hours proposed is based on the contractor's standard practices to estimate workable hours per year?

RESPONSE-The referenced statement could not be found anywhere in the subject RFP. When discussing the level of effort, the RFP clearly states the estimations provided are for "INFORMATIONAL PURPOSES ONLY".

The RFP further states that "it is the offeror's responsibility to ensure the actual hours and labor categories proposed is appropriate to accomplish the requirements and is consistent with the SOW". Please submit proposals accordingly.

5. Please clarify the formula suggested to bidders as a means to budget annual level of effort, reconciling the following:

a. In the RFP, section L.1.d Level of Effort (p. 46) estimates 24,960 direct labor hours per year.

RESPONSE--The number of 24,960 direct labor hours per year is correct.

b. In Attachment 11 Additional Business Proposal Instructions, section A. Yearly Activities, estimates 68 projects across nine task areas at an average of 400 hours per project, totaling 27,200 hours.

RESPONSE--The number of 68 estimated projects per year across the nine task areas is correct.

The number of 400 hours per project was a rough estimate. A more accurate estimate is 367 hours per project from 24,960 hours/68 projects. Therefore, 24,960 direct labor hours per year (not 27,200 hours) should be used.

c. In Attachment 3 Statement of Work, section B. Specific Technical requirements, 12 task areas are listed with estimated project counts. Nine of these correspond to those in Additional Business Proposal Instructions. Three of these areas (9. Informatics data extraction, 10. Support for Study Designs, 11. Support for New Bioinformatics Method Development) do not seem to be included in the estimated 68 projects, and potentially total an additional 13-19 projects.

RESPONSE--The other 3 tasks including #9. - informatics data extraction, #10. - support for study design, and #11. - methods development, are general tasks to be incorporated as needed among the 68 projects. Offerors are not expected to account for additional hours (not more than 24,960 hours per year) for these three general areas of need represented in these 3 tasks.

6. RFP Page 48: Please confirm that the Government requires a different number of copies for Technical and Business volumes. Also, please confirm the number of paper and electronic copies for the Technical volume.

RESPONSE-Please submit the following:

a. TECHNICAL PROPOSAL For the technical proposal: Include ONE (1) ORIGINAL AND FOUR (4) COPIES PLUS 2 CD copies (not to exceed 25MB).All CD copies shall be submitted using a .PDF searchable format and password protected (Use Password BIOINFO2016). The technical proposal, including any necessary appendices, shall be formatted by sections, cross-referenced and shall consist of a cover page, a table of contents, the information requested in the Technical Proposal Instructions, and the information specified in Section J, List of Attachments-Technical Proposal Attachments.

b. BUSINESS PROPOSAL For the business proposal: Include ONE (1) ORIGINAL AND FOUR (4) COPIES PLUS 2 CD copies. The CD copies shall be submitted using a .PDF searchable format and password protected (Use Password BIOINFO2016). The business proposal, including any necessary appendices, shall be formatted by sections, cross-referenced and shall

- 3 -consist of a cover page, a table of contents, and the information requested in the Business Proposal Instructions and as specified in Section J, List of Attachments.

c. SAMPLE ASSIGNMENT DOCUMENTATION For Sample Assignments, Offerors may submit additional back-up documentation as follows:

• Datasets #1 and #3 - submit these two datasets together on the same CD, total file size for both Datasets shall not exceed 25MB. Submit 2 CD copies. Files should be either .PDF, Microsoft Word or Excel format. Files shall be password protected (Use Password BIOINFO2016).

• Dataset #2 - Submit 2 CD copies, file size not to exceed 25MB. Files should be either .PDF, Microsoft Word or Excel format. Files shall be password protected (Use Password BIOINFO2016).

• Dataset #4 - Submit 2 CD copies, file size not to exceed 25MB. Files should be either .PDF, Microsoft Word or Excel format. Files shall be password protected (Use Password BIOINFO2016).

7. May grants be included as past performance under the requirement listed on Page 52, Section 14?

RESPONSE-Offerors shall provide any of the information that is outlined on page 52, under Item 14 as part of Past Performance Information.

8. In the RFP (Pages 63 through 64): Please confirm only the technical proposal may not exceed 25MB in size, but that the total proposal inclusive of other sections may exceed 25 MB in size.

RESPONSE-The file sizes have been revised from Amendment #1. Please see response to Question 6 above clarifying the file sizes for each section.

9. Would you please confirm that the Data Information Security Plan requirement (RFP, Page. 64, Technical Proposal Instructions) is for prime bidders only and not proposed subcontractors?

RESPONSE-- The contractor is responsible for ensuring that information security requirements are met as outlined in the RFP. Thus, this may require any subcontractors performing under this contract to also be subject to the information security requirements. Each offeror is responsible for assessing how the information security requirements may apply to any proposed subcontractor(s). The information security plan submitted must provide the offeror's approach for addressing the information security requirements for all personnel working on the contract. The information security plan submitted by the offeror will be evaluated for appropriateness in accordance with Section M-Evaluation Factors.

10. In the RFP, Page 66 (508 Compliance): Please confirm that the proposal response itself is not required to be 508 compliant.

RESPONSE-For this RFP, the proposal is not required to be 508 compliant. However, offerors are encouraged to format documents for Section 508-conformance and accessibility.

11. The Small Business Subcontracting Plan (Page 1): "A subcontracting Plan is required if the estimated cost of the contract may exceed $650,000 ($1,500,000 for construction)." Pages 71 and 73 of the RFP also contain the value of $650,000.00. Please confirm that the dollar value should be updated to read $700,000.00 in both areas in accordance with the requirements of Federal Acquisition Regulation (FAR) 52.219-9 Small Business Subcontracting Plan (Oct 2015).

RESPONSE-Acknowledged. The Small Business Subcontracting plan and pages 71 through 73 of the RFP are updated to a value of $700,000 instead of $650,000.

12. RFP Pages 74-75, Section 9(b)(1) (Total Compensation Plan) states, "Proposals offering total compensation levels less than currently being paid by the predecessor Contractor for the same work will be evaluated, in addition to the above, on the basis of maintaining program continuity, uninterrupted work of high quality, and availability of required competent professional employees." Out of fairness to the offerors with relation to this criteria, please provide current compensation levels for staff.

RESPONSE-While other contracts have conducted specific bioinformatics projects, this proposed contract for bioinformatics support is considered a new procurement. As such, there is no predecessor contract/ contractor for this work as referenced under the "Total Compensation Plan". Furthermore, the purpose of the

- 4 -language on pages 74-75 is to ensure that offerors are aware of the importance of establishing and proposing realistic compensation levels for professional employees in order to obtain and retain quality personnel that will meet the objectives of the requirement. It is up to each offeror to determine what constitutes a fair and reasonable compensation plan for their professional employees, and to develop a proposal based on such a plan.

13. Regarding RFP Pages 74-75 (Total Compensation Plan and related evaluation of such), in the absence of providing total compensation information on the current staff, we ask the Government to at a minimum provide salary information for current staff out of interest of fairness to offerors.

RESPONSE-See response to question 12 above.

14. In the RFP, Page 79, Section 12e (Pertinent Grants) states "You are cautioned that omission or an inadequate or inaccurate response to this very important RFP requirement could have a negative effect on the overall selection process." Please confirm that a prime contractor may use contract experience provided under 12d in lieu of the requirements contained in 12e.

RESPONSE-Offerors shall submit information pertinent to all of the subparagraphs mentioned on page 78 under Item 12-Qualifications of the Offeror. This includes items 12.a. through 12.e., which allows for submission of experience on both contracts and grants in order to evaluate the overall experience of the offeror.

15. Please confirm that subcontractor requirements under RFP Page 79, Section 13f (as highlighted in the provision below) only apply to major subcontractors, consistent with the definition on Page 52, Section 14a (i.e., greater than $100,000.00 and similar in nature to the solicitation workscope).

"Subcontractors If subcontractors are proposed, please include a commitment letter from the subcontractor detailing:

a. Willingness to perform as a subcontractor for specific duties (list duties).

b. What priority the work will be given and how it will relate to other work.

c. The amount of time and facilities available to this project.

d. Information on their cognizant field audit offices.

e. How rights to publications and patents are to be handled.

f. A complete cost proposal in the same format as the offeror's cost proposal."

RESPONSE-The submission requirements on page 79, item 13.f. are not related to the past performance information requested on page 52. There are no specific dollar values specified on page 79. Therefore, if subcontractors (of any type) are proposed, offerors are to provide the information specified on page 79 in the format specified. This information is necessary in order to allow for adequate evaluation of all proposed subcontractor arrangements and subcontractor costs.

16. In regard to RFP Page 79, Section 13f, we have several additional questions:

a. Please confirm that only pricing in the same format as the prime is required for major subcontractors and not complete business proposal narrative information, except insomuch that certain business proposal provisions may have specific flow-down requirements for subcontractors, which are explicitly required in the RFP.

b. If subcontracts are not of a similar nature to the solicitation workshare or are anticipated to be less than $100,000.00, or are anticipated to result in a firm-fixed-price or time-and-materials award, please confirm that no subcontractor business proposal narrative is required.

c. If subcontracts are not of a similar nature to the solicitation workshare or are anticipated to be less than $100,000.00 please confirm that the only applicable business proposal requirement is Federal Acquisition Regulation

(FAR 15.404-3).

RESPONSE-See response to question 15 above.

Additional Technical Proposal Instructions Questions

17. The note at the bottom on Pages 3 and 4 of the Additional Technical Proposal Instructions (Attachment 7) states:

"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,"

- 5 -along with the following verbiage from Page 5: "As key personnel, the PI is considered essential to the contract and shall be an employee of the contractor." We have several questions about this provision which follow:

i. Do you mean to include within the definition of "contractor" the "subcontractor" so that a subcontractor's personnel might be proposed as Key Personnel (i.e., Principal Investigator, Lead Bioinformatician, Lead Biostatistician)?

a. If so, would you please clarify the RFP to make this clear? (The remainder of this question has been redacted by the Government).

RESPONSE-It was not the Government's intent to include "subcontractor" within the definition of "contractor". This office relies on the definition of 'subcontract' and 'subcontractor' outlined in FAR 44 and further clarified on page 71 of this RFP.

ii. If you did not mean to include "subcontractor" within the definition of "contractor," would you please revise the RFP so that one may propose subcontractor staff as Key Personnel? (The remainder of this question has been redacted by the Government).

RESPONSE-As stated in the RFP, the Principal Investigator is responsible for the overall implementation of the contract and is the key contact for technical aspects of the project. The Lead Bioinformatician and the Lead Biostatistician will also have key roles as outlined in the RFP. These positions are considered essential to the contract and the Government has determined that the daily interaction, constant coordination of efforts, and the management of these positions makes it critical that they be physically and organizationally together. Therefore, the RFP has designated that these three key personnel positions should be employees of the contractor .

iii. To the extent you insist that Key Personnel be employees of the prime contractor, will you authorize the secondment (i.e., official transfer of personnel) of staff from one company to the prime contractor to become one of its employees for the contract pursuant to a written agreement with mandatory confidentiality and other applicable contractual protections to which the seconded employee would be bound? This will meet requirement for the personnel to be an employee of prime contractor.

RESPONSE-Our office is unfamiliar with arrangements termed "secondments", as they relate to procurements within the Federal Government and whether the referenced structure would conform to the management and characteristics of an employer-employee relationship. Therefore, we will neither authorize nor prohibit the proposal of such an arrangement if an offeror believes that it meets the requirements of the RFP. As stated in the RFP, offerors are to propose how the project is to be organized, staffed, and managed in a way that reflects a clear understanding of the nature of the work being undertaken.

You may also, at your discretion, submit alternate proposals. For specific restrictions regarding alternate proposals, see page 49, item 5 of the RFP.

iv. Please confirm that the Key Personnel may be proposed at a part-time level of effort deemed appropriate by the prime contractor to support the resultant contract.

RESPONSE-As previously stated, it is the offeror's responsibility to ensure that the actual hours and labor categories proposed are appropriate to accomplish the requirements and are consistent with the SOW.

Sample Assignment Questions

18. Please confirm that the intent of Sample Assignment 1(a)(i) is to derive differentially methylated regions from the given BigWig files. (The remainder of this question has been redacted by the Government).

RESPONSE: The intent of the Dataset#1.a.i is to find differentially methylation regions from files in this dataset. The .bw files are a general format that are supported by many visualization tools.

19. Regarding Sample Assignment outputs:

• Sample assignment 2(a): This dataset task specifically asks for a tab-delimited file "similar to the provided input file" of the inferred transcriptome dataset.

• Dataset 4: the README file specifies that the output from these data analyses are to be provided as either amendments to the input tab-delimited file or as separate tab-delimited files with specific column headings (six TSV files in total, plus an appended input file). Task E specifies an excel spreadsheet file as output.

- 6 -

• Our understanding is that these tab-delimited files and excel spreadsheets are not included in the 25-page sample assignment limit, as this would be impractical for these large files. Please confirm that the files described above (tab-delimited files and excel spreadsheets) are to be provided as separate electronic files on CD, and not included in the proposal hardcopy.

RESPONSE:

The submission requirements for the Sample Assignments have been revised. Please see response to Question 6.

General Questions

20. If the Government permits Subcontractor personnel to be bid as Principal Investigator, please confirm the Standard Form (SF) 2043 should be signed by relevant Subcontractor staff.

RESPONSE-Refer to the Government's response to Question 17 above. In addition, respondents to this RFP shall adhere to the requirements and submission instructions for subcontracts outlined in the RFP , and addressed throughout this response.

21. The RFP does not specify how an offeror should address Intellectual Property - technical data and / or computer software - which it may have developed at its own expense and which it may desire to use in performing the contract.

FAR 52.227-14 does not include the restricted use clause in Alt 3 to the clause. Please advise / clarify how offerors are to address this situation.

RESPONSE: Offerors may use software they have developed independently before initiation of the contract in the performance of the contract. If the contractor develops new software as a result of NIEHS contract expenditures, the new software is subject to government claims and use. Specific terms and conditions regarding Intellectual Property will be outlined in the resultant award.

22. In the interest of satisfying any applicable small business subcontracting requirements, and given the limited number of vendors listed under the Interested Parties tab associated with this opportunity on Fedbizopps, we respectfully request that the Government share the names of all small business vendors who responded to the sources sought notice.

RESPONSE-All offerors that would like to have their information shared are able to provide that information under the "Interested Vendors" tab. That information is also available on the Fed Biz Opps link for the Sources Sought Notice. In light of the competitive nature of this requirement and in the interest of ensuring fair competition for all parties, our office does not release lists of interested parties while in the midst of the solicitation process due to the possibility of creating an unfair advantage based on the information released.

23. Given the significant impact that the Government's answers to questions will have on applicable requirements, as well as offerors' responses, we request that the Government grant a three week extension for proposal submission through 3:30 PM EST on Monday, May 23, 2016.

RESPONSE-Due to time constraints regarding the award date of this requirement, we are unable to grant a three week extension. However, a one week extension has been granted. See the amendment notice.