Amendment__1_BAA-NIAID-DAIT-NIHAI2013167.pdf

Amendment #1 to BAA-NIAID-DAIT-NIHAI2013167 Large Scale T Cell Epitope Discovery

Amendment to Solicitation No.: BAA-NIAID-DAIT-NIHAI2013167

Amendment No.: 1

Issue Date: June 19, 2013

Effective Date:

Proposal Due Date:

June 19, 2013

October 01, 2013 at 3:00 P.M. local time

Issued By: Tom Bahrami, MBA Contracting Officer

NIH/NIAID

Office of Acquisitions 6700 B Rockledge Drive Room 3109 Bethesda, Maryland 20892-7612

Point of Contact: Brandon de White, Contract Specialist whitebra@niaid.nih.gov

Name and Address of Offeror: To All Potential Offerors

The above numbered solicitation is amended as set forth below. The hour and date specified for receipt of proposals remains unchanged. Offerors must acknowledge receipt of this amendment. Failure to receive your acknowledgement of this amendment may result in the rejection of your offer.

SECTION 1 – AMENDMENTS TO THE SOLICITATION

This section of the amendment provides modifications to the above referenced solicitation. All of other terms and conditions of the solicitation remain unchanged.

Item 1: The attachment labeled ATTACHMENT 8: REPORTING REQUIREMENTS AND DELIVERIES in the solicitation document is hereby deleted and replaced by the document labeled ATTACHMENT 8: REPORTING REQUIREMENTS AND DELIVERABLES which is the updated document included in this amendment.

Item 2: “SECTION M – TECHNICAL EVALUATION FACTORES FOR AWARD” (BAA pages 102-103), 8.

TECHNICAL EVALUATION FACTORS is amended as follows;

1. TECHNICAL EVALUATION CRITERIA:

The technical evaluation criteria are used by the peer review group when reviewing the technical proposals. The criteria below are listed in the order of relative importance with weights assigned for evaluation purposes.

OFFERORS AND REVIEWERS ARE ADVISED TO REFER TO THE ATTACHMENT ENTITLED “ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS” OF THIS SOLICITATION PACKAGE FOR GUIDANCE AND INFORMATION

RELATED TO THE PREPARATION OF TECHNICAL PROPOSALS.

CRITERIA WEIGHT

CRITERION 1: SCIENTIFIC AND TECHNICAL MERIT 50

The appropriateness and completeness of the Offeror’s proposed Statement of Work (SOW) and technical approach to fulfill the requirements of the solicitation, including: the adequacy, feasibility, and scientific and technical merit of the offeror’s proposed methods and approaches to meet the overall research and technical objectives of the BAA; adequacy and feasibility of the proposed techniques and approaches that demonstrate both an awareness of and solutions for resolving potential methodological and inferential problems related to epitope identification and validation; if included in the proposal, feasibility of the methods for computational model or algorithm development/refinement; and the potential for the proposed research to increase knowledge and understanding of T cell epitopes and host immune response to microorganisms responsible for emerging and re-emerging infectious diseases and potential agents of bioterrorism and their toxins.

CRITERION 2: SCIENTIFIC AND TECHNICAL PERSONNEL 25

A. Principal Investigator (PI): Appropriateness and adequacy of the education, training, experience, expertise, qualifications and effort of the proposed PI to successfully administer a project of this size and complexity and to accomplish the research and technical objectives.

B. Other Scientific and Technical Personnel: Appropriateness and adequacy of the education, training, experience, expertise, qualifications and effort of all proposed scientific and technical personnel, and proposed staff to oversee and manage a project of comparable size and complexity as well as appropriate time commitment, including any proposed subcontractors and consultants, to accomplish the research and technical objectives.

CRITERION 3: PROJECT MANAGEMENT 15

Adequacy and feasibility of the: management approach in terms of staffing, organization, communication among staff and with the Government, responsibilities, leadership, and lines of authority, as well as management of subcontracts and consultants; proposed methods of coordination, monitoring, and central management of all activities, including appropriate milestones and timelines, and plans for the collection, management, security, and dissemination of data.

CRITERION 4: FACILITIES 10

Availability and adequacy, including safety and security of the necessary facilities, equipment, and other resources for the contractor and all subcontractors to successfully execute the proposed research.

TOTAL POSSIBLE POINTS: 100

SECTION 2- QUESTIONS AND RESPONSES

This section of the amendment provides questions submitted by potential applicants/offerors and the responses provided by NIAID. The responses are offered for information only and do not modify or become part of this solicitation. This Amendment will be updated as needed to add further questions and their related responses. All potential offerors are advised to refer back to this Amendment #1 for additional Questions & Answers.

Question 1: Will the NIAID accept applications with a focus on tuberculosis?

Answer: The NIAID will accept applications on tuberculosis including drug resistant TB as a focus for large scale T cell epitope discovery. Pathogens from the NIAID Emerging and Re-Emerging Infectious Diseases list must account for at least 50% of the pathogens in the proposed studies.

Question 2: How is the NIAID prioritizing research projects based on the disease causing organisms in the NIAID Category A-C Priority Pathogen list and the List of Emerging and Reemerging Pathogens list?

Answer: The selection of proposals for award is based upon the evaluation factors (found in Section M of the BAA), importance to the agency programs (programmatic balance), and fund availability. Although these technical factors are of paramount consideration in the award of the contract, cost/price, past performance, and SDB (small disadvantaged business) participation are also important to the overall contract award decision. The merit of each technical proposal will be evaluated by a peer review panel.

Question 3: Will the NIAID consider proposals for T cell epitope discovery in variola/vaccinia?

Answer: This solicitation will not support the discovery and validation of MHC class I pox virus T cell epitopes, but will accept applications that support the large scale discovery of MHC class II and/or peptide or non-peptide epitopes/ligands presented by non-classical MHC molecules from pox viruses (found in Attachment 5, section 1 – Research Design).

Question 4: Will the NIAID support ongoing epitope characterization studies for current Large Scale T cell Epitope Discovery Programs.

Answer: This solicitation will not support the validation of previously identified T cell epitopes (found in Attachment 5, section 1 – Research Design).

REPORTING REQUIREMENTS ATTACHMENT 8

AND DELIVERABLES Page 1 of 4

BAA-NIAID-DAIT-NIHAI2013167

ATTACHMENT 8: REPORTING REQUIREMENTS AND DELIVERABLES

LARGE SCALE T CELL EPITOPE DISCOVERY

BAA-NIHAI2013167

1. SECTION C - REPORTING REQUIREMENTS

a. Technical Progress Reports

Format of Cover page: All reports shall include a cover page prepared in accordance with the following format:

• Contract Number and Project Title

• Title of Report

• Period of Performance Being Reported

• Contractor’s Name and Address

• Author(s)

• Date of Submission

• Delivery Address

Type and Number of Copies:

Electronic Copy to Contracting Officer Representative and Contracting Officer 1 Hard Copy to Contracting Officer Representative 1 Original Hard Copy to Contracting Officer

1) Monthly Progress Report

This report shall include a description of the activities during the reporting period and the activities planned for the ensuing reporting period. The first reporting period consists of the first full month of performance plus any fractional part of the initial month. Thereafter, the reporting period shall consist of each calendar month. Reports are due on or before the ____ calendar/working day of the month.

2) Quarterly Progress Report

a) This report shall include a description of the activities during the reporting period and the activities planned for the ensuing reporting period. The first reporting period consists of the first full three months of performance including any fractional part of the initial month. Thereafter, the reporting period shall consist of three full calendar months. Reports are due on or before the 15th calendar/working day of the month following the end of the reporting period.

REPORTING REQUIREMENTS ATTACHMENT 8

AND DELIVERABLES Page 2 of 4

b) A monthly report will not be submitted for the final month of a quarter.

3) Semi-Annual Progress Report

a) This report shall include a [ summation of the monthly progress reports a description of the activities during the reporting period] and the activities planned for the ensuing reporting period. The initial report will be submitted for the first full six months of the contract performance including any fractional part of the initial month. Thereafter, the reporting period shall consist of six full calendar months. Reports are due on or before the calendar/working day of the month following the end of the reporting period.

b) Monthly reports, Quarterly reports will not be submitted the month the semi-annual report is due.

4) Annual Progress Report

This report includes a summation of the results of the entire contract work for the period covered. An Annual Progress Report will not be required for the period when the Final Report is due. A [ Monthly Quarterly Semi-Annual] Report shall not be submitted when an Annual Report is due. Reports are due on or before the 15th calendar/working day of the month following the end of the reporting period.

5) Annual Technical Progress Report for Clinical Research Study Populations (Required for use in all contracts for clinical research involving human subjects)

6) Final Report

This report is to include a summation of the work performed and the results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Final Report shall be submitted in accordance with the DELIVERIES Article in SECTION F of the contract. An annual report will not be required for the period when the Final Report is due. The contractor shall submit, with the Final Report, a summary (not to exceed 250 words) of salient results achieved during the performance of the contract.

Use the below narrative if a draft final report is requested.

The contractor shall provide the Contracting Officer with an electronic copy of the Final Report in draft form in accordance with the DELIVERIES Article in SECTION F of this contract 90 calendar days prior to the completion date of this contract. The Contracting Officer Representative will review the draft report and provide the Contracting Officer with comments within 30 calendar days after

REPORTING REQUIREMENTS ATTACHMENT 8

AND DELIVERABLES Page 3 of 4 receipt. The Final Report shall be corrected by the contractor, if necessary, and the final version delivered as specified in the above paragraph.

Draft Final Report shall be due on or before the 30 calendar/working day of the month.

Source Code and Object Code - Use when software is used, produced, modified or enhanced

b. Other Reports and Deliverables

1. Provide raw data and specific analyses of data generated with contract funding to the Contracting Officer’s Representative (COR).

2. Other Reports and Deliverables may be required. This may include special reports required by regulation or policy and deliverables such as data, vaccine, etc. These will be developed after proposal receipt as a result of finalization of the Statement of Work during negotiations. Special instructions, if applicable, will be provided to offerors in the Attachment entitled “Additional Technical Proposal Instructions.”

All contractors supported by the Large Scale T Cell Epitope Discovery Program shall submit detailed epitope information to the IEDB (www.iedb.org) describing each newly identified epitope along with a summary of the results of the studies validating epitope antigenicity.

Submissions shall include epitope identification software tools (such as predictive algorithms, mathematic models, and artificial neural network programs). Contractors will have to register with the IEDB (free registration) in order to submit data (submission information available at:

http://submission.iedb.org/). The current IEDB submission format utilizes either a spreadsheet or an XML file to transfer datasets to the IEDB. The current IEDB submission schema is available at (http://submission.iedb.org/UserGuide.aspx or http://help.iedb.org/entries/31691-field-guide-for-dst-beta (this link provides access to a PDF document describing the epitope submission fields).

The following immune epitope information and epitope prediction tools shall be submitted to the IEDB (www.iedb.org):

i. epitope sequence, and any post-translational modifications important for epitope recognition or antigen processing

ii. pathogen species and strain from which the epitope was identified

iii. antigen from which the epitope was derived

iv. MHC allele(s) that binds and presents the epitope

v. epitope identification methods

vi. validation methods (e.g., test recognition by T cells, and role in protective immunity) and summary of results

vii. Extensive annotation may also be required, as determined in consultation with the Contracting Officer Representative. This annotation may include: MHC/peptide binding affinity; three-dimensional structure of the antigen or epitope; pathogen replication http://www.iedb.org/ http://submission.iedb.org/UserGuide.aspx http://help.iedb.org/entries/31691-field-guide-for-dst-beta http://www.iedb.org/

REPORTING REQUIREMENTS ATTACHMENT 8

AND DELIVERABLES Page 4 of 4 state in which the epitope is expressed; and disease state in which the epitope is expressed or recognized by the host.

viii. For any research involving development and testing of algorithms, mathematical models and neural networks for predicting T cell epitopes (NOTE: development of novel or improved methods or algorithms/models is not required for this BAA): the algorithms, mathematical models, and/or artificial neural networks shall be submitted in a format that allows the scientific community to use these tools in their individual research projects for epitope prediction.

Documentation and a tutorial on use of the computational tool shall be included with the submission. Tools shall be submitted to the IEDB for consideration to add the tools to the website for public use.

Please provide an alternative method for supplying public access to the tool in the event that the IEDB decides not to host the tool.

For projects that include the development or refinement of epitope prediction tools:

to the extent possible, the contractor shall provide software under a license certified by the Open Source Initiative (http://www.opensource.org/licenses/), to the IEDB or other public source (see viii above and Advanced Understandings), to guarantee the right to read, redistribute, modify, and freely use the software. In addition, these computational tools shall have detailed documentation and a user interface that allows the broader scientific community to use the tools in their individual research projects.

2. SECTION D - PACKAGING, MARKING, AND SHIPPING

If special instructions regarding packaging, marking and shipping are required, these will be developed after receipt of proposals as a result of finalization of the Statement of Work during negotiations. Special instructions, if applicable, will be provided to offerors in the Attachment entitled “Additional Technical Proposal Instructions.”

3. SECTION F - DELIVERY SCHEDULE

Delivery of other reports and deliverables will be proposed by the offerors in their technical proposal. They will be developed further after receipt of proposals as a result of finalization of the Statement of Work and other terms and conditions of any resultant contract during negotiations. Specific instructions, if applicable, will be provided to offerors in the Attachment entitled “Additional Technical Proposal Instructions.”

http://www.opensource.org/licenses/

Amendment #1 to BAA-NIAID-DAIT-NIHAI2013167