Bioinformatics and Assays Development Program 2

(BIAD2)

Broad Agency Announcement 06-01

(BAA 06-01)

Proposal Information Pamphlet (PIP)

Department of Homeland Security

Homeland Security Advanced Research Projects Agency (HSARPA)

31 January 2006

For Questions Regarding This Solicitation:

BAA06-01@dhs.gov

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T A B L E O F C O N T E N T S 1 Background ........................................................................................................ 4 2 Program Structure............................................................................................... 5

2.1 TTA 2-1: Assays for Novel, Emerging, or Engineered Threats ......................... 5 2.2 TTA 2-2: Assays to Detect Functional Signatures ............................................. 5 2.3 TTA 2-3: Bioinformatics Tools .......................................................................... 5 2.4 TTA 2-4: Actionable Assays for the Public and Private Sector ......................... 5 2.5 TTA 2-5: Methodology for the Independent Evaluation and Verification of

Assays................................................................................................................. 5 3 Program Schedule and Approach ....................................................................... 5

3.1 Program Schedule and Phases ............................................................................ 6 3.2 Government Furnished Equipment and Resources............................................. 6 3.3 Review Panel ...................................................................................................... 6 3.4 Test and Evaluation Facilities............................................................................. 7

4 BIAD2 Program Goals ....................................................................................... 7 4.1 TTA 2-1: Assays for novel, emerging, or engineered threats............................. 7 4.2 TTA 2-2: Assays to detect functional signatures................................................ 8 4.3 TTA 2-3: Bioinformatics tools............................................................................ 9 4.4 TTA 2-4: Actionable assays for the public and private sector.......................... 10 4.5 TTA 2-5: Mechanism for the Independent Evaluation and Verification of

Assays............................................................................................................... 11 5 Deliverables...................................................................................................... 12

5.1 Phase I Technical and Management Deliverables ............................................ 12 5.2 Phase II Technical and Management Deliverables........................................... 13 5.3 Phase III Technical and Management Deliverables.......................................... 13

6 Information for Offerors................................................................................... 14 6.1 Eligible Applicants............................................................................................ 14 6.2 Current BIAD BAA (04-03) Performer Eligibility........................................... 14 6.3 Organizational Conflict of Interest ................................................................... 14 6.4 Anticipated Awards .......................................................................................... 14 6.5 Types of Awards ............................................................................................... 14 6.6 BAA Information .............................................................................................. 15 6.7 Submitting a Response to this BAA ................................................................. 15 6.8 Security ............................................................................................................. 16 6.9 Solicitation and Awards Schedule .................................................................... 17 6.10 White Paper Guidance and Content.................................................................. 17 6.11 Proposal Guidance and Content........................................................................ 19 6.12 Contact Information .......................................................................................... 23 6.13 Information for White Paper and Proposal Respondents.................................. 24

7 Evaluation Criteria and Selection Process........................................................ 24 7.1 White Papers ..................................................................................................... 24 7.2 Proposals ........................................................................................................... 24 7.3 Review and Selection Process .......................................................................... 25

8 List of Attachments .......................................................................................... 26 8.1 Appendix A: List of Excluded Offerors........................................................... 27

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8.2 Appendix B: List of Acronyms........................................................................ 30 8.3 Appendix C: Quad Chart Format..................................................................... 32 8.4 Appendix D: Organizational Conflict of Interest............................................. 33

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1 BACKGROUND The Homeland Security Advanced Research Projects Agency (HSARPA) invests in programs offering the potential for revolutionary changes in technologies that promote homeland security and accelerate the prototyping and deployment of technologies that reduce homeland vulnerabilities. HSARPA has a unique capability to perform these functions in part by awarding procurement contracts, grants, cooperative agreements, or other transactions for research or prototypes to public or private entities, businesses, federally funded research and development centers and universities. A critical area of focus for DHS is the protection of the homeland from the release of a biological agent. This focus is demonstrated by the BioWatch surveillance system and a number of programs initiated by HSARPA that are developing new sensor technologies. These include the Bioagent Autonomous Networked Detectors (BAND) and Rapid Automated Biological Identification System (RABIS) programs under solicitation RA03-01, as well as Instantaneous Bio-Aerosol Detector Systems (IBADS; BAA 04-18), Low-Cost Bio-Aerosol Detector Systems (LBADS; BAA 05-08), and Food Biological Agent Detection Sensors (FBADS; BAA 05-06) programs. As a complement to the technology program initiated under RA03-01, HSARPA initiated the Bioinformatics and Assays Development program (BIAD; BAA 04-03) to extend the existing family of detection and forensics assays as well as to develop next generation assays and new tools for assay development. (See www.hsarpabaa.com for details about these past solicitations.) Development of new sensor systems is not a priority for the BIAD2 program. HSARPA is initiating a new Bioinformatics and Assay Development solicitation, BIAD2 (BAA 06-01), to address a number of technology gaps and requirements for biodetection. This solicitation will leverage the vast research and development capabilities of the private sector and academia in order to meet the needs of HSARPA and Homeland Security. In order to meet these requirements, performers selected as a result of this solicitation will:

• Develop and validate actionable assays for the public and private sector • Develop and validate new assays and novel assay methodologies to enhance

existing detection systems and enable future detection platforms • Develop next generation assays which are robust against novel, emerging, and

engineered threats • Develop novel assays that detect low levels of ribonucleic acid (RNA)-based viral

threats in complex backgrounds • Develop novel assays to characterize the viability, degree of virulence or toxicity,

and countermeasure resistance of a biological agent • Develop new bioinformatics tools to support assay development and assay

validation

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2 PROGRAM STRUCTURE This BAA comprises five separate Technical Topic Areas (TTAs). Each TTA solicits a specific approach or tool to augment our detection and analysis capabilities. TTA designations are prefixed with a ‘2’ to denote their association with the BIAD2 BAA.

2.1 TTA 2-1: Assays for Novel, Emerging, or Engineered Threats We seek strategies and new approaches for the detection and characterization of previously unknown, emerging, or engineered biological threats.

2.2 TTA 2-2: Assays to Detect Functional Signatures We seek assay technologies that functionally characterize the viability, degree of virulence or toxicity, and countermeasure resistance of a biological agent following an attack in order to allow a rapid and appropriate response by decision makers.

2.3 TTA 2-3: Bioinformatics Tools We seek bioinformatics tools that will enhance assay development and validation by providing functional, genomic, proteomic, and other related information and processing, as well as tools that provide a capability to store and integrate assay-relevant data. A high priority will be placed on approaches that offer a means to provide tools that can be utilized by the broader developer community.

2.4 TTA 2-4: Actionable Assays for the Public and Private Sector We seek to develop and evaluate biodetection assays that can ultimately be used by the public and private sector and meet the requirements of Homeland Security. Towards that goal, we highly desire to leverage technologies developed for other biodetection or biotechnology applications. These assays, after successful evaluation in Phase I, may be used within a pilot process (TTA 2-5) for the independent evaluation and verification of assays.

2.5 TTA 2-5: Methodology for the Independent Evaluation and Verification of Assays

We seek to develop a plan and methodology for the independent evaluation of assay technologies directed against biothreat agents, with the ultimate goal of establishing a national capability to provide actionable assays to the public and private sector. The evaluation plan will be piloted using selected assays from the public or private sector.

3 PROGRAM SCHEDULE AND APPROACH The objective of the HSARPA BIAD2 program is to augment, extend, and enable new capabilities of existing and near-term systems to counter a biological attack using advances and tools from bioinformatics and new assay development. Continuation of work initiated under Phase I of this solicitation will depend upon the level of technical accomplishments achieved during Phase I, the availability of funds, and other programmatic considerations. Such considerations may include indications of which

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types of assays provide the best opportunities for enhanced countermeasures, as determined by HSARPA. HSARPA anticipates making multiple Phase I awards under this solicitation. All awards will be subject to negotiations, availability of funding, and programmatic priorities.

3.1 Program Schedule and Phases

FY09FY07FY06 FY10FY08

Phase I Phase II Phase IIILegend

TTA 2-1

Transition to Public Sector

Database/Tool Delivery

DemonstrationConcept & Strategy Development Assay Formulation Test & Evaluation

of Assays

MethodDevelopment Pilot Process

Database Concept/Tool Design Populate, Test, and Implement

DemonstrationConcept & Strategy Development Assay Formulation Test & Evaluation

of Assays

Pilot Support

TTA 2-2

TTA 2-4

TTA 2-3

TTA 2-5

Development and Evaluation (Variable Length)

Decision Point on Integration into TTA 2-5 Pilot Program at End of Evaluation

FY09FY07FY06 FY10FY08 FY09FY07FY06 FY10FY08

Phase I Phase II Phase IIILegend Phase I Phase II Phase IIILegend

TTA 2-1

Transition to Public Sector

Database/Tool Delivery

DemonstrationConcept & Strategy Development Assay Formulation Test & Evaluation

of Assays

MethodDevelopment Pilot Process

Database Concept/Tool Design Populate, Test, and Implement

DemonstrationConcept & Strategy Development Assay Formulation Test & Evaluation

of Assays

Pilot Support

TTA 2-2

TTA 2-4

TTA 2-3

TTA 2-5

Development and Evaluation (Variable Length)

Decision Point on Integration into TTA 2-5 Pilot Program at End of Evaluation

Figure 1. A notional schedule of the program execution timeline. Offerors are encouraged to propose their own schedule based upon their detailed understanding of the technical challenges and their realistic estimate of the technical effort required to solve the problem they propose to address.

3.2 Government Furnished Equipment and Resources In support of the TTAs, the Government will consider requests from principal investigators or from teams for Government Furnished Resources (GFR) and Government Furnished Technologies (GFT). As part of this solicitation, HSARPA may publish a list of potentially applicable technologies and allow offerors to propose accelerated schedule options based upon the availability of GFR and GFT, when possible. This information, if any, will be published on the HSARPA website http://www.hsarpabaa.com soon after the release of this BAA. Please see Appendix A for more information on restricted offerors, and the process for leveraging ‘transition-ready technologies’ from DHS strategic partner laboratories.

3.3 Review Panel A review panel drawn from Government and non-Government experts who have signed appropriate non-disclosure agreements will support the HSARPA Program Manager in performing technical evaluations of the proposed efforts. Non-government experts may include Scientific and Engineering Technical Assistance (SETA) contractors from Booz, Allen & Hamilton, among others. Should any offeror desire to have their White Paper or

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Proposal reviewed exclusively by Government personnel, all pages must be clearly marked to indicate the following: “In accord with BAA 06-01, this submission is to be evaluated exclusively by Government personnel.”

3.4 Test and Evaluation Facilities DHS S&T will make available appropriate test and evaluation facilities to support this program. Offerors should provide any specific requirements needed for Government furnished equipment (GFE) or information for development, test, and/or evaluation of their proposed concept.

4 BIAD2 PROGRAM GOALS

Concepts are requested that address as many of the goals specified below as possible for each TTA. Proposals should clearly indicate how the proposed concept augments or exceeds existing capabilities.

4.1 TTA 2-1: Assays for Novel, Emerging, or Engineered Threats We seek strategies and novel approaches for the detection of previously unknown, emerging, or engineered biological threats. Emerging and previously unknown chemical threats are also of interest if biological receptors might be used as part of the detection technologies. Current detection methods involve identification via nucleic acids (polymerase chain reaction (PCR)-based, gene-chip, sequencing), proteins or carbohydrates (antibodies, aptamers, immunochromatography), and whole organisms (spectroscopy, culture, living cell response). While these methods are more or less effective at identifying known pathogens, advances to these, as well as the development of novel assays, are needed to detect unknown or engineered pathogens. Desired advancements include improvements in speed, accuracy, multiplexing and sensitivity, while also being able to operate in the presence of background organisms, complex matrices, and environmental contaminants. Additionally, we seek new technologies or concepts that allow the rapid development and deployment of reagents, or other detection moieties, primarily for integration into existing detection systems. These platforms or technologies would have the capability to provide a more rapid creation of detection elements against novel chemical or biological threat agents. To clarify, HSARPA does not seek development of new sensor platforms, but new concepts in creating the detection elements that define sensor specificity to new threats. The highest priority will be placed on efforts that develop and demonstrate assay capabilities that enhance existing or developmental systems, or enable new detection concepts. Efforts that are primarily focused on the development of hardware platforms are of lower priority. In order to determine the presence of an engineered or newly-emergent threat, a detection technology might be designed to detect genomic or other biomarkers that are characteristic of potential pathogens or weaponized agents. Possible classes of these characteristics include, but are not limited to, the following:

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• Virulence - detection of specific virulence factors among typically non-pathogenic organisms

• Viability - presence of strains exhibiting aberrant or extraordinary durability, ruggedness, or enhanced survivability

• Infection - routes of infection (non-natural host pathogen receptors or pathways) during disease outbreaks that are uncharacteristic of wild-type organisms

• Resistance - presence of antibiotic resistance genes or other immuno-modulating factors

• Genetic manipulation – presence of nucleic acids common to cloning vectors or changes in the genetic structure of an organism

Preference will be given to assays that are universal and able to detect a large number of threats simultaneously from complex mixtures of background clutter. Broad-spectrum approaches are preferred, with the ability to identify known and unknown agents quickly and accurately with minimal false alarms. Of particular interest are emerging RNA viral threats; for example, avian influenza. The majority of current molecular assays for the detection of RNA viruses involve antibodies and immunoassays or the reverse transcription of the viral nucleic acid to generate complementary DNA (cDNA) followed by standard PCR techniques. These assays are currently employed in human diagnostics; however, their cost, sensitivity, and other attributes, may make them less applicable for environmental surveillance. We seek assays that can detect the nucleic acid or proteins of RNA virus at low levels of viral particles in the presence of complex environmental matrices and other background organisms while also improving the speed of detection and cost of the assay. Approaches that improve the sensitivity and other characteristics of current assays, as well as novel methodologies, are desired.

4.2 TTA 2-2: Assays to Detect Functional Signatures In order to mount a rapid and appropriate response to the release of a biological agent, the threat needs to be quickly identified and characterized as to its viability, degree of virulence or toxicity, and potential resistance to countermeasures. This type of information is critical to allow decision makers to take the best course of action to most efficiently counter an incident. Tests to determine the viability of an organism, its virulence, and its resistance to countermeasures using current technologies, can take days to weeks to complete. We seek to identify functional signatures and develop corresponding assays that can not only minimize the time of characterization, but also maximize the sensitivity and specificity of detection and characterization of the Category A and B agents. Of particular interest are the bacteria B. anthracis, Y. pestis, F. tularensis, Brucella species, and Burkholderia species, as well as Variola and Foot and Mouth Disease (FMD) viruses. Assays that characterize the toxicity of agents such as botulinum toxin, staphylococcus enterotoxin B (SEB), and ricin are also desired. Other attributes to assay performance might also include:

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• Ability to multiplex for multiple functional signatures of one threat and functional signatures across multiple agents

• Capability to operate in the presence of near-neighbors, innocuous background organisms, complex matrices, and environmental contaminants

• Automating and/or streamlining assays so that they require little human supervision or intervention, and minimal training for result interpretation

4.3 TTA 2-3: Bioinformatics Tools We seek bioinformatics tools that will enhance assay development and validation to provide a more thorough understanding of assay system performance, with the eventual goal of being able to predict and optimize detection-system performance. Databases We are seeking new and novel databases to enable creation, development, testing, and validation of assays for detection of threat agents. For all these databases, we seek capture of the currently available data, as opposed to new research in the area designated for data collection. Several areas of interest for HSARPA include, but are not limited to:

• A database of common assay interferents from the environment, their sources, distribution, effects, and mitigation (if any)

• A database of environmental background containing published data on biological clutter, including known near neighbors, naturally-occurring threat agents, and other data relevant to establishing ground truth for sensor evaluation

• A spectral signature database to incorporate data such as infrared, raman, ultraviolet florescence, induced breakdown spectroscopy, or other spectral data used for identification or measurement of sample purity of simulants, agents, and their associated backgrounds

• A database of functional signatures, to include known genomic and proteomic markers of pathogenicity or other threat-related properties

• A reagent database cataloging known data and sources for reagents, to include antibodies, proteins, and enzymes relevant to environmental monitoring of threat agents

With all bioinformatics databases, we seek to enable the widest applicability of these databases to the development of bioassays for DHS critical needs. Offerors should include in their Proposals a plan for allowing maximal access to databases by other developers in the public and private sectors while maintaining appropriate control over any distribution-restricted data. In addition, all proposers should include a plan for allowing the integration of their databases with other bioinformatic databases to permit data to be related, compared, and used to enhance efforts to develop, evaluate, and validate current and future assays. Proposers should describe an integration strategy that maximally utilizes existing infrastructure and resources.

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Bioinformatics tools and instrumentation Development of bioinformatics tools involves not only software and computational analysis tools, but also the instrumentation, assays, and protocols that complement data collection and analysis. We encourage offerors to propose not only a set of algorithms or data mining activities, but also a set of tightly coupled, high throughput laboratory measurement methods to provide data for analysis. We seek innovative approaches that might propose to:

• Develop genomic- and/or proteomic-based informatics tools that enhance assay development and that can be applied to platforms that rapidly and accurately detect biothreat agents. These platforms might include DNA and protein microarrays, mass spectrometry, or PCR-based technologies. Efforts might also focus on pathogen biology as well as host responses. Applicants should also consider issues relating to instrumentation and describe how these proposed tools can be incorporated cost effectively into simple detection devices.

• Develop software tools that are coupled to the platforms and technologies described above. We particularly seek data analysis tools that aid in optimizing the sensitivity and specificity of detection assays. Areas of focus include algorithms for complex pattern recognition and profile-based classification.

• Develop software tools for large-scale comparative genomics and phylogenetic analysis to facilitate the development of genomic signature-based assays. We seek strategies that identify signature sequences from existing or limited sequence information, including complete and partial genomic sequences.

• Develop computational tools that model the function and activity of macromolecular components and, if applicable, the cellular responses of detection systems to assist the development of novel biodetection systems by providing the ability to predict effectively the behavior of the system under a wide variety of conditions. These might include system response in the presence of confounding analytes, background levels of non-pathogenic organisms, potential inhibitors of assay reactions, and temperature and other environmental extremes.

• Develop other bioinformatics tools for which the applicant can provide a strong argument for their importance in enhancing our current Biological Countermeasures capabilities.

4.4 TTA 2-4: Actionable Assays for the Public and Private Sector A major requirement for Homeland Security is the development of bioassays for the public and private sector that give high-confidence detection and are recognized by the Centers for Disease Control (CDC) and the United States Government (USG) as public health actionable. These assays are sought by private and public-sector customers that desire to develop and deploy biological countermeasure systems because they do not have access to the current CDC/Laboratory Response Network (LRN) confirmatory assays used for BioWatch. In order to address this critical requirement, the BIAD2 program intends to develop a mechanism for the independent evaluation and validation of publicly-available assays. Towards that goal, HSARPA seeks to leverage:

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• Assays primarily developed for clinical application that may be transferred to environmental matrices.

• Assays that have been developed and tested in the laboratory setting or undergone limited environmental tests, but require additional testing.

• Next generation assays that significantly improve current DHS operational capabilities.

In support of the assay types listed above, HSARPA prefers more mature or commercialized assays, but will still consider novel, yet well-demonstrated and well-tested, technologies. Assay technologies which are not typically associated with current DHS environmental testing will also be considered. Preference will be given to low cost, rapid, and high-confidence assays that will improve DHS operating capability. In terms of detection targets, preference will be given to those assays that target the bacteria B. anthracis, Y. pestis, F. tularensis, Brucella species, and Burkholderia species; Variola, Foot and Mouth Disease (FMD) and avian influenza viruses; and the biological toxins SEB, ricin, and botulinum toxin. However, assays to all Category A and B agents are desired and will be considered. Offerors should propose a rigorous technical evaluation of their assays. At a minimum, assays should be tested to characterize the limit of detection, the probability of detection, the rate of false negative and false positive results in the presence and absence of near-neighbors, background organisms, complex matrices, and environmental contaminants. Performers should carefully describe their evaluation plan and describe other efforts to evaluate the proposed assay. Assays evaluated under TTA 2-4 will be considered for entry into the independent evaluation and verification process described below in TTA 2-5. Therefore, offerors are encouraged to propose several assays in which they have the most experience and confidence. If a proposed effort is encouraged during the White Paper stage, encouraged offerors will receive additional guidance relating to the most desired assay and target-agent scope. If an offeror’s Proposal includes the use of Government furnished resources (GFR), of any nature, the Proposal must include schedule, cost, and detailed plan for said GFR. Proposers are encouraged to engage needed resources directly, subject to restrictions described in Appendix A describing excluded offerors.

4.5 TTA 2-5: Mechanism for the Independent Evaluation and Verification of Assays

In conjunction with TTA 2-4, HSARPA seeks to leverage private-sector validation capabilities by funding entities to develop and pilot a plan for the independent evaluation of assays specific to the interests and needs of Homeland Security. The plan should address but not be limited to topics such as:

• Pilot evaluation of assays that detect biothreats listed in TTA 2-4

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• Pilot evaluation of the limit of detection, the probability of detection, the rate of false negative and false positive results in the presence and absence of near-neighbors, background organisms, complex matrices, and environmental contaminants

• Procedures to ensure a fair, independent evaluation process • Procedures for developing appropriate evaluation test plans • Procedures for coordinating and managing the reagents, protocols, evaluation

data, and reports of the evaluation program • Procedures for coordinating with all the relevant USG stakeholders (e.g., DHS,

CDC, Department of Defense (DoD), United States Postal Service (USPS), Department of Justice (DoJ), and Office of Science and Technology Policy (OSTP))

As a pilot demonstration, performers will exercise the evaluation process developed under this TTA using assays that have gone through the extensive in-house evaluation described in TTA 2-4 or other assays provided by the government. The ultimate goal of this effort will be to establish a framework that will be used to aid in the procurement of a national capacity to provide high-confidence actionable assays to the public and private sector for their biodetection needs.

5 DELIVERABLES To the exclusion of exceptions negotiated at time of award, any of the deliverables associated with this program may be released to outside organizations, both U. S. Government and non-Government, in support of DHS missions. The performer may recommend a preferred format for each deliverable, but the Government will determine the final format at least 90 days prior to delivery. For each Phase, monthly status reports are due within one week after the last day of each month; quarterly reports are due one week prior to the time of the quarterly reviews; and comprehensive Phase deliverables are due within two weeks of the conclusion of each Phase.

5.1 Phase I Technical and Management Deliverables Brief (not more than one page) narrative reports are required to be electronically submitted to the HSARPA Program Manager within one week after the last day of each month. These reports will describe the previous 30 calendar days’ activity, technical progress achieved against project goals, difficulties encountered, recovery plans (if needed), and explicit technical plans for the next 30 day period. Quarterly reports (not to exceed 5 pages) are required to be electronically submitted to the HSARPA Program Manager and are due one week prior to the time of the quarterly reviews, with the first review occurring not more than 90 days after contract signing. These reports will describe the previous 90 calendar days’ activity, technical principals involved in the actual work of the period, technical progress achieved against goals, difficulties encountered, funds expended against each sub-task in the previous 90 day

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period, recovery plans (if needed), and explicit plans for the next 90 day period. Quarterly reviews will be provided in person to the HSARPA Program Manager with a venue, duration, and format determined in consultation with the HSARPA Program Manager. For a final report, each principal investigator or Team will provide a Final Technical Report of their work performed during Phase I. This will include, where appropriate, system performance predictions, estimates of cost of ownership, a description of the design trades that resulted in the selected design, and an enumeration of remaining unknowns and uncertainties. This final report will be a cumulative, stand-alone document that describes the work of the entire Phase leading up to it. It should detail how the design concept was refined and why the refinement was undertaken. It must include any technical data gathered, such as measurements taken, models developed, simulation results, and formulations developed. This final report should also include “lessons learned” from the effort, recommendations for future research in this area, and a comprehensive and detailed account of all funds expended. In cases where performers believe results derived in Phase I justify a Phase II effort, they must also include in their final report a plan for executing Phase II & III: an experimental plan for developing and testing the assays or techniques and an activity schedule and a budget containing a detailed cost breakdown. Each principal investigator or Team will submit a detailed work plan, including a Statement of Work for conducting their Phase II effort, should they be selected.

5.2 Phase II Technical and Management Deliverables All documents will be in a format determined by the contractor. The government shall review the documents within two weeks of receipt and provide any additions, deletions or editorial changes. Lack of a response by the government will constitute acceptance.

5.2.1 Testing Report Contractors shall provide a report of the results of all assay, algorithm or database system tests conducted in Phase II. These shall include all components of the reports required for Phase I, including written Quarterly Reports and in-person Quarterly Reviews.

5.2.2 Phase II Final Report A Final Report covering the activities conducted in Phase II and the results of Phase II work will be delivered to the HSARPA Program Manager following the guidance provided for Phase I final reports in Section 5.1 above.

5.3 Phase III Technical and Management Deliverables In addition to the periodic deliverables required from Phases I and II, the Phase III deliverables should include a final report and documentations on all assay protocols, data-mining algorithms, databases, and other relevant materials. The complete list of

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deliverables should be clearly stated in Volume I, Technical Proposal. This list is subject to negotiation and update by all parties in the later stages of program execution.

6 INFORMATION FOR OFFERORS

6.1 Eligible Applicants Single investigators or teams from private sector organizations, Government Laboratories, Federally Funded Research and Development Centers (FFRDCs), and academic institutions, are encouraged to respond. DoE Laboratories may also respond with the exception of those listed in Appendix A. Historically Black Colleges and Universities (HBCU), Minority Institutions (MI), small and disadvantaged businesses (SDB), women-owned businesses (WB), and HUB-zone enterprises are encouraged to submit Proposals, and to join others as team members in submitting Proposals; however, no portion of the BAA will be set-aside for these special entities because of the impracticality of reserving discrete or severable areas of research and development under this topic.

6.2 Current BIAD BAA (04-03) Performer Eligibility Current BIAD performers (those performers selected under HSARPA BAA 04-03) are eligible to propose to this solicitation. Efforts proposed under this solicitation (BIAD2) will be carefully reviewed for overlapping efforts with previous BIAD performance.

6.3 Organizational Conflict of Interest Organizational Conflict of Interest issues will be evaluated on a case by case basis as outlined in Appendix D. Offerors who have existing contract(s) to provide Scientific, Engineering, Technical and/or Administrative support directly to the program managers or other operational activities of the Science and Technology Directorate will receive particular scrutiny.

6.4 Anticipated Awards Multiple awards are anticipated. Awards will be made based on Proposal evaluation, funds availability, and other programmatic considerations. The Government reserves the right to fund none, some, parts, or all of the Proposals received. Portions of resulting awards are likely to be segregated into optional tasks. It is the intention upon completion of the Proposal evaluation to notify offerors of an initiation of negotiation for awards or rejection of their Proposal. In a limited number of cases, decisions about Proposals will be delayed pending the outcome of other negotiations and the availability of funds. HSARPA requests that such Proposals remain valid for twelve months after the Proposal closing date.

6.5 Types of Awards Awards may be executed as contracts, grants, or cooperative agreements. Proposals should clearly identify which of these instruments is preferred by the offeror. The

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Government Contracting Officer will make the final determination as to the type of award instrument.

6.6 BAA Information Copies of this BAA may be downloaded from the FedBizOpps website http://www.fedbizopps.gov or from http://www.hsarpabaa.com. Paper copies of the BAA may be obtained by contacting: Booz Allen Hamilton, 4001 Fairfax Drive, Suite 750 Arlington, VA 22203 POC: Robert Taylor Phone: (202) 254-5697

6.7 Submitting a Response to this BAA Offerors are required to register online, using the HSARPA BAA Website at http://www.hsarpabaa.com, in order to submit a White Paper or Proposal. Instructions for registration are provided on the website. Offerors who have not registered by the deadline, February 23, 2006 for White Papers and April 21, 2006 for Proposals, will not be permitted to submit White Papers or Proposals. It is very important to follow the registration instructions prior to White Paper and Proposal submittal. Offerors must coordinate with all members of their team to ensure the registration process is done correctly and in a timely manner. Upon successful registration, a file will be sent to the registered email address. Receipt of this file confirms your registration. This email will contain a registration number that is required for uploading. You must register once for White Papers and a second time for Proposals. You can not use the same registration number for both the White Paper and the Proposal. Please check the contents of the file. If they are incorrect, return to the website and make corrections. Any questions concerning the registration process should be directed to HSARPA by emailing BAA06-01@dhs.gov. Following successful registration, White Papers and Proposals may be submitted electronically at http://www.hsarpabaa.com. The submission of a White Paper is not required for submitting a full Proposal. Upon successful submission, a file will be sent to the registered email address. Receipt of this file confirms your White Paper or Proposal submission. Please check the contents of the file. If they are incorrect, return to the website and make corrections.

6.7.1 Proprietary Information Protection All competitive submissions uploaded to the HSARPA BAA Website are protected from public view or download. All submissions will be considered proprietary/source selection sensitive and protected accordingly. Documents may only be reviewed by the registrant, authorized Government representatives, and assigned evaluators, or if marked appropriately, only by authorized Government representatives.

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6.7.2 Multiple Submissions Organizations are permitted to submit more than one Proposal or White Paper to this solicitation. In the case where a single concept applies to multiple TTAs, offerors may submit a single White Paper or Proposal selecting a primary TTA for evaluation. In the Proposal, the offeror is invited to describe the relevance of the concept to other TTAs in addition to the primary TTA. In the case where an offeror or team would like to submit multiple White Papers or Proposals to a single TTA, we strongly encourage coordination to minimize submissions, but multiple submissions are allowed.

6.7.3 Offeror’s Conference HSARPA will hold an Offeror’s Conference for the BIAD2 BAA at the Hyatt Regency, Washington D.C., on February 21, 2006. All interested attendees must register on line by linking to a site from http://www.hsarpabaa.com. The site will include directions to the location from local airports and names and contact information for area hotels. The point of contact for the Offeror’s Conference is: Kimberly Owen Booz-Allen Hamilton 3811 Fairfax Drive, Suite 600 Arlington, VA 22203 Phone: 703-816-5462 owen_kimberly@bah.com

For those unable to attend the Offeror’s Conference, the presentations made at the conference will be posted afterward on http://www.hsarpabaa.com.

6.8 Security Some projects funded under this BAA may require access to, and the generation of, classified data (up to SECRET). Offerors to this solicitation will need to provide an appropriate security plan if access to this classified data is required. DHS may require future phases of this program be performed at a SECRET level. HSARPA will not accept classified White Papers or Proposals in response to this solicitation.

For additional questions regarding security, please contact Angel Santiago-Pinto.

Angel Santiago-Pinto, HSARPA Security Officer angel.santiago-pinto@associates.dhs.gov Phone: 202-254-2191

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6.9 Solicitation and Awards Schedule

Table 1. Schedule of Events.

HSARPA plans to review all White Papers in accordance with this BAA using the evaluation criteria described in Section 7. After the White Paper review, HSARPA will notify offerors, electronically or in writing, at its discretion, either encouraging or discouraging submission of full Proposals based upon this review. HSARPA does not intend to provide further feedback or debrief to submitters of White Papers for which full Proposals are not encouraged. HSARPA plans to review all Proposals in accordance with this BAA. Proposals will be evaluated by a review panel using the criteria specified under Evaluation Criteria in Section 7. Following this review, offerors will be notified whether or not their Proposal has been selected for negotiation.

6.10 White Paper Guidance and Content HSARPA strongly encourages offerors to register and submit White Papers in advance of full Proposals using the instructions in section 6.7 above. Discussion, suggestions, or advice given during communication between the Government and offerors on White Paper topics is not binding. Offerors are free to submit a full Proposal without regard to any feedback or advice about White Papers that they may have received. Even if a full Proposal is discouraged by the Government, a full Proposal may still be submitted and will be evaluated uniformly with all other Proposal submissions. White Papers should capture the essence of a Proposal, and are designed to permit offerors an opportunity to obtain feedback from HSARPA on their planned technology development without having to go to the expense and effort of writing a complete Proposal. A White Paper should consist of not more than five pages and a one page Quad Chart, for a total of six pages. If received by the White Paper submission deadline, the White Paper will be evaluated by a review panel comprised of Government employees and Government contractors.

DATE TIME EVENT 31 Jan 2006 (Tue) BAA released 21 Feb 2006 (Tue) Offeror’s Conference held 23 Feb 2006 (Thu) 4 pm ET White Paper Website Registration deadline 28 Feb 2006 (Tue) 4 pm ET White Paper submissions due 30 Mar 2006 (Thu) White Paper feedback provided 21 Apr 2006 (Fri) 4 pm ET Proposal Website Registration deadline 28 Apr 2006 (Fri) 4 pm ET Proposals due 14 July 2006 (Fri) Selections announced

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Offerors may request a Government-only review, but must indicate so when submitting on the website, and must clearly mark all pages of the White Paper to this effect. After this evaluation, offerors will be promptly notified either encouraging or discouraging the submission of a full Proposal. Notwithstanding a request for a Government-only review, the Government intends to use employees and subcontractors of a support contractor to assist in administering the evaluation of White Papers and Proposals. These personnel will have signed, and will be subject to, the terms and conditions of non-disclosure agreements.

6.10.1 Format and size limitations: A White Paper is an electronic file in Portable Document Format (PDF), readable by IBM-compatible Personal Computers (PC), and in a type font no smaller than 12 point. The individual file size must be no more than 5 Megabytes (MB). White Papers may not exceed five pages and must be accompanied by a one page Quad Chart. Therefore, the entire White Paper submission will not exceed six pages. The White Paper should contain the following information in the following order:

• Quad Chart (one page) • White Paper body (limit of five pages)

o Title, performer, total cost information o Abstract o Technical Approach o Summary of Personnel and Performer Qualifications and Experience o Cost Summary for Phase I

6.10.1.1 Quad Chart For instructions and sample of a Quad Chart, please refer to Appendix C, or go to http://www.hsarpabaa.com .

6.10.1.2 Title, performer, total cost Provide a Title and give names and addresses of the principal investigator and team members, the name of the performing organization, and the total cost and duration (in months) of Phase I.

6.10.1.3 Abstract Provide a concise description of the scientific, technical, engineering and management approaches you propose to address the TTA. Describe the various components of the system proposed and relevant details about how they will function together to achieve the goals of the TTA. Point out what is unique about your proposed solution. Include a brief summary of your concept’s anticipated performance relative to the TTA goals.

6.10.1.4 Technical Approach Phase I:

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Describe the basic scientific or technical concepts that will be used in each component or subsystem comprising your proposed solution to the problem described in the TTA. What is unique about your solution and what advantages might it afford compared to alternate approaches other workers in this field have taken? What has been the extent of your or your team’s past experience in working with or developing the technologies comprising your system? What particular scientific, technical and/or engineering issues need to be addressed and resolved in Phase I to demonstrate feasibility? Explain how the performance of your proposed solution can be expected to meet and be measured against each of the specific technical attributes and/or performance enhancements described in the TTA section of the BAA. What are the key scientific, technical, or engineering challenges and the timing for each that must be met in order to successfully complete this project? Describe all required material and information, which must be provided by the Government to support the proposed work. Provide a brief summary of the costs to execute Phase I, summarized by task. Phase II: Briefly explain your concept of how you will develop and demonstrate a system or system component if you are awarded Phase II funding. Point out the critical path technologies or key technical challenges you will face when building this system or component and your plans for meeting these challenges. Explain how you will demonstrate the Phase II system or component performance relative to the performance or enhancement goals described in the BAA.

6.10.1.5 Summary of Personnel and Performer Qualifications and Experience Briefly describe the offeror’s qualifications and experience in similar development efforts. Present the qualifications of the principal team leaders. Describe the extent of your team’s past experience in working with, or developing the technologies and/or concepts proposed in your technical approach.

6.10.1.6 Cost Summary Provide a brief summary of the cost (labor, materials, consumables, equipment, subcontracts, and any Government furnished resources (GFR)) of the planned effort.

6.11 Proposal Guidance and Content Offerors are encouraged to initiate Proposal Registration at www.hsarpabaa.com only after the deadline for White Paper feedback, March 30, 2006. Following Proposal registration, offerors may begin submitting Proposals, which must be submitted prior to the Proposal deadline, April 28, 2006. Offerors must register separately for Proposal submission. Offerors can choose to alter their ideas, concepts, technical approaches, etc. or expand on their original ideas between submission of a White Paper and submission of the full Proposal. Discussion, suggestions, or advice given during communication between the Government and offerors on White Paper topics are not binding. Proposals consist of three separate documents described in detail below:

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• Volume I: Core Technical Proposal • Volume II: Management Proposal and Supplementary Technical Data • Volume III: Cost Proposal

Volume I is the primary document to be used by the reviewers, with Volumes II and III providing supporting information. The supplemental material in Volumes II and III are to be used at the discretion of the reviewer. The three-volume Proposal comprises PDF files, or, if more convenient for Volume III, a Microsoft Excel file. Each volume must be a separate file, and submitted to the appropriate field on the website. The maximum file size for each volume is 5 MB.

6.11.1 Volume I, Technical and Management Proposal (25 page limit inclusive) Volume I provides the primary technical description of the Proposal. The Volume I, Core Technical Proposal, shall not exceed twenty-five (25) pages, including the cover sheet and table of contents, but not the transmittal letter, in a font no smaller than 12 point. Proposals for which Volume I exceeds the 25 page limit will be considered non-responsive to the BAA. A Quad Chart must be included within the 25 page limit. Volume II may not exceed fifty (50) pages. There is no page limit on Volume III. The twenty-five page limitation for Volume I includes all pictures, figures, tables, and charts in a legible size. Graphic images inserted into the file should minimize file size and support clear display and document printing. Nonconforming Proposals may be rejected without review. The submission of other supporting materials with the Proposal is strongly discouraged and if submitted, will not be reviewed.

6.11.1.1 Section I. Official Transmittal Letter: Official transmittal letter with authorizing official signature and the Proposal Title.

6.11.1.2 Section II. Quad Chart See Appendix C.

6.11.1.3 Section III. Abstract of Proposal: A one page synopsis of the entire Proposal, including total costs proposed for each phase. Provide a description of the scientific, technical, engineering and management approach you propose to address the goals of the TTA. Describe the various components of the system proposed and relevant details about how they will function together to achieve the goals of the TTA. Point out what is unique about your proposed solution. Include a brief summary of your concept’s anticipated performance relative to the TTA goals.

6.11.1.4 Section IV. Proposal This section describes the proposed work and the associated technical and management issues.

a. Ability of proposed work to meet the program goals. This section is the centerpiece of the Proposal and should describe the overall methodology and how it will meet the desired attributes and functionality goals specified in the TTA.

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b. Detailed technical descriptions and approach for Phase I. Identifies the critical issues and plans for executing the Phase I effort.

c. Overview of Phase II and Phase III technical approach. d. Deliverables. Provide a brief summary of all deliverables proposed under this

effort, including data, software, and reports consistent with the objectives of the work involved.

e. Management Plan. Provide a brief summary of the management plan, including an explicit description of what role each participant or team member will play in the project, their past experience in technical areas related to this Proposal, and which type of award mechanism you propose to use (see section 6.11.3.2).

f. Requirements for Government Furnished Resources. Provide a brief summary of required information and data which must be provided by the Government to support the proposed work, if any.

g. Cost Summary. Summarizes the projected total costs for each task in each year of the effort, including a summary of subcontracts, man hours, and consumables.

6.11.2 Volume II, Management Proposal (50 page limit inclusive)

a. Technical Approach for Phase II. Provide a preliminary description of the Phase II effort, including Gantt charts and milestones.

b. Statement of Work (SOW), Schedule and Milestones. Provide an integrated display for the proposed research, showing each task in Phase I, including major milestones. Include a summary schedule for Phase II with anticipated milestones. Include a section clearly marked as the Phase I Statement of Work (SOW) you propose to undertake. The SOW must include the following information: cost breakdown, deliverables, period of performance, technical and contracting points of contact (POC’s). It is important to note that the SOW will be used for the initiation of contract negotiations for selected Proposals.

c. Management Plan and Key personnel. Describe how the total team effort will be managed and provide rationale for participation of key team members. Provide resumes or curricula vitae (CVs) for each of the key personnel.

d. Relevant Past Experience. Present the offeror’s previous accomplishments and work in this and closely related research areas. Describe other related government funded efforts and their relationship to the proposed effort, and clearly describe how the proposed effort is delineated from these other activities.

e. Facilities. Describe key facilities that will be used in the proposed effort. Delineate between classified and unclassified facilities.

f. Requirements for Government Furnished Resources. Describe all required information and data with the respective classification level, if known, which must be provided by the Government to support the proposed work, if any.

g. Security Plan. Describe the rationale for what aspects of the work, if any, need to be protected, at what level, and propose a strategy for doing so. Provide the collateral clearance level held, if any, by each team member.

h. Additional technical information or data.

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6.11.3 Volume III, Cost Proposal (no page limit)

6.11.3.1 Section I. Cost Response: The cost response should be in the offerors format. Detailed Bases of Estimates are not required. Certified cost or pricing data are not required. However, in order for the Government to determine the reasonableness, realism and completeness of the Cost Proposal, the following data must be provided for the principal investigator and for each team member and in a cumulative summary: Labor: Total labor includes direct labor and all indirect expenses associated with labor, to be used in the Phase I period of performance. Labor hours shall be allocated to each work outline element and segmented by team member. A labor summary by work outline is required. Provide a breakdown of labor and rates for each category of personnel to be used on this project. Direct Materials: Provide total direct material costs that will be acquired and/or consumed in the Phase I period of performance. Limit this information to major items of material only, and explain how the estimated expense was derived. For this agreement, a major item exceeds $25,000. Material costs shall be assigned to specific work outline elements. Subcontracts: Describe major efforts to be subcontracted, the source, estimated cost and the basis for this estimate. For this agreement, a major effort exceeds $250,000. Subcontract labor and material shall be accounted for per the two paragraphs above. A summary chart showing each major subcontractor labor and material effort by work outline is required. Indirect Cost: The Prime Contractor and subcontractor(s) shall include a copy of its most current Negotiated Indirect Cost Rate Agreement (NICRA) or other documentation from the offeror's cognizant Government Audit Agency, if any, stating the offeror's most recent final indirect cost rates and/or the current provisional or predetermined rates accepted by the cognizant Government Audit Agency. Travel: Provide total proposed travel expenditures relating to the Phase I period of performance. Limit this information to the number of trips, location, duration, and purpose of each trip. Other Costs: Include any direct costs not included above. List the item, the estimated cost, and basis for the estimate. The Cost Proposal should be consistent with your proposed SOW presented in Vol II. Activities such as demonstrations required to reduce the various technical risks should be identified in the SOW and reflected in the Cost Proposal. The offeror should provide a total estimated price for the major Independent Research & Development (IR&D) activities associated with the program. The offeror should state whether each program is a dedicated IR&D or if it is being pursued to benefit other programs as well. Cost Share: Cost sharing is neither required nor encouraged. Individuals or Teams proposing to cost share should identify the amount, timing, and source of funds, and

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provide the supporting rationale for cost share. Costs shared by the team shall be allocated to each relevant work outline element.

6.11.3.2 Section II. Proposed Agreement w/ Attachments: Awards may be issued as a FAR contract, cooperative agreement, or grant. Offerors should request a specific award mechanism. Teams requesting a non-FAR based award must submit the rationale for their selection.

6.12 Contact Information The electronic address for all correspondence related to this BIAD2 BAA is:

BAA06-01@dhs.gov

To ensure proper logging and prompt response to questions about this BAA, potential offerors are encouraged to use this email address for all correspondence.

The HSARPA Program Managers who lead this effort are: Dr. Matthew Davenport (HSARPA Program Manager) matthew.davenport@dhs.gov Phone: 202-254-6093 Mr. Michael Mcloughlin (HSARPA Program Manager) michael.mcloughlin@dhs.gov Phone: 202-254-6134 The Contracting Officer for this effort is: Mr. Gilbert Hovermale gilbert.hovermale@DET.AMEDD.ARMY.MIL Any objections to the terms of this solicitation or to the conduct of receipt, evaluation, or award of agreements must be presented in writing within 10 calendar days of (1) the release of this solicitation or (2) the date the objector knows or should have known the basis for its objection. Objections should be provided in letter format, clearly stating that it is an objection to this solicitation or to the conduct of the evaluation or award of an agreement and providing a clear, detailed, and factual statement of the basis for objection. Failure to comply with these directions is a basis for summary dismissal of the objection. Bidders should mail objections to: Mr. Gilbert Hovermale U.S. Army Medical Research Acquisition Activity (USAMRAA) Contracting Officer gilbert.hovermale@DET.AMEDD.ARMY.MIL 301-619-2090 Mailing Address:

USA MED RESEARCH ACQ ACTIVITY

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820 Chandler Street Fort Detrick, MD 21702

6.13 Information for White Paper and Proposal Respondents This BAA is for planning purposes only and shall not be construed as an obligation on the part of the government to acquire any products or services. No entitlement to payment of direct or indirect costs or charges by the government will arise as a result of submission of responses to this BAA and the government’s use of such information. Respondents to this BAA may be requested to provide additional information based on their submittals. Unnecessarily elaborate responses containing extensive marketing materials are not desired.

7 EVALUATION CRITERIA AND SELECTION PROCESS

7.1 White Papers The evaluation of White Papers will be accomplished through an independent technical review of each White Paper, using the following criteria, which are listed in descending order of relative importance:

• Potential of the proposed concept to address the program goals described in this document.

• Sound technical and managerial approach to the proposed work, including a demonstrated understanding of the critical technology challenges required to address the desired system performance parameters, and a strategy to address those issues, including a risk mitigation strategy.

• Capability to perform proposed work and history of performance of the Team and Team members in developing related technologies and systems.

7.2 Proposals Volume I, II, and III will be used to evaluate each Proposal. The evaluation of Proposals will be accomplished through an independent technical review of each, using the following criteria, which are listed in descending order of relative importance:

• Potential of the proposed concept to address the program goals described in this document.

• Sound technical and managerial approach to the proposed work, including a demonstrated understanding of the critical technology challenges required to address the desired system performance parameters, and a strategy to address those issues, including a risk mitigation strategy

• Capability to perform proposed work and history of performance of the Team and Team members in developing related technologies and systems.

• Cost realism. Each price response will be reviewed for price/cost realism, reasonableness, and overall best value to the government.

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The final evaluation will be based upon an assessment of the overall best value to the Government, based upon these criteria.

7.3 Review and Selection Process It is the policy of HSARPA to ensure an impartial, equitable, and comprehensive evaluation of all Proposals and to select the source (or combination of sources) whose offer(s) is most advantageous to the Government. In order to provide the desired evaluation, Government evaluators and subject matter expert advisors from the employees and subcontractors of a support contractor will review each submission. These personnel will have signed, and will be subject to, the terms and conditions of non-disclosure agreements. Offerors may request a Government-only review, but must indicate so during the White Paper and/or Proposal registration at http://www.hsarpabaa.com.

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8 LIST OF ATTACHMENTS

8.1 Appendix A: List of Excluded Offerors 8.2 Appendix B: List of Acronyms 8.3 Appendix C: Quad Chart Format 8.4 Appendix D: Organizational Conflict of Interest

Appendix A

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8.1 Appendix A: List of Excluded Offerors This solicitation is a Broad Agency Announcement (BAA) considered to be full and open competition. Therefore any entity other than the following DoE National Laboratories may submit responses to this solicitation:

1) Lawrence Livermore National Laboratory 2) Los Alamos National Laboratory 3) Oak Ridge National Laboratory 4) Pacific Northwest National Laboratory 5) Sandia National Laboratory 6) Brookhaven National Laboratory 7) Argonne National Laboratory 8) Idaho National Environmental and Engineering Laboratory 9) Remote Sensing Laboratory 10) Savannah River National Laboratory

The DoE National Laboratories listed above, termed DHS strategic partner laboratories, are prohibited because of their direct participation in DHS programs through the Office of Research and Development (ORD). These DHS strategic partner laboratories are not permitted to propose as the lead or prime contractor under this solicitation, nor may they be included on any team, except under the very limited circumstances of providing transition-ready technologies as described in detail below. The ten DHS strategic partner laboratories are permitted to participate in this solicitation only under the very limited circumstances described in this Appendix. The principles which guide this participation are:

• Due to the potential for access to internal DHS data and the provision of stewardship funding, DHS strategic partner laboratories may not participate in HSARPA solicitations except under the very limited circumstances described below.

• DHS strategic partner laboratories may not propose directly to this solicitation or participate in any manner in the development of responses to this solicitation outside of the process here defined.

• DHS strategic partner laboratories may collaborate with HSARPA offerors by providing explicitly identified transition-ready technologies, subject to DoE and DHS approval. It is on the initiative of the providing laboratory to identify which technologies are transition-ready.

• DHS strategic partner laboratories may collaborate with HSARPA offerors by providing explicitly identified and unique supporting capabilities, subject to DoE and DHS approval. It is on the initiative of the providing laboratory to identify which supporting capabilities are available to HSARPA offerors.

• HSARPA will neither encourage nor discourage offerors from incorporating DHS strategic partner laboratory technologies. The inclusion of these technologies is at the sole discretion of offerors in their evaluation of best value and best technical response to the Government under this solicitation.

Appendix A

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• All collaborations between HSARPA performers and DHS strategic partner laboratories are subject to any additional restrictions imposed by either the collaborating laboratory or the DoE.

• Laboratories other than those identified as DHS strategic partners may participate directly in this solicitation, similar to any other FFRDC, subject to any restrictions imposed by the policies of the individual laboratory and the DoE.

The process for DHS strategic partner participation in this HSARPA solicitation is defined below:

1) The ten DHS strategic partner laboratories, at their initiative, will propose a list of

transition ready technologies or unique supporting capabilities. This list is subject to the approval of DHS S&T (ORD & HSARPA). Once approved, this list is published at www.hsarpabaa.com with supporting technical documentation.

2) Offerors may request the addition of technologies not listed as part of this BAA. This request must be submitted to HSARPA and is subject to the approvals identified in 1).

3) Offerors may NOT directly contact the DHS strategic partner laboratories with regard to this solicitation. Bids which include DHS strategic partner laboratory participation outside of this process will be rejected without review.

4) For the purposes of the White Paper submission, offerors may identify as part of their technical solution any of the listed transition-ready technologies or unique supporting technologies without laboratory, DHS or DoE consultation or approval. This consultation and approval will be required prior to submission of a full Proposal.

5) Offerors may request from HSARPA a technical POC for any of the listed technologies. Based upon the number of inquiries and other factors, individual DHS strategic partner laboratories may elect not to provide additional technical data beyond the public technical disclosures at the White Paper stage.

6) White Papers will be evaluated assuming the requested technologies will be made available to the proposer.

7) White Papers submitters who are encouraged to submit a full Proposal which includes DHS strategic partner participation will be provided a DHS strategic partner laboratory POC for the identified technologies.

8) Offerors who wish to submit a full Proposal without an encouraged White Paper may directly request, and will be provided, a DHS strategic partner laboratory POC for the identified technologies from HSARPA.

9) HSARPA will provide a single DHS strategic partner laboratory POC for each laboratory to all requestors. This POC is responsible for ensuring that technical discussion with the offerors are limited to the technologies and capabilities listed and must explicitly ensure that no discussions involve any internal DHS data provided to the lab.

10) Prior to submission of a full Proposal, offerors must negotiate a statement of work including costs with the appropriate lab partner, which must be submitted as part of the full Proposal. This negotiation is subject to all normal laboratory and DoE policies with regard to collaboration and technology transition.

Appendix A

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11) Selected Proposals which include DHS strategic partner laboratory participation are subject to final approval of either the source selection authority (SSA) or the HSARPA Director with regards to the level of effort and scope of the DHS strategic partner’s participation.

12) Selected Proposals may be subject to final negotiation of any technology transfer or collaborative agreements needed to implement the proposed work.

Appendix B

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8.2 Appendix B: List of Acronyms BAA Broad Agency Announcement BAND BioAgent Autonomous Networked Detectors BIAD Bioinformatics and Assay Development Program CDC Centers for Disease Control cDNA Complementary Deoxyribonucleic Acid CV Curricula Vitae DHS Department of Homeland Security DHS S&T Department of Homeland Security Science and Technology DNA Deoxyribonucleic Acid DoD Department of Defense DoE Department of Energy DoJ Department of Justice ET Eastern Time (U.S.) FAR Federal Acquisition Regulation FBADS Food Biological Detection Sensors FFRDC Federally Funded Research and Development Centers FMD Foot and Mouth Disease GFE Government Furnished Equipment GFI Government Furnished Information GFM Government Furnished Materials GFR Government Furnished Resources GFT Government Furnished Technologies HBCU Historically Black Colleges and Universities HSARPA Homeland Security Advanced Research Projects Agency HUB-zone Historically Underutilized Business Zone IR&D Independent Research & Development LBADS Low-Cost Bio-Aerosol Detector Systems LRN Laboratory Response Network MB Megabyte MI Minority Institutions NIRCA Negotiated Indirect Cost Rate Agreement OSTP Office of Science and Technology Policy PC Personal Computer PCR Polymerase Chain Reaction PDF Portable Document Format PIP Proposer Information Pamphlet POC Point of Contact RABIS Rapid Automated Biological Identification System RNA Ribonucleic Acid SDB Small and Disadvantaged Businesses SEB Staphylococcus Enterotoxin B SETA Scientific and Engineering Technical Assistance SOW Statement of Work SSA Source Selection Authority

Appendix B

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TTA Technical Topic Area USG United States Government USPS United States Postal Service WB Women-Owned Businesses

Appendix C

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8.3 Appendix C: Quad Chart Format This template will be available in Microsoft PowerPoint Format at www.hsarpabaa.com.

Photograph or Artist’s Concept:Provide a simple but sufficiently detailed graphic that will convey the main idea of the final capability/use of the prototype, and its technological methodology.

Operational Capability:Provide information on how the prototype or prototype component would meet the goals listed in Section 3:

1) Performance Targets2) Cost of Ownership3) Prototype Characteristics

Proposed Technical Approach:Specifically, how the problem will be approached. Describe tasks to be performed. Describe any actions done to date. Describe any related on-going effort by the offeror. Describe the technology involved and how it will be used to solve the problem. Describe the key technical challenges.

Cost and Schedule:Provide any milestone decision points that will be required. Describe period of performance and total costs. Include the base performance period cost and length, and estimates of cost and lengths of possible option.Deliverables:Include all hardware, software, and data deliverables. Corporate Information:You must include Offeror Name, POC full name, address, phone numbers and email.

BAA Number: BAA06-01TTA: (Insert TTA Number)Title: (Brief/Short Title to Describe Offeror’s Proposed Effort)

Offeror Name:Date:

Appendix D

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8.4 Appendix D: Organizational Conflict of Interest ORGANIZATIONAL CONFLICT OF INTEREST

(a) Determination. The Government has determined that this effort may result in an actual or potential conflict of interest, or may provide one or more offerors with the potential to attain an unfair competitive advantage.

(b) If any such conflict of interest is found to exist, the Contracting Officer may (1) disqualify the offeror, or (2) determine that it is otherwise in the best interest of the United States to contract with the offeror and include the appropriate provisions to mitigate or avoid such conflict in the contract awarded. After discussion with the offeror, the Contracting Officer may determine that the actual conflict cannot be avoided, neutralized, mitigated or otherwise resolved to the satisfaction of the Government, and the offeror may be found ineligible for award.

(c) Disclosure: The offeror hereby represents, to the best of its knowledge that:

(1) It is not aware of any facts which create any actual or potential organizational conflicts of interest relating to the award of this contract, or

(2) It has included information in its Proposal, providing all current information bearing on the existence of any actual or potential organizational conflicts of interest, and has included the mitigation plan in accordance with paragraph (d) of this provision.

(d) Mitigation/Waiver. If an offeror with a potential or actual conflict of interest or unfair competitive advantage believes it can be mitigated, neutralized, or avoided, the offeror shall submit a mitigation plan to the Government for review. Award of a contract where an actual or potential conflict of interest exists shall not occur before Government approval of the mitigation plan. If a mitigation plan is approved, the restrictions of this provision do not apply to the extent defined in the mitigation plan. If not defined, then this provision applies fully.

(e) Other Relevant Information: In addition to the mitigation plan, the Contracting Officer may require further relevant information from the offeror. The Contracting Officer will use all information submitted by the offeror, and any other relevant information known to DHS, to determine whether an award to the offeror may take place, and whether the mitigation plan adequately neutralizes or mitigates the conflict.

(f) Corporation Change. The successful offeror shall inform the Contracting Officer within thirty (30) calendar days of the effective date of any corporate mergers, acquisitions, and/or divestures that may affect this provision.

(g) Flow-down. The contractor shall insert the substance of this clause in each first tier subcontract that exceeds the simplified acquisition threshold.