DARPA-BAA-11-60_Living Foundries_FinalForPosting_2 Sept 11.pdf

Broad Agency Announcement

Living Foundries: Advanced Tools and Capabilities for Generalizable Platforms (ATCG)

Microsystems Technology Office (MTO)

DARPA-BAA-11-60

September 2, 2011

Table of Contents:

Part I: Overview Information……………………………………………………………………...3 Part II: Full Text of Announcement Sec. I: FUNDING OPPORTUNITY DESCRIPTION…………………………………….4 Sec. II: AWARD INFORMATION……………………………………………………...12 Sec. III: ELIGIBILITY INFORMATION……………………………………………….13

A. Eligible Applicants B. Procurement Integrity, Standards of Conduct, Ethical Considerations, and

Organizational Conflicts of Interest C. Cost Sharing/Matching

Sec. IV. APPLICATION AND SUBMISSION INFORMATION……………………...15 A. Address to Request Application Package B. Security and Proprietary Issues C. Proposal Abstract and Full Proposal Submission Information

Sec. V. APPLICATION REVIEW INFORMATION…………………………………...26 A. Evaluation Criteria B. Review and Selection Process

Sec. VI. AWARD ADMINISTRATION INFORMATION……………………………..28 A. Selection Notices B. Administrative and National Policy Requirements C. Reporting D. Electronic Systems

Sec. VII. AGENCY CONTACTS……………………………………………………….34 Sec. VIII. OTHER INFORMATION……………………………………………………35

A. Intellectual Property B. Non-Procurement Contract Proposers – Noncommercial and Commercial

Items (Technical Data and Computer Software) C. All Proposers – Patents D. All Proposers – Intellectual Property Representations E. Other Transaction Agreements (OTAs)

NOTE: PROPOSERS ARE CAUTIONED THAT EVALUATION RATING MAY BE LOWERED

AND/OR PROPOSALS REJECTED IF ALL PROPOSAL PREPARATION AND/OR

SUBMITTAL INSTRUCTIONS LISTED HEREIN ARE NOT FOLLOWED.

THOSE INTENDING TO SUBMIT A PROPOSAL FOR AN ASSISTANCE INSTRUMENT

(GRANT OR COOPERATIVE AGREEMENT) ARE STRONGLY ENCOURAGED TO READ

THE INSTRUCTIONS PROVIDED AT SECTION IV(B)(4) REGARDING THE TIME

REQUIRED TO RECEIVE VALIDATION OF SUBMISSIONS MADE THROUGH

GRANTS.GOV. PROPOSALS THAT ARE VALIDATED AFTER THE PROPOSAL DUE

DATE/TIME WILL BE CONSIDERED LATE AND, AS SUCH, WILL NOT BE CONSIDERED

DURING THE INITIAL ROUND OF REVIEWS.

Part I: Overview Information

Federal Agency Name – Defense Advanced Research Projects Agency (DARPA), Microsystems Technology Office (MTO)

Funding Opportunity Title – Living Foundries: Advanced Tools and Capabilities for Generalizable Platforms (ATCG)

Announcement Type – Initial announcement Funding Opportunity Number – Broad Agency Announcement (BAA) 11-60 Catalog of Federal Domestic Assistance Numbers (CFDA) – 12.910 Research and

Technology Development Dates o Posting Date: September 2, 2011 o Industry Day Date: June 28, 2011 (DARPA-SN-11-44) o Proposal Abstract Due Date: On or before 4:00 PM Eastern, September 26, 2011 o Proposal Due Date: On or before 4:00 PM Eastern, November 17, 2011

Concise description of the funding opportunity –DARPA is soliciting innovative research proposals to develop new tools, technologies and methodologies to transform biology into an engineering practice, speeding the biological design-build-test cycle and expanding the complexity of systems that can be engineered. The goal is to enable the rapid development of previously unattainable technologies and products, leveraging biology to solve challenges associated with production of new materials, novel capabilities, fuel and medicines. For example, one motivating, widespread and currently intractable problem is that of corrosion/materials degradation—a challenge which costs the DoD nearly $23 B/yr. Living Foundries, with its ability to truly program and engineer biology, may enable the capability to design and engineer systems to rapidly and dynamically prevent, seek out, identify and repair corrosion/materials degradation.

Ultimately, in turning biology into an engineering endeavor, Living Foundries aims to enable on-demand production of new and high-value materials, devices and capabilities for the Department of Defense (DoD). This announcement, Living Foundries: ATCG, focuses on the development of the component, advanced tools and capabilities for rapidly engineering new biological systems. Example areas of interest include: design and automation tools, modular genetic parts and devices, standardized test platforms and chassis, tools for rapid physical construction, editing and manipulation of genetic designs, and new characterization and debugging tools for synthetic networks.

Anticipated individual awards – Multiple awards are anticipated.

Types of instruments that may be awarded – Procurement contract, grant, cooperative agreement or other transaction.

Question and Answer Page – https://safe.sysplan.com/livingfoundries Agency contact

Dr. Alicia Jackson, Program Manager

DARPA/MTO

ATTN: DARPA-BAA-11-60

3701 North Fairfax Drive Arlington, VA 22203-1714

The BAA Coordinator for this effort can be reached by electronic mail:

DARPA-BAA-11-60@darpa.mil

Part II: Full Text of Announcement

I. FUNDING OPPORTUNITY DESCRIPTION

The Defense Advanced Research Projects Agency often selects its research efforts through the Broad Agency Announcement (BAA) process. The BAA will appear first on the FedBizOpps website, http://www.fedbizopps.gov/, and the Grants.gov website http://www.grants.gov/. The following information is for those wishing to respond to the BAA.

Introduction

As part of its Living Foundries Program, DARPA is soliciting innovative research proposals to develop new tools, technologies and methodologies to transform biology into an engineering practice, speeding the biological design-build-test cycle and expanding the complexity of systems that can be engineered. The goal is to enable the rapid development of previously unattainable technologies and products, leveraging biology to solve challenges associated with production of new materials, novel capabilities, fuel and medicines. For example, one motivating, widespread and currently intractable problem is that of corrosion/materials degradation. The DoD must operate in all environments, including some of the most corrosively aggressive on Earth, and do so with increasingly complex heterogeneous materials systems. This multifaceted and ubiquitous problem, which affects nearly all systems, costs the DoD nearly $23 B/yr. Living Foundries, with its ability to truly program and engineer biology, may enable the capability to design and engineer systems to rapidly and dynamically prevent, seek out, identify and repair corrosion/materials degradation. In turning biology into an engineering endeavor, Living Foundries aims to enable on-demand production of new and high-value materials, devices and capabilities for the Department of Defense (DoD).

The Living Foundries’ portfolio consists of a set of programs, of which this BAA is the first, whose ultimate goal is to harness the use of biology as a technology and drive its advance as a manufacturing platform. This announcement, Living Foundries: Advanced Tools and Capabilities for Generalizable Platforms (ATCG), calls for the development of the advanced, translatable tools and capabilities that will make up an end-to-end technology platform for rapidly, safely, and predictably engineering new biological systems. The goals of these advanced tools and capabilities are to accelerate the biological design-build-test cycle (the process of taking a new biological design from conception to execution) and to expand the complexity of designs that can be built. DARPA anticipates a second BAA comprised of challenge demonstrations necessitating the integration of these tools and capabilities into a platform to prove-out the Living Foundries goal of rapid biological design and engineering for the production of materials and new biological functionalities; for example, such a platform would may enable the rapid design and fabrication of systems to prevent, seek out, identify and repair corrosion/materials degradation for a variety of environments and materials, as well as be capable of the design and fabrication of additional systems for unrelated applications.

Accomplishing the vision of Living Foundries requires a program that is more than multidisciplinary – it requires a new engineering discipline built upon the integration of new ideas, approaches and tools from fields spanning computer science and electrical engineering to chemistry and the biological sciences, in order to overcome current limitations and to create revolutionary capabilities in our ability to engineer biology. Key to success will be opening up the biological design and manufacturing process to new researchers, allowing information to be readily shared, and establishing a design ethos founded on predictability and reproducibility.

Research proposed in the ATCG BAA should investigate innovative approaches that produce transformative advances in our ability to engineer biology. Specifically excluded is research that will primarily result in evolutionary improvements to the existing state of practice.

Background

Current approaches to engineering biology rely on an ad hoc, laborious, trial-and-error process, wherein one successful project often does not translate to enabling subsequent new designs. As a result, the state of the art development cycle for engineering a new biologically manufactured product often takes 7+ years and tens to hundreds of millions of dollars (e.g. microbial production of artemisinic acid for the treatment of malaria and the non-petroleum-based production 1,3-propanediol). The impact of current approaches is two-fold. First, the number of new entrants and innovators into the biomanufacturing space is immediately limited – few have the expertise, capital and/or time necessary to develop and engineer a new product. Second, combined with the complexity of biological systems, an ad hoc approach results in one-off efforts limited to modifying only a small set of genes and constructing simple, isolated genetic circuits and metabolic pathways. Consequently, while progress has been made, we are constrained to producing only a tiny fraction of the vast number of possible chemicals, materials, and functional systems that would be enabled by the ability to truly engineer biology. A new approach is needed.

This new approach is Living Foundries: develop and apply an engineering framework to biology that decouples biological design from fabrication, yields design rules and tools, and manages biological complexity through abstraction and standardization. One analogy is that Living Foundries aims to do for biological design what very-large-scale integration (VLSI) did for integrated circuits. Applying an engineering framework to biology will remove barriers to researchers outside the biological sciences, bringing diverse expertise and new methods to biological design. The best innovations will introduce new architectures and tools that will form the foundational technology for engineering biology.

The vision of Living Foundries is one where new and multiple cellular functions are readily constructed, combined, and controlled by an integrated genetic circuitry. The ultimate effect of which will be to open up the full space of biologically produced materials and systems. To achieve this, new tools, technologies and methodologies that directly address our current limitations and expand our capabilities must be developed. The outcome should be an open technology platform that integrates these tools and capabilities, allowing new designs to rapidly move from conception to execution.

Program Scope & Structure

DARPA is soliciting innovative research and development proposals for the Living Foundries:

ATCG program that focus on the development of new tools, technologies and methodologies to compress the biological design-build-test cycle by at least 10x in both time and cost while increasing the complexity of systems that can be designed and executed by orders of magnitude.

These advancements should enable the ability to rapidly design and build new systems to create novel capabilities and to address complex challenges that today have no or few solutions (e.g.

corrosion).

Each proposal may address one or more areas of interest, examples of which are described below. If addressing more than one area within a single proposal, proposers must ensure that they are proposing one coherent vision, and demonstrate that each area is necessary and inseparable from the other(s) to achieve that vision. Disjointed efforts submitted under a single proposal will not be supported. Since the tools and capabilities required ultimately must be integrated and demonstrated with a proof-of-concept, proposals must also address how the need for future integration will inform the design and development of these individual tools/capabilities from their conception. Simultaneously developing multiple interrelated tools, technologies and/or methodologies in close concert is one (not the only) way to address this requirement. Successful proposals will consist of a multidisciplinary team with expertise both inside and outside of the biological sciences and will ensure a tight coupling between any proposed design tool development and experimental work. Again, DARPA is only interested in proposals that will result in transformative advances in our ability to engineer biology

The ATCG Program should not exceed 30 months. Proposals should be separated into two execution phases with the first phase (Phase I) expected to last no more than 12 months. Phase I may last up to 18 months only if the extra time is justified by the technical nature of the effort.

Funding for a second phase is contingent on meeting the milestones proposed in Phase I. Phase I should focus on the development of new tools and capabilities and include a proof-of-concept to demonstrate utility to the Living Foundries’ goals. The remainder of the effort should focus on refining the tools and capabilities to demonstrate appropriate robustness and the ability to translate across multiple platforms and systems in preparation for the Demonstration projects in the anticipated BAA #2 and their associated target applications. Note that work performed under the ATCG BAA should not be confined to one particular challenge demonstration or application (e.g. corrosion) that results in a one-off capability; tools and capabilities proposed should enable the ability to tackle a broad array of challenges. Each proposal should include a discussion of how the proposed tools/capabilities advance the vision of the Living Foundries program, a detailed evaluation of the state of the art for the respective tool, technology or methodology, a plan for the safe and responsible development of the proposed tools/capabilities, as well as quantitative performance and evaluation metrics.

Collaboration

Collaborative efforts/teaming are encouraged if the proposed tools/capabilities require a team to ensure successful execution. Any teams should be sized according to the scale of the technical effort proposed and expertise required. A teaming website has been established at https://safe.sysplan.com/livingfoundries/ to facilitate the formation of teaming arrangements between interested parties. Specific content, communications, networking, and team formation are the sole responsibility of the proposer. Neither DARPA nor the Department of Defense (DoD) endorses the destination web site or the information and organizations contained therein, nor does DARPA or the DoD exercise any responsibility at the destination. This website is provided consistent with the stated purpose of this BAA.

Example Areas of Interest

Developing engineered biological solutions to the diverse challenges we face, such as corrosion, requires the rapid and predictable design and implementation of systems that can sense and respond to their environment, perform complex logic functions, synthesize materials in situ, signal, and exhibit a host of other engineered behaviors. The design and implementation of these functionalities today is extremely difficult. The state of the art biological design cycle consists of a highly coupled design and fabrication process that is lengthy, empirical, ad hoc, and constrained to producing simple designs and products. This cycle consists of (1) identifying and modifying potential genes, pathways and regulatory elements of interest from nature, (2) “designing” genetic networks and pathways, (3) synthesizing and assembling the corresponding DNA sequence, and (4) testing and optimizing the implemented design. From idea conception to final construct, the entire process takes 7+ years. To achieve the Living Foundries: ATCG goals of compressing the design-build-test cycle timeline by at least an order of magnitude and increasing the complexity of designs that we can build, new approaches, tools and capabilities are needed.

Listed below are several example areas of interest for developing new tools and capabilities.

This list is not comprehensive and additional/alternative areas of research and development are welcome that will revolutionize the capability to rapidly and predictably engineer biology. If proposing additional/alternative areas of research, proposers should be explicit in detailing what problem they are addressing, why it is important to the goals of Living Foundries, and what the impact will be if successful.

(1) Design tools that span from high-level description to synthetic circuit modeling to automated fabrication in cells, i.e. interoperable tools and databases for design, modeling, and fabrication

Current software approaches to designing genetic systems rely on boutique, custom solutions produced by individual groups tailored to their specific methodologies and tools. This results in a myriad of design tools that are not readily adopted or combined with other software, preventing their widespread use and the subsequent democratization of the biological design or fabrication process. Furthermore, there is significant opportunity for automation of many wet-lab tasks, reducing variability between experiments and increasing the speed and throughput of constructing new designs. Challenges to developing a standardized, widespread suite of design/modeling/fabrication tools include: 1) core data models must include sufficient granularity of information to encompass the diverse needs of researchers, but retain enough abstraction to limit the computational performance needed, 2) tools must be interoperable via a defined application programming interface (API) and 3) tools must both inform and be informed by experimental work and wet-lab methodologies to ensure their utility. To encourage interoperability, all applicable design tools and databases developed under the ATCG program should be compatible with Synthetic Biology Open Language (SBOL) core data model.

(2) Modular genetic parts, regulators, devices, and circuits (and the new methods to develop and refine these) that allow a combination of systems to be designed and reproducibly assembled increasing the efficiency, sophistication, and scale of possible designs. In particular, DARPA is looking to approaches that harness and take advantage of the networks of DNA, RNA and proteins that work in concert to give rise to biological function.

A key challenge is a lack of sufficient, robust sets of parts, regulators, devices and circuits to rapidly design new genetic systems of complexity beyond a few tens of genes, single circuits, or simple tweaking of existing pathways. Orthogonal biological parts, regulators and circuits with well-characterized function for a variety of host systems and conditions would make biological engineering more predictable and enable the construction and integration of more complex systems than are currently possible. Current approaches to parts development involve extensive mining and harvesting of naturally occurring genes, whose behavior is often not predictable outside their native context. Furthermore, existing genes/genetic parts, devices and circuits have not evolved or been designed with sufficient robustness for use with CAD tools, restricting the ability to decouple biological design from fabrication. New approaches that incorporate techniques such as directed evolution are needed to create new and refine existing modular genetic parts, regulators and circuits to expand the diversity of available building blocks applicable to an array of genetic regulatory mechanisms.

(3) Well understood test platforms, ‘cell-like’ systems, and chassis that readily integrate new genetic designs in a predictable fashion

Current challenges in predictably engineering new biological systems include unintended interactions and possible failure modes that result from complex cellular backgrounds interacting with engineered genetic networks. Genetic designs are typically inserted into a few well-known chassis (e.g. E. coli, S. cerivisiae) with largely only experiential expectations of how the genetic pathways will perform in the host. Proposals should address the technical challenges associated with implementing genetic designs into cell or cell-like systems in a predictable and robust fashion. The ultimate goal is to have platforms that are well understood and whose inner machinery will predictably interact with designed genetic networks thereby removing the significant time spent tackling unintended interactions from the design-build-test cycle.

(4) Rapid physical construction, editing and manipulation of genetic designs of up to genome scale complexity including: low cost, rapid DNA synthesis and assembly techniques that produce up to megabase pair lengths of DNA, facile modification and manipulation of genetic designs into a system/chassis, and designs engineered to readily translate between different systems/chassis

Engineering biology with useful complexity requires new approaches for synthesizing, assembling, and manipulating genetic designs rapidly, cheaply, and accurately. The goal is to shift the designers’ mindset towards design and experimentation and facilitate more complex, previously unattainable system designs and architectures. Unlike computer programming, where writing and producing variants of new code is essentially free, DNA synthesis and assembly (the writing of ‘biological code’) is expensive ($0.40-$0.80 per bp), slow (2wks-2mos turn time), error prone (~10-2-10-3), and limited in length and complexity (<25kb). These limitations restrict biological designers to constructing conservative, evolutionary designs, with little room for multiple design refinements, variants or new ideas. Furthermore, the ability to facilely manipulate and integrate genetic code is restricted to only a handful of organisms, limiting the number of possible useful systems and products. The ability to synthesize, modify and test many new designs (up to the genome scale) with little overhead will help to inform and create the biological design rules and tools that are necessary for complex design.

(5) Routine system characterization and debugging of synthetic gene networks that feeds back and informs the design cycle

Current methods for testing new genetic designs revolve around fluorescence or mass spectrometry techniques and require the physical fabrication and incorporation of the complete genetic design into the host system to measure outcomes/final product(s) while producing only a limited amount of quantitative information on expression levels, interactions within the cell, and effect on cell state. Furthermore, the limited throughput of these techniques combined with their analytical limitations, hinder and even prevent large scale screening projects (e.g., for directed enzyme evolution), as the throughput of the assays make these projects unrealistic for many researchers. To enable increases in genetic design complexity, pathway debugging is needed to determine failure points – information that can be fed back to the designer and to design tools to inform re-design. Additionally, new analytical techniques are needed to accurately query the concentrations and interactions of mRNA, proteins, and metabolites within a biological system cheaply and quickly to understand how synthetic gene networks function and interact with the host system in non-specific ways outside of their intended purpose. Proposals in this area should not simply apply high-throughput, parallelization techniques to traditional mass spectrometry or fluorescence; rather they should provide new and enhanced techniques tailored to biological characterization and the needs of Living Foundries.

Program Metrics and Justification

Proposers should address the following questions in describing their proposal’s vision and for each tool, technology, or methodology to be developed:

(1) What is the end goal and how does this compare against the current state of the art?

Include quantitative metrics.

(2) Why is the specific tool/capability proposed important and what problem does it solve?

Be quantitative.

(3) What is the impact? Be quantitative. By how much will each tool/capability speed the biological design, build, test cycle and/or expand the complexity of designs that can be built?

(4) What is the new technical idea behind the proposed tool/capability and why can it succeed now? Provide examples of recent scientific advances that will enable success.

(5) How will each specific tool/capability be developed to ensure its ability to integrate with and support other tools/capabilities?

(6) What is the proposed proof-of-concept to be demonstrated by the end of Phase I to demonstrate the utility of the proposed tools/capabilities to the Living Foundries goals?

(7) Looking ahead to the challenge demonstrations in BAA #2 – if successful, what specific new target applications will be possible that cannot be achieved today?

Furthermore, proposers should identify appropriate quantitative milestones that facilitate tracking of the research progress towards the overall phase and program goals. This includes quantitative performance criteria for each phase as well as intermediate goals and milestones. Proposers should also include a comparison against the state of the art. As an example, if proposing a new DNA synthesis and assembly technique, potential quantitative, end goal metrics/milestones might include: >100x cost reduction (<$0.008/bp), 2 day turn time, >1Mbp length and error rates of 10-5-10-6. This would result in being able to synthesize 10 small (10Mbp) genomes at a cost of only $200K (as opposed to $20M).

A successful proposal will thoroughly discuss all details for meeting the metrics set forth for the program as well as the associated risks and risk-mitigation strategies to meeting those metrics and related milestones. Proposers should provide detailed technical rationale supporting the ability to achieve each milestone and plan for the testing and evaluation of their tools, capabilities, and/or constructs at each milestone.

Bio-Safety and Security

Proposers must ensure and demonstrate throughout the program that all methods and demonstrations of capability comply with national guidance for manipulation of genes and organisms and follow all guidance for biological safety and biosecurity. Proposals should address any potential safety/security issues that the development of the proposed tools/capabilities might pose and include a discussion of approaches and strategies to manage, mitigate and monitor these risks during technology development. In addition, demonstrations and testbeds must meet any applicable regulations designed to protect human health and the environment promulgated by the Environmental Protection Agency, National Institutes of Health, or other relevant agencies of the federal government. Proposers must also comply with any state or municipal regulations or ordinances governing biotechnology practices.

Proposers should be sure to refer to the following documents:

1. Presidential Bioethics Commission Report on Synthetic Biology:

(http://www.bioethics.gov/documents/synthetic-biology/PCSBI-Synthetic-Biology-Report-12- 16-10.pdf )

2. NIH "Dual Use Research: A Dialogue" (a 7 minute video):

http://oba.od.nih.gov/biosecurity/biosecurity.html

3. NIH Office of Biotechnology Assessment (OBA) "Does Your Research Have Dual Use Potential?" http://oba.od.nih.gov/biosecurity/pdf/EducationalBrochureDualUseResearch.pdf

4. National Science Advisory Board for Biosecurity (NSABB): "Addressing Biosecurity Concerns Related to Synthetic Biology" http://oba.od.nih.gov/biosecurity/pdf/NSABB%20SynBio%20DRAFT%20Report- FINAL%20(2)_6-7-10.pdf

5. United States Department of Health and Human Services Guidance Document on Synthetic Biology and Synthetic dsDNA Research:

(http://www.phe.gov/Preparedness/legal/guidance/syndna/Documents/syndna-guidance.pdf ).

6. Coordinated Framework for the Regulation of Biotechnology: http://usbiotechreg.nbii.gov/

7. Biotechnology Program under the Toxic Substances Control Act (TSCA):

http://epa.gov/biotech_rule/pubs/biorule.htm

8. International Treaty and on Prevention of Biological Weapons/ Biological Weapons Convention including all Appendices (1969-2008;

http://www.state.gov/www/global/arms/treaties/bwc1.html)

Intellectual Property and Data Sharing

DARPA expects its investment in the tools and capabilities developed under the ATCG program to be multiplied many-fold by adoption and improvement by researchers across the US. In order to achieve this vision, the Living Foundries program aims to facilitate interoperability and open the field to new entrants. As such, all proposals should contain an intellectual property and data dissemination plan that strives to maximize these aims. For example, even in cases of pre-existing IP, nonassertion covenants have successfully been used to enhance openness.

Commitments to nonexclusive, nondiscriminatory licensing represent another mechanism for ensuring that IP does not prevent widespread dissemination of, and improvement upon, basic platform technologies. However, in cases where are strong reasons for maintaining or acquiring exclusive IP, justification and proof of compatibility and interoperability may be sufficient.

To facilitate interoperability, all applicable design tools and databases developed under the ATCG program should be compatible with Synthetic Biology Open Language (SBOL) core data model.

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II. AWARD INFORMATION

Multiple awards are anticipated. The amount of resources made available under this BAA will depend on the quality of the proposals received and the availability of funds.

The Government reserves the right to select for negotiation all, some, one, or none of the proposals received in response to this solicitation, and to make awards without discussions with proposers. The Government also reserves the right to conduct discussions if it is later determined to be necessary. If warranted, portions of resulting awards may be segregated into pre-priced options. Additionally, DARPA reserves the right to accept proposals in their entirety or to select only portions of proposals for award. In the event that DARPA desires to award only portions of a proposal, negotiations may be opened with that proposer. The Government reserves the right to fund proposals in phases with options for continued work at the end of one or more of the phases.

Awards under this BAA will be made to proposers on the basis of the evaluation criteria listed below (see section labeled “Application Review Information”, Sec. V.), and program balance to provide overall value to the Government. Proposals identified for negotiation may result in a procurement contract, grant, cooperative agreement, or other transaction depending upon the nature of the work proposed, the required degree of interaction between parties, and other factors. The Government reserves the right to request any additional, necessary documentation once it makes the award instrument determination. Such additional information may include but is not limited to Representations and Certifications. The Government reserves the right to remove proposers from award consideration should the parties fail to reach agreement on award terms, conditions and cost/price within a reasonable time or the proposer fails to timely provide requested additional information.

As of the date of publication of this BAA, DARPA expects that program goals for this BAA may be met by proposers intending to perform 'fundamental research,' i.e., basic or applied research performed on campus in science and engineering, the results of which ordinarily are published and shared broadly within the scientific community, as distinguished from proprietary research and from industrial development, design, production, and product utilization the results of which ordinarily are restricted for proprietary or national security reasons. Notwithstanding this statement of expectation, DARPA is not prohibited from considering and selecting research proposals that, while perhaps not qualifying as 'fundamental research' under the foregoing definition, still meet the BAA criteria for submissions. If proposals are selected for award that offer other than a fundamental research solution, then DARPA will either work with the proposer to modify the proposed statement of work to bring the research back into line with fundamental research or else the proposer will agree to restrictions in order to receive an award. See Section VI.B.4 for further information on fundamental, non-fundamental and restricted research. In all cases, the DARPA contracting officer shall have sole discretion to select award instrument type and to negotiate all instrument provisions with selectees.

III. ELIGIBILITY INFORMATION

A. Eligible Applicants

All responsible sources capable of satisfying the Government's needs may submit a proposal that shall be considered by DARPA. Historically Black Colleges and Universities (HBCUs), Small Businesses, Small Disadvantaged Businesses and Minority Institutions (MIs) are encouraged to submit proposals and join others in submitting proposals; however, no portion of this announcement will be set aside for these organizations’ participation due to the impracticality of reserving discrete or severable areas of this research for exclusive competition among these entities.

Federally Funded Research and Development Centers (FFRDCs) and Government entities (Government/National laboratories, military educational institutions, etc.) are subject to applicable direct competition limitations and cannot propose to this BAA in any capacity unless they address the following conditions. FFRDCs must clearly demonstrate that the proposed work is not otherwise available from the private sector AND must also provide a letter on letterhead from their sponsoring organization citing the specific authority establishing their eligibility to propose to government solicitations and compete with industry, and compliance with the associated FFRDC sponsor agreement and terms and conditions. This information is required for FFRDCs proposing to be prime or subcontractors. Government entities must clearly demonstrate that the work is not otherwise available from the private sector and provide written documentation citing the specific statutory authority (as well as, where relevant, contractual authority) establishing their ability to propose to Government solicitations. At the present time, DARPA does not consider 15 U.S.C. 3710a to be sufficient legal authority to show eligibility.

While 10 U.S.C. 2539b may be the appropriate statutory starting point for some entities, specific supporting regulatory guidance, together with evidence of agency approval, will still be required to fully establish eligibility. DARPA will consider eligibility submissions on a case-by-case basis; however, the burden to prove eligibility for all team members rests solely with the Proposer.

B. Procurement Integrity, Standards of Conduct, Ethical Considerations, and Organizational Conflicts of Interest

Current federal employees are prohibited from participating in particular matters involving conflicting financial, employment, and representational interests (18 USC 203, 205, and 208).

The DARPA Program Manager for this BAA is Dr. Alicia Jackson. Once the proposals have been received, and prior to the start of proposal evaluations, the Government will assess potential conflicts of interest and will promptly notify the Proposer if any appear to exist. (Please note, the Government assessment does NOT affect, offset, or mitigate the Proposer’s own duty to give full notice and planned mitigation for all potential organizational conflicts, as discussed below.)

Without prior approval or a waiver from the DARPA Director, in accordance with FAR 9.503, a Contractor cannot simultaneously provide scientific, engineering, technical assistance (SETA) or similar support and also be a technical performer. Therefore, all Proposers as well as proposed subcontractors and consultants must affirm whether they (their organizations and individual team members) are providing SETA or similar support to any DARPA technical office(s) through an active contract or subcontract. All affirmations must state which office(s) the Proposer, subcontractor, consultant, or individual supports and identify the prime contract number(s).

Affirmations shall be furnished at the time of proposal submission. All facts relevant to the existence or potential existence of organizational conflicts of interest (FAR 9.5) must be disclosed. The disclosure must include a description of the action the Proposer has taken or proposes to take to avoid, neutralize, or mitigate such conflict. If in the sole opinion of the Government after full consideration of the circumstances, a proposal fails to fully disclose potential conflicts of interest and/or any identified conflict situation cannot be effectively mitigated, the proposal will be rejected without technical evaluation and withdrawn from further consideration for award.

If a prospective Proposer believes that any conflict of interest exists or may exist (whether organizational or otherwise) or has questions on what constitutes a conflict of interest, the Proposer should promptly raise the issue with DARPA by sending his/her contact information and a summary of the potential conflict by email to the BAA mailbox at DARPA-BAA-11- 60@darpa.mil before time and effort are expended in preparing a proposal and mitigation plan.

C. Cost Sharing/Matching

Cost sharing is not required for this particular program; however, cost sharing will be carefully considered where there is an applicable statutory condition relating to the selected funding instrument (e.g., for any Other Transactions under the authority of 10 U.S.C. § 2371). Cost sharing is encouraged where there is a reasonable probability of a potential commercial application related to the proposed research and development effort.

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IV. APPLICATION AND SUBMISSION INFORMATION

A. Address to Request Application Package

This solicitation contains all information required to submit a proposal. No additional forms, kits, or other materials are needed. This notice constitutes the total BAA. No additional information is available, nor will a formal Request for Proposal (RFP) or additional solicitation regarding this announcement be issued. Requests for same will be disregarded.

B. Security and Proprietary Issues

Security: The Government anticipates proposals submitted under this BAA will be unclassified.

No classified proposals will be accepted.

Proprietary Data: All proposals containing proprietary data should have the cover page and each page containing proprietary data clearly marked as containing proprietary data. It is the Proposer’s responsibility to clearly define to the Government what is considered proprietary data.

It is the policy of DARPA to treat all proposals as competitive information, and to disclose their contents only for the purpose of evaluation. Proposals will not be returned. The original of each proposal received will be retained at DARPA and all other non-required copies destroyed.

A certification of destruction may be requested, provided the formal request is received at this office within 5 days after unsuccessful notification.

C. Proposal Abstract and Full Proposal Submission Information

It is STRONGLY ENCOURAGED that a proposal abstract be submitted to determine the acceptability of the proposed concept to the BAA. This procedure is intended to minimize unnecessary effort in proposal preparation and review. Proposal Abstracts are due on or before 4:00 p.m., ET, September 26, 2011. Full proposals are due on or before 4:00 p.m., ET, November 17, 2011. Further information regarding abstract and full proposal submission dates and instructions is specified in Section IV. C.5.

DARPA will respond to abstracts with a statement as to whether DARPA is interested in the idea. DARPA will attempt to reply to abstracts via e-mail within thirty (30) calendar days of receipt. Should a proposer be discouraged from submitting a full proposal, the letter must contain feedback for the proposer regarding the rationale for the decision not to recommend a full proposal be submitted. Abstracts will be reviewed in the order they are received. Regardless of DARPA’s response to an abstract, proposers may submit a full proposal. DARPA will review all full proposals submitted using the published evaluation criteria and without regard to any comments resulting from the review of an abstract.

Proposers are required to submit full proposals by the time and date specified in the BAA in order to be considered during the initial round of selections. DARPA may evaluate proposals received after this date for a period up to 180 days from date of posting on FedBizOpps and Grants.gov. Ability to review late submissions remains contingent on availability of funds.

Proposals and abstracts may not be submitted by fax or e-mail; any so sent will be disregarded.

Proposal abstracts and full proposals not meeting the format described in the BAA may not be reviewed.

1. Proposal Abstract Format

Proposal abstracts should follow the same general format as described for Volume I under FULL PROPOSAL FORMAT (see below), but include ONLY Section I and Section II with significant focus on Parts A and B, key personnel, and program metrics and milestones in enough detail to provide a representative overview of the proposed effort. Note that no formal transmittal letter is required for proposal abstracts. The cover sheet should be clearly marked “PROPOSAL ABSTRACT” and the total length should not exceed 8 pages, excluding cover page and Summary PowerPoint slide.

2. Full Proposal Format

All full proposals must be in the format given below. Nonconforming proposals may be rejected without review. Proposals shall consist of two separate files, Volume I (Technical and Management Proposal) and Volume II (Cost Proposal). All pages shall be printed on single-spaced, 8-1/2 by 11 inch paper with the type not smaller than 12 point font. Smaller font may be used for figures, tables, and charts. Volume I, Technical Management Proposal, may include an attached bibliography of relevant technical papers or research notes (published and unpublished) which document the technical ideas and approach upon which the proposal is based. Intellectual Property/Patents Requirements and the bibliography are not included in the page counts. The submission of other supporting materials along with the proposals is strongly discouraged and will not be considered for review. Volume I shall not exceed 30 pages, excluding the bibliography, summary PowerPoint slide and Section I.

Volume I, Technical and Management Proposal

Section I, Administrative

COVER SHEET TO INCLUDE:

A. Cover sheet to include:

(1) BAA number

(2) Technical area

(3) Lead organization submitting proposal

(4) Type of business, selected among the following categories: “LARGE

BUSINESS”, “SMALL DISADVANTAGED BUSINESS”, “OTHER SMALL

BUSINESS”, “HBCU”, “MI”, “OTHER EDUCATIONAL”, OR “OTHER

NONPROFIT”

(5) Contractor’s reference number (if any)

(6) Other team members (if applicable) and type of business for each

(7) Proposal title

(8) Technical point of contact to include: salutation, last name, first name, street address, city, state, zip code, telephone, fax, electronic mail

(9) Administrative point of contact to include: salutation, last name, first name, street address, city, state, zip code, telephone, fax, electronic mail

(10) Total funds requested from DARPA, separated by Base Award and Options (if any), and the amount of cost share (if any); AND

(11) Date proposal was submitted

B. Official Signed Transmittal Letter. (Note: An official transmittal letter is not required when submitting a Proposal Abstract.)

Section II. Summary of Proposal

This section should clearly and concisely highlight and address the following:

A. Innovative claims for the proposed research. This section should succinctly describe the uniqueness and benefits of the proposed approach relative to the current state-of-art alternate approaches. The following points should be specifically addressed:

(1) What is the end goal and how does this compare against the state of the art?

Include quantitative metrics.

(2) What is the impact? Be quantitative. By how much will each tool/capability speed the biological design, build, test cycle and/or expand the complexity of designs that can be built?

(3) What is the new technical idea behind the proposed tool/capability and why can it succeed now? Provide examples of recent scientific advances that will enable success.

(4) What are the major technical risk elements?

(5) How will each specific tool/capability be developed to ensure its ability to integrate with and support other tools/capabilities?

(6) What is the proposed proof-of-concept to be demonstrated by the end of Phase I to demonstrate the utility of the proposed tools/capabilities to the Living Foundries goals?

(7) Looking ahead to the challenge demonstrations in BAA #2 – if successful, what specific new target applications will be possible that cannot be achieved today?

B. Strategy/description for how tools/capabilities will be disseminated and safely used by the community and ultimately, industry;

C. Technical and Management Approach, including a discussion of how the program will be organized, key personnel and capabilities, and proposed teaming approach;

D. Cost, schedule and measurable milestones for the proposed research, including estimates of cost for each task in each year of the effort delineated by the prime and subcontractors, total cost and cost share, if applicable. (Note: Measurable milestones should capture key development points in tasks and should be clearly articulated and defined in time relative to start of effort.);

E. PowerPoint summary slides summarizing the program and effort; download and use the template provided with the subject BAA, Attachment 2. Submit the PowerPoint (or equivalent) file in addition to Volume I and Volume II of your full proposal.

Section III. Detailed Proposal Information

A. Technical Rationale and Approach. This section is the centerpiece of the proposal and should succinctly describe the uniqueness and benefits of the proposed approach relative to the current state-of-art alternate approaches. A concise section, enhancing that of Section II, outlining the scientific and technical challenges, unique approaches, and potential anticipated technical solutions to the challenges that will be addressed. This section should demonstrate that the proposer has a clear understanding of the state of the art; and should provide sufficient technical details so as to permit complete evaluation of the feasibility of the idea.

B. Program metrics and milestones. All program metrics must be associated with demonstrable, quantitative measures of performance and should be summarized in a single table. Proposals should clearly explain the technical approach(es) that will be employed to meet or exceed each defined metric and provide ample justification as to why the approach(es) is/are feasible. Additionally, comparison with other ongoing research shall be provided indicating advantages and disadvantages of the proposed effort.

C. Program Plan & Risk Assessment. Detailed program plan and risk assessment enhancing that of Section II. Summary of Proposal. A narrative explaining the explicit timelines, milestone achievements, and quantitative program metrics (to include proposer defined metrics, if applicable) by which progress toward the goals can be evaluated. The proposed period of performance of the overall program, and each program stage, should be clearly stated. The narrative plan should include a test plan/approach detailing how all program metrics will be accurately measured. This section should also identify major technical risk elements specific to the proposed technical and management approach, estimate the risk magnitude for each such element, and describe specific plans to mitigate risks. All program metrics should be described/discussed in detail so government reviewers can assess risks associated with meeting them.

D. Bio-safety/security. Proposals should address any potential bio-safety/security issues that the development of the proposed tools/capabilities might pose and include a discussion of approaches and strategies to manage, mitigate and monitor these risks during technology development. Proposers should include a discussion of their proposed work in the context of the NSABB definition of dual use research of concern:

(http://oba.od.nih.gov/biosecurity/nsabb_faq.html#NSABB_FAQ001). See NIH Office of Biotechnology Activities’ (OBA's) "Does Your Research Have Dual Use Potential?"

(http://oba.od.nih.gov/biosecurity/pdf/EducationalBrochureDualUseResearch.pdf). Will it meet this definition? How will the risks be assessed? And if it does meet this definition, how will the risks be mitigated (e.g., communication plan, etc)?