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1000 Molecules Proposers’ Day
Alicia Jackson DARPA/MTO
July 24, 2013
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Engineering Biology
Design and construct genetic pathways, networks and systems to harness the powerful synthetic and
functional capabilities of biology.
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What You Need to Know
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Proposals Due September 17, 2013
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Vision
Requirements
Proposal Instructions
Evaluation Criteria
Read the BAA
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Enable transformative and currently inaccessible projects across chemicals, materials, sensing
capabilities and therapeutics
Vision
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Key Technical Components and Capabilities—p. 8
Teaming and Partnerships—pp. 11 and 12
Intermediate Milestones—pp. 14 and 15
Requirements
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Follow Them
Proposal Instructions
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• Overall Scientific and Technical Merit
• Potential Contribution and Relevance to the DARPA Mission
• Proposer’s Capabilities and/or Related Experience
• Cost Realism
• Realism of Proposed Schedule
• Plans and Capability to Accomplish Technology Transition
Evaluation Criteria: p. 47 of BAA
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If you have Questions: DARPA-BAA-13-37@darpa.mil
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Living Foundries: 1000 Molecules
The Details
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Building a new technology base to enable transformative applications
Living Foundries: ATCG
Foundries
Demo New Capability
New tools to enable rapid engineering of biology
Enable scale and rapid prototyping of genetic designs
never before accessible
1000 Molecules 1000 new chemical building
blocks for new materials 100x faster DBT cycle for engineering biology
Fundamental shift in chemical/materials industry
. . . Enable Impossible Projects
Living Foundries: 1000 Molecules
IMPACT:
Engage and Seed industrial/academic partnerships
Open up new avenues for innovation Enable access/new entrants
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Petro-materials paradigm dominates today
Inputs Commodity Chemicals
Materials Products
MATERIEL/INFRASTRUCTURE
FIELD GEAR
Today’s materials are built from a limited set of building blocks
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Petrochemical starting molecules are limited
Finished Motor Gasoline (42.0%)
Distillate Fuel Oil (27.0%)
Kerosene-type Jet Fuel
(8.8%)
Petroleum Coke (5.1%)
Still Gas (4.1%)
Liquefied Refinery Gases (3.7%)
Naphtha – bp ≤ 401º F (1.2%)
Oils – bp ≥ 401º F (0.7%)
Special Naphthas (0.2%)
US Petroleum Refinery Yield
42 US Gallons
Olefins: alkenes including those with 2, 3, 4, and >4 carbons
Aromatics: conjugated, planar, cyclic compounds
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Biology provides a far richer palette of starting points
Olefins: alkenes including those with 2, 3, 4, and >4 carbons
Aromatics: conjugated, planar, cyclic compounds
Caprolactam
Ladderanes Fluorocarbons
1,3-Propanediol
Farnesene
Riboflavin
Phosphatidylinositol
Heme
Creatine Coniine
Shikimic acid
Adenine Biotin
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New materials produced using engineered biosystems can enhance DoD capabilities
New chemical structures and functions enable new avenues for innovation
Materials Commodity Chemicals
Products Products
Speed DoD Technology
Development
Commodity Chemicals
>103 increase in intermediates
(from 10’s to 10,000’s)
Expanded Chemical Palette
Inputs Inputs
Carbon sources: Corn, Sugarcane,
Biomass, CO2, Nat Gas, etc.
Chemical Factories: Yeast, Algae, new
exotic microorganisms and in-vitro systems
Inherently Flexible, Adaptable Platform
Materials
New Materials with new properties
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Engineering biology could enable the next advance
Biology Petroleum & Natural Gas Engineering Biology
Inflection point
2040
Inflection point
Source: Morgan Stanley Research
Genetically Encoded Materials
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Infrastructure: Scaled, rapid prototyping of genetic designs
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GOAL: Scalable and accessible technology base
• Bridge the gap from initial, laboratory-level, proof-of-concept experimentation to industrial pilot production.
• Enable scale and sophistication of engineering orders of magnitude > SOA
• Automated, integrated processes across design, fabrication, testing, and analysis.
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Key elements/expectations
GOAL: Scalable and accessible technology base
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Key elements/expectations (2)
Successful proposals:
• Advanced process design utilizing best industrial
manufacturing practices,
• Integration and modularization of component technologies,
• Identification of driving technical and scientific challenges.
Key tech components/challenges
1. Design Innovation: Enable forward engineering of new systems
• Novel biosynthetic pathway prediction
• Gene cluster discovery
• Chemical structure prediction
• Tools for design and control of complex networked systems
2. Scalable, Automated Construction: Parallelized construction of combinatorial genetic designs
• Large-scale DNA construction
• Optimized genetic chassis
• Genome-scale, parallel editing tools
• Flexible across organisms/designs
3. Design Evaluation: Massively parallel test and QC of designs
• Integrated, high-throughput detection and analysis
• Automated QC of parts, assembly, and integration
• Validation/verification of engineered systems
4. Integrated Feedback: Harness massive data generation to inform future design
• Analysis of all data, including failure modes
• Machine learning and data mining algorithms
• Generate design rules Approved for Public Release, Distribution Unlimited 21
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Meta-elements/expectations
Beyond the technology and process infrastructure
Infrastructure should:
• Be applicable to addressing diverse applications beyond biosynthesis of new molecules e.g. synthetic biological circuits and networks, creation of libraries, recoding and refactoring of genomes, etc.
• Readily import, test, and integrate new methods and tech
• Engage and partner with end users, technology developers and infrastructure providers
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Teams • Mix of Institutions/Partners – academic, non-profit, and industrial
collaborations
• Multidisciplinary - computer science, engineering, automation, industrial process development, chemistry/chemical engineering, biological sciences, etc
• Core team members and researchers are expected to be co-located with the centralized rapid design and prototyping infrastructure maximize interactions and project focus.
Leadership • Teams may be led by industrial, academic, or non-profit entities • Leadership Team should have significant experience and expertise in:
• Directing operations and technology development, • Leading large and diverse teams with both academic and industrial
partners, and • Industrial process design
Teaming and management expectations
Commitment: Expect significant time commitment from core team
Overview/Purpose: Provides a measure of capabilities
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1000 Molecules
• Generate >350 unique molecules demonstrating a breadth of structural and functional diversity
• >1000 unique molecules in total generated across all facilities
• Demonstrate infrastructure capabilities in • throughput, • rapid product generation, and • platform flexibility and generalizability
Across numerous designs, pathways, and products
3 Challenge Areas: 1. Rapid, improved prototyping of known molecules.
• Known biosynthetic pathways. • Includes: molecules previously synthesized biologically and natural products. • Demonstrate improved production (e.g., yield, cost, purity, etc.) relative to
state-of-the-art production methods by using a biosynthetic route.
2. Prototyping of known, but currently inaccessible, molecules. • Not routinely synthesized biologically • Includes synthetic pathways constructed from multiple, unique organisms. • Of particular interest to DARPA: molecules that are currently very difficult,
impossible, or prohibitively expensive to synthesize chemically.
3. Prototyping of novel molecules. •Effectively unattainable through synthetic chemistry and cannot be synthesized using existing biological chemistry.
•Examples: novel enzymes to enable inaccessible pathways, incorporation of novel elements from the periodic table, or high-efficiency incorporation of non-natural amino acids into products
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1000 Molecules challenge areas
Task Area 2: Demonstration of capabilities
Phase I Phase II
FY15 18 mos 18 mos
Phase III 24 mos
FY18
Challenge Area 1: Rapid, improved prototyping of known molecules Super absorbent materials – Polyitaconic acid
Insecticides – Spinocyn
Coating/Fibers – Muconic acid
Natural Products – Artmesinin
Challenge Area 3: Prototyping of novel materials from new chemistries Sequence defined, nonnatural polymers –
New nanomaterials –
Novel Catalysts –
Hybrid materials systems
Electro/Optical molecules– Anti-corrosive coatings – Thermopolymers – High-strength polymers –
Challenge Area 2: Prototyping of known, but currently inaccessible, molecules
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• Phase 1: >10 molecules from Areas 1 or 2
• Phase 2: >60 molecules, including >15 molecules from Area 2.
• Phase 3: >10 molecules from Area 3 and > 200 additional molecules from Challenge Areas 1 and 2.
>350 unique molecules total by end of Phase III
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Anticipated program structure
Phase I Phase II
FY14 18 mos 18 mos
Phase III
24 mos
FY18
Task Area 1
6 mos
Task Area 2
Task Area 1 (TA1): Initial infrastructure and technical design exploration • Infrastructure plan and technical path are refined
• Culminates in a technical report detailing the proposed technical approach, physical capabilities, and management structure.
Task Area 2 (TA2): Require centers to develop/demonstrate capabilities Consists of three phases:
• Phase 1: “pressure test” - produce at least 10 molecules by the end of Phase 1.
• Phase 2 - Produce > 60 molecules, including > 15 known, but currently inaccessible, molecules (i.e. Challenge Area 2).
• Phase 3 – Produce > 10 completely novel molecules (i.e. Challenge Area 3) and > 200 additional molecules from Challenge Areas 1 and 2.
Performers that complete Task Area 1 may submit proposals to Task Area 2
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Proposing to Task Area 1: Design and study phase
Provide: Brief and concise overview of anticipated project plan and approach to meet the goals and milestones of the Living Foundries: 1000 Molecules program. Task Area 1 Study: Identify anticipated technical elements, milestones and metrics to be refined and/or generated during the Task Area 1 design and study phase of the program. Technical Rationale and Approach: Outline of the anticipated technical approach and plan for Task Area 2, including how the Task Area 1 study work fits into the overall project plan.
Technical approach and plan must address: • Description of the proposed infrastructure to be developed • Overview of and timeline for the technical approach • Description of and justification for the types of molecules that will be targeted
during each phase of Task Area 2 • Initial steps/proof-of-concept experiments toward developing the proposed
infrastructure • Anticipated academic and industrial partners
DARPA requires proposers to submit all initial proposals to TA1
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Task Area 2 proposals must address:
(1) Complete Technical approach and plan that addresses the following:
• Description of proposed infrastructure
• Overview of the technical approach, milestones, and timeline both related to infrastructure capabilities and to the 1000 molecules goal
• Major Technical Risk Elements
• Description of and justification for the types/classes of molecules that will be targeted during each phase of TA2
• How the proposed infrastructure can be used to address applications beyond the biosynthesis of new molecules.
• Proposed intermediate and end-of-project demos and proofs-of-concept
(2) Program Plan: A plan with clear timelines, milestones and risks identified for demonstrating the functional capabilities and performance of the proposed rapid design and prototyping facility as a whole, as well as for individual components
(3) Teaming and Management plan
(5) Tech Transition Plan: How the infrastructure facility will maintain viability following cessation of DARPA funding?
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Task Area 2 proposals must address: (cont’d)
(6) SOW • A general description of the objective • A brief and concise description of the approach • Identification of the primary organization responsible for task execution • The completion criteria for each task/activity - a product, event or milestone that defines
its completion; • Define all deliverables (reporting, data, reports, software, etc.) to be provided to the
Government in support of the proposed research tasks/activities; and • An estimate of cost
(7) Discussion of proposer team’s previous accomplishments and work in closely related research areas.
(8) Description of the facilities and capabilities that would be used for the proposed effort.
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TA Phase Timeline Milestones
TA1 Up to 6 mo • Project plan • Proof of concept (option) • Initiate infrastructure (option)
TA2 Phase I Up to 18 mo
• Produce 10 target molecules (Areas 1/2) • Demonstrate infrastructure capabilities (2 proposer-
defined milestones)
TA2 Phase II Up to 18 mo
• Produce 60 target molecules, including at least • 15 previously inaccessible target molecules (Area 2)
• Further demonstration of infrastructure capabilities (2 proposer-defined milestones)
TA2 Phase III Up to 24 mo
• Produce 200 target molecules, including at least • 30 previously inaccessible target molecules (Area 2) • 10 novel target molecules (Area 3)
• Further demonstration of infrastructure capabilities (3 proposer-defined milestones)
Program End Up to 60 mo
• Produce 350 target molecules, including at least • 45 previously inaccessible target molecules (Area 2) • 10 novel target molecules (Area 3)
Anticipated program milestones
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Comprehensive Efforts vs. Advanced Studies
2 categories of proposals for this solicitation:
(1) Comprehensive proposals (2) Advanced Studies: Innovative component technologies • Markedly improve the performance of the rapid design and
prototyping infrastructure • Can be readily automated, parallelized, scaled-up, and/or
utilized in reduced reaction volumes • Limited to a maximum of 24 months in length • Only a limited number is expected be funded
The Government strongly prefers an integrated approach to systematically address all program goals in their entirety
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• Advanced studies: address one or more novel component technologies targeted as part of infrastructure development.
• Clearly indicate Advanced Studies proposal submission on title page • Explain the relevance of the work to the overall program goals, as well as propose
detailed objectives and quantitative metrics.
• Groups proposing advanced studies are encouraged to identify teams proposing rapid design and prototyping centers that may be able to leverage the tools and technologies resulting from such a study.
Advanced Studies
Phase I Phase II
FY14 18 mos 18 mos
Phase III
24 mos
FY18
TA1
6 mos
TA2
Phase I Phase II
FY14 12 mos
Advanced Studies
12 mos FY16
Duration: maximum of 24 months and should consist of 2 phases, each no longer than 12 months.
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Proposers should focus on 3 aspects:
• Designing and demonstrating a rapid design and prototyping infrastructure that will enable a radical improvement in capabilities over SOA
• Outlining the technical approach(es) to be pursued to meet the infrastructure and DARPA 1000 goals
• Identifying and justifying the molecules and chemical building blocks proposed for each DARPA 1000 Challenge Area
Key points
The Government expects to fund several types of rapid design and prototyping infrastructure, spanning a range of approaches, foci, and users
All proposed infrastructure should be generalizable in that it can address a
range of designs, pathways, organisms/systems and/or products
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Key dates
BAA Released
10 July 2013
BAA Process and Proposal Preparation/Submission Overview Webinar
31 July 2013
Proposals for TA1 and Advanced Studies Due
17 Sept 2013
Estimated Start date for TA1 and Advanced Studies
17 March 2014
Note: BAA will remain open until 21 Oct 2014
www.darpa.mil
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