# Presentation: 429823

## The Energy Biosciences InstitutePreparing for Startup

- The Energy Biosciences InstitutePreparing for Startup

- Chris Somerville

- Carnegie, Stanford, LBNL, EBI

## The Energy Bioscience Institute

- Partnership between UCB, UI, LBL
- BP has committed $500M over 10 years to facilitate a broad investigation of the application of molecular biosciences and biotechnology to challenges and opportunities in the energy sector

## Research Complementarity

## Status

- BP & UCB in discussion about terms of agreement
- Executive committee organizing operational aspects
- Expect July 1 startup

## UC Principles for

- University Agreements w/ External Parties

- Open Dissemination of Research Results and Information
- Commitment to Students
- Accessibility for Research Purposes
- Public Benefit
- Informed participation
- Legal Integrity
- Fair Consideration for University Research Results
- Objective Decision-Making

- URL:  _[http://www.ucop.edu/ott/genresources/082699a.html](http://www.ucop.edu/ott/genresources/082699a.html)_

## Funding to UCB, LBNL & UIUC will flow to individual projects based on future, individual project proposals

- who will be involved in the project & for how long
- what funding will be used
- where the work will be performed
- the scope of work (including expected milestones to be achieved and when)
- • written and proposed by faculty based on own interest and capabilities
- • signed by all institutions performing the research
- • informed participation agreement signed by researchers

- Funding to UCB, LBNL & UIUC will flow to individual projects based on _future_, individual project proposals

- Once the Master Agreement is signed, EBI individual research projects can be initiated quickly and easily
- completing an IMPLEMENTING LETTER

- Each implementing letter launches a project to be performed under the terms of the Master Agreement, obviating the need to negotiate a dedicated sponsored research agreement for each  EBI project.

## UC BerkeleyCampus

- UC BerkeleyCampus

- LBL

- University of California at Berkeley and Lawrence Berkeley National Laboratory

## Site of EBI-East

## UIUC Farmland

## Goals of the EBI

- Envisioning the future
- Identifying and solving the scientific and technical problems required to enable the development of a cellulosic biofuels industry
- Developing new biotechnologies for enhanced oil recovery, fossil fuel processing & biosequestration
- Educating scientists, policymakers, and the public
- Training a new generation of students

## EBI Funding

**Lawrence Berkeley**

**National Laboratory**

**Other **

**BP Components**

**BP **

**Proprietary Component**

**UC Berkeley**

**Host Institution**

**BP Subsidiary**

**University of Illinois**

**Urbana**

**-**

**Champaign**

**funds**

**Other **

**Entities **

**contracts**

**contracts**

**subcontracts**

**contracts**

**contracts**

**OPEN RESEARCH**

**PROPRIETARY RESEARCH**

**ENERGY BIOSCIENCES INSTITUTE (EBI)**

**subcontracts**

## Intellectual Property and Contract Management

- Master Agreement
- Between UCB and BP

- LBNL

- UIUC

- Terms and conditions flow down
- through subcontracts and inter-institutional agreements

**UCB will serve as a single point of contact for BP on**
**all contract management and IP matters**

**Notes:**
IP and contract management

UCB, LBNL and UIUC share BP’s vision of creating robust and long-term technological solutions to global energy challenges

To implement this vision we propose a master agreement between UCB and BP

## EBI Governance and Oversight

**EBI **

**DIRECTOR**

**Governance Board**

- UCB Vice Chancellor for Research

- LBNL Director & Assoc Director

- UIUC Vice Chancellor

- -

- Research

- BP Reps (4)

- EBI Director, ex

- -

- officio

- EBI Assoc. Director, ex

- -

- officio

- EBI Deputy Director, ex

- -

- officio

**EBI**

**ASSOC DIRECTOR**

- Scientific Advisory

- Board

**Program Director**

**BP Team (1)**

**Program Director**

**BP Team (2)**

**Program Director**

**BP Team (3)**

**Executive Committee**

**Program Director**

**Discover & Development **

**Support Centers**

**Program Director**

**Discover & Development **

**Support Centers**

**EBI **

**DEPUTY **

**DIRECTOR**

- Strategic

- Science

- Advisors

**Program Director**

**Biofuels**

**Production**

**Program Director**

**Biofuels**

**Production**

**Program Director**

**Feedstock Development**

**Program Director**

**Feedstock Development**

**Program Director**

**Fossil Fuel **

**Bioprocessing**

**& **

**Carbon Sequestration**

**Program Director**

**Fossil Fuel **

**Bioprocessing**

**& **

**Carbon Sequestration**

**Program Director**

**Socio**

**-**

**Economic Systems**

**Program Director**

**Socio**

**-**

**Economic Systems**

**Program Director**

**Biomass **

**Depolymerization**

**Program Director**

**Biomass **

**Depolymerization**

## EBI Operations Committee

## Implementing the program

- Recruit excellent, committed people
- 10 faculty appointments
- All internal and external programs will have EBI-defined goals & milestones
- Budgets will be developed annually based on evolving opportunities
- Create a culture that facilitates discovery
- Clear goals and common vision
- All programs co-located at the two sites
- Seminars & workshops
- Active leadership and mentoring
- EBI fellows and BP investigators will crosscut

## Research Overview

- Feedstocks
- What species? How to grow, harvest, store
- Deconstruction
- How to convert biomass to fermentation substrates?
- Fuel production
- Optimize fermentation, new fuels
- Social and economic Issues
- Social effects, contracts, land use, logistics, trade policies, international scope, food vs fuel issues, ...
- Enhanced oil recovery, bioprocessing and biosequestration
- Exploit recent advances in omics, synthetic biology

## Scientific Program

## Applications Laboratory

- Staffed by BP employees (“BP investigators”) who report to EBI Associate Director
- EBI investigators bound by confidentiality agreements during activities in Applications Lab
- BP investigators affiliated with one or more EBI Laboratories
- Goals
- Proprietary research and development
- Interaction with companies

## Outreach to Local Biotech Industry

- 53,000 jobs
- $3.6B R&D investments (52% of US)
- >100 spinoffs from UC Berkeley, UC San Francisco, and UC Santa Cruz, most within 35 miles of the founding campus.

**Notes:**
Susan Marqusee and I guess others from HIS think these numbers
reflect poorly on UCB, UCSF & UCSC’s achievements in industry. 
Graham doesn’t seem to think so.  What do you think Kristin?  

## EBI Broad Education Goals

- Provide BP investigators broad access to intellectual resources
- Educate the next generation of energy scientists
- Postdoctoral
- Ph. D.
- B. S.
- Educate the public
- general public
- public policy students
- policy makers
- K-12
- Provide extension activities targeting the greater agricultural community

## Implementing the program

- Open call for preproposals that address broad goals
- Based on preproposals, PIs will be invited to submit either a project or program proposal
- Suggestions from executive committee may be attached.
- Projects will be defined term (EBI associates)
- Programs will be rolling 3 years with annual reviews (EBI investigators)
- Proposals will be peer reviewed
- EBI investigators will co-locate in EBI space
- EBI associates will have participation obligations

## Timeline for Initiating Science  Programs

- May 1 - Call for preproposals
- June 8 – Preproposals received
- June 8 – 21 Preproposal review
- June 22 – Invitations for proposals extended
- Aug 1 – Proposals received
- September 28 – Funding for projects and proposals approved

## The EBI: An Opportunity to Contribute to Sustainability

- John Stringer & Linda Horton

## But... Alignment with Industry poses Challenges

- <date/time>

- <footer>

## EBI vs JBEI

- JBEI will design, develop and employ advanced high-throughput technologies to move the most promising approaches today for biofuels (primarily ethanol and butanol) production from the laboratory to commercial practice. JBEI will rely on recent advances in synthetic biology to overcome the economic hurdles in producing these fuels from lignocellulosic biomass. The capabilities of JBEI’s six partners will be key to the near-term (3-5 year) success of JBEI’s efforts.  JBEI will be operationally integrated through the use of electronic data capture and transparent integration of data and informatics tools.  The institute will be structured and managed in the model of a start-up technology company, using success metrics and stage-gate milestones to enable agile decision-making.
- EBI will provide the broad-based scientific underpinnings for developing energy crops and converting them to a variety of transportation fuels. Other efforts will address carbon sequestration and biological processing of fossil fuels. This is a long-term (10 year) research undertaking that will also address public policy issues.  Research will be investigator-driven and performed in the context of traditional academic research groups.

- IAB, multiple strategic relationships and industry membership levels that bringl expertise, resources, and licensing commercialization opportunities

- BP is sole industry sponsor

- Industrial partnerships

- Multi-pronged education strategy

- Multi-pronged education strategy

- Education

- No effort

- Significant effort

- Public policy

- No effort

- Significant effort

- Economics

*Business, Economics & Public Policy*

- No effort

- Significant effort

- Fossil fuel bioprocessing

- No effort

- Significant effort

- Microbial enhanced oil recovery

- No effort

- Significant effort

- Biological carbon sequestration

*Non-biofuels activities*

-   3                                                                 3

- Other investigators in common

-   4                                                                 4

- Core investigators                  in common

- 27

- 24

- Total core investigators

- 6:  LBNL (Lead), SNL, LLNL, UCB, UCD, Stanford

- 3:  UCB (Lead), LBNL, UIUC

- Partners

*Management and partnership*

**JBEI**

**EBI**

**Activity**

## JBEI

- Limited effort based on live-cell imaging methods and genetics studies of single genes. Synergistic with JBEI studies.

- Determine enzymes involved in plant cell wall synthesis

*Feedstocks*

- No effort

- Significant effort for Miscanthus, switchgrass, other energy crops

- Agronomic studies

- Large scale project to produce transgenic plants for most carbohydrate-active enzymes and lignin oxidases.

- Limited to single gene studies of selected enzymes involved in lignin and polysaccharide synthesis. Synergistic with JBEI studies.

- Plant engineering

- Major effort to understand enzymes responsible for polymerization of lignin monomers and secretion of lignin monomers by systematic analysis of all candidate genes using high throughput technologies

- Development of novel forms of lignin by characterizing novel pathways of precursor synthesis and transport. Synergistic with JBEI studies.

- Lignin biochemistry

- No effort

- Major investigations of effects of biomass removal on long term soil fertility. Also studies of disease pressure on bioenergy crops.

- Sustainability studies

- No effort

- Significant effort to breed improved energy crops

- Plant breeding

- No effort

- Significant effort including design and testing of new farm machinery

- Harvesting and storage

**JBEI**

**EBI**

**Activity**

## JBEI

**JBEI**

**EBI**

**Activity**

| Deconstruction |  |  |
| --- | --- | --- |
| New cellulases, hemicellulases, and ligninases | Forward design and engineering | Discovery and development of improved cellulolytic enzymes in organisms from cellulose-rich environments (compost and forest floors) and extremophiles |
| Non-enzyme catalysts | Development of homogeneous and heterogeneous non-biological catalysts | No effort |
| Tools for screening new lignocellulolytic enzymes | No effort | Development of high throughput chips (lignochips and glycochips) for screening enzymes and next generation microsystem platforms for on-chip enzyme engineering. |
| Biomass pretreatment | Development of new approaches to  biomass pretreatment and processing. Cellulose solubilization and partial acid hydrolysis. | Acquisition of parallel data sets of pretreatment and biomass matrices to enable a predictive multi-physics, multi-scale computational model. Investigation into ionic liquids, AFEX, dilute acid, and hydrothermolysis against targeted feedstocks. |

## JBEI

**JBEI**

**EBI**

**Activity**

- Electronic laboratory notebooks as basis for center-wide integrated informatics

- NA

- Integrated Informatics/LIMS

- Omics used in every project area; data maintained in central repository

- Investigator and project specific

- Omics

- Center wide use of novel, high-throughput discovery capabilities

- NA

- High-throughput Technologies

- Extensive use of bioinformatics and computational biophysics

- Investigator-specific

- Computational Biology and Bionformatics

*Technologies*

- Targeted effort to develop assays that probe enzyme-substrate interactions and are amenable for use in high-throughput technology platforms

- Broad-spectrum effort on novel assays that provide activity and kinetic information

- Develop novel assays for enzyme screening

- No effort

- Major effort in organic synthesis

- Develop novel catalysts

- Chemistry and Biochemistry

- Focus on ethanol & butanol, plus three other target fuel molecules

- Many, but not ethanol

- Fuel molecules

- No effort

- Significant effort

- Organism reconstruction

- Significant effort

- Some effort

- Creation of novel pathways

- Transcriptomics, proteomics, metabolomics, fluxomics

- No effort

- Omics of fuel toxicity

*Fuel Synthesis*

## JBEI

- Microfluidics for chip-based enzyme discovery and protein expression and characterization

- Microsystems Engineering and Science Applications facility (MESA), SNL

- High-throughput sequencing
- Standard Biological Parts Fab
- Metagenomics
- Bioinformatics

- Joint Genome Institute, LBNL/LLNL

- Nanoscale science and technology
- (LigninChips and GlycanChips)

- Biomass engineering; lignin, enzyme engineering; pretreatment; integrated bioprocessing; chemistry; computation

- Molecular Foundry, LBNL
- Biomolecular Nanofabrication Center, UCB

- Applied environmental microbiology (VIMSS/ESPP)

- LBNL, UCB: Extremophile bioreactors

- Data management modeling and analysis, e.g.; modeling feedstock deconstruction; bioinformatics

- LBNL:
- National Energy Research Computing Center (NERSC)
- Biological Data Management & Technology Center (BDMTC)
- MicrobesOnline (VIMSS)
- SNL:  Computer Science Research Institute (CSRI)

- Biomass engineering; Lignin, Enzyme engineering; feedstock pretreatment,imaging

- Biomass engineering; Lignin, Enzyme engineering; feedstock pretreatment, imaging

- National Center for Electron Microscopy (NCEM), LBNL

- SAXS, SANS, small particle electron microscopy, x-ray tomography

- LBNL:
- Advanced Light Source (ALS)
- Berkeley Center for Structural Biology (BCSB)
- National Center for X-ray Tomography (NCXT)

**JBEI**

**EBI**

**Facility/Capability**

## JBEI

| Hyperspectral Fluorescence Spectroscopy (HFS), SNL |  | Imaging plant cell walls |
| --- | --- | --- |
| Combustion Research Facility (CRF), SNL/LLNL |  | Characterizing biofuels |

- Polysaccharide MS, high-throughput genotyping, proteomics

- UCD Genome Center

- Specialized plant production

- Specialized plant production

- Jane Gray Research Greenhouse, Oxford Tract, UCB

- Specialized plant production

- Greenhouse facilities, UCD

- Biomass processing and conversion

- UCD Biomass Laboratory

- Fuel combustion mechanisms

- Center for Accelerator Mass Spectroscopy (CAMS), LLNL

- Large-scale fermentation

- Livermore Bioreactor Facility (LBF), LLNL

- Nimblegen DNA array

- Livermore Microarray Facility (LMAC), LLNL

**JBEI**

**EBI**

**Facility/Capability**

## JBEI

- Enzyme discovery & engineering; feedstock pretreatment; integrated bioprocessing;

- Integrated Bioprocessing Research Laboratory, UIUC

- Feedstock production, harvesting transport & storage

- Off-road Agricultural Vehicle Development Facility, UIUC

- Feedstock production, genetics & plant breeding; biotic stress, harvesting transport & storage

- Open-air Feedstock R&D Center, UIUC

- Biomass engineering, environmental & sustainability assessment

- Morrow Plots, UIUC

- Feedstock genetics, plant breeding, environmental & sustainability assessment

- Carver Biotechnology Center, UIUC

**JBEI**

**EBI**

**Facility/Capability**

## Summary: EBI and JBEI are Complementary

- Different people (and institutions)
- Different modus operandi
- Different breadth
- Largely different goals
- One industrial relationship vs many

## Licensing of EBI Inventions

- For inventions that are solely owned by UCB, LBNL and/or UIUC
- that are fully funded by BP

**Non-Exclusive**
- 	We will grant to BP a _Non-Exclusive_, Royalty Free (NERF) commercial license in BP’s areas of interest with two qualifications:
- BP will be required to diligently pursue commercialization of the licensed invention(s)
- Inventor institution will not be obligated to file for patents unless it has a commitment from at least one licensee to underwrite patent costs

**Exclusive**
- UCB, LBNL and UIUC agree that BP may obtain _Exclusive_ license rights to our sole or joint interests in EBI inventions
- Will  feature pre-negotiateed capped fees and/or royalty rate ranges in technology areas where it is possible to estimate those ranges

## Licensing of EBI Inventions

**Exclusive Licensing Option**
- Time limited, first right to negotiate an exclusive license to resultant IP
- Patents: conceived and first reduced to practice in the performance of a pre-defined scope of work, that is fully funded by BP
- Pursuant to prenegotiated, capped fees or royalty ranges in technology fields where it is possible to estimate those ranges
- The “exclusive licensing option” also includes the right to elect an option agreement to obtain an exclusive  license in the future
- It allows BP to evaluate the commercial potential of a given invention and defers the execution of an exclusive license until both the licensor and the licensee know more about the likelihood of commercial success, the appropriate milestones that will be required in the license, if the invention will be commercialized by the licensee alone, or must be co-developed with others, etc.
- Option agreements are often appropriate when a given research result is very early stage, embryonic, and not developed to a commercial standard, and is thus appropriate for much of the research emerging from University research.

## Excerpts from: Academic Freedom and Academic Principles are Preserved in 

**Corporate Sponsored Research Agreements**
**The University owns intellectual property (IP)** developed by its employees in our facilities, even if that IP arises from corporate funded research.
- As the owner of the IP, even when the University licenses IP rights to the sponsor (or to any entity) the University always **reserves the right to practice the IP rights on our own behalf and to allow others in the nonprofit sector to use them for their own education and research purposes.**
**Publication at the University is a fundamental right**.  Sponsor preview right is time limited and doesn’t allow editorial rights.
**Grants to sponsor a time-limited, first right to negotiate a commercial license to IP developed in the funded project.**
**Resultant licenses to such IP always indemnify the University from commercial acts, and require that the licensee diligently commercialize the rights**.
**The University is an open, academic institution with limited mechanisms to safeguard confidential information.**
**Standard research compliance procedures, such as standard conflict of interest procedures.**
- Moreover, all contracts with unusual clauses are vetted by legal and policy experts.  The most robust enforcer of academic freedom in place on campus is **the academic tradition itself, that all principal investigators are familiar with, and have a strong motivation to preserve.**