eScience
Request for Proposals 2006
Computational Challenges in Synthetic Biology

This RFP has been awarded. To view the award recipients, see eScience Computational Challenges in Synthetic Biology 2006 Awards.

Synthetic Biology lies at a junction between engineering and biology. Much of modern biology is based on three breakthroughs: (1) understanding the structure and operation of DNA, (2) manipulating DNA with restriction enzymes and the Polymerase Chain Reaction, and (3) understanding the genome through DNA sequencing. Synthetic Biology is based on three new developments: (1) direct synthesis of DNA, (2) abstraction of biological function, and (3) the growth of an industry of standard biological parts. Long-term research goals include how to best design and build engineered biological systems and to promote the open and transparent development of tools for engineering biology. Long-term social goals include enabling new industries based on the rational engineering of biological systems and materials, and constructing a society that can productively apply biological technology.

Goals & Objectives
Microsoft invites proposals to identify and address computational challenges in two areas of synthetic biology. The first relates to the re-engineering of natural biological pathways to produce interoperable, composable, standard biological parts. Examples of research topics include, but are not limited to, the specification, simulation, construction, and dissemination of biological components or systems of interacting components. The second area for proposals focuses on tools and information repositories relating to the use of DNA in the fabrication of nanostructures and nanodevices. In both cases, proposals combining computational methods with biological experimentation are seen as particularly valuable.

Awards
The total amount available under this request for proposals (RFP) is $500,000. Microsoft Research anticipates making approximately five awards averaging $90,000, with a maximum of $120,000 for any single award. All awards will be made in $US. Awards are generally made as unrestricted gifts to the institution. Outside the United States other local restrictions may apply to the terms of the award. For current policy regarding non-U.S. countries, please refer to http://research.microsoft.com/ur/us/fundingopps/faq.aspx.

For all awards, payment of indirect costs (“overhead”) is not permitted.

Microsoft will take into account the reasonableness of the amount requested in any proposal in light of stated deliverables, local costs, etc and reserves the right to fund proposals at an amount lower than requested if appropriate.

Awards are made for the purpose of seed-funding larger initiatives, proofs of concept, or demonstrations of feasibility. It is important to understand that funding will continue after the first year only in exceptional circumstances, and that the principal investigators should therefore make every effort to leverage Microsoft funds as one component of a diverse funding base in a larger or longer-running project.

Eligibility
Conditions of eligibility listed below will be strictly adhered to, so please read them carefully. Proposals not meeting all these criteria will not be considered.

1. The proposing institution must be an accredited baccalaureate-granting college or university (or international equivalent) with non-profit status. All qualifying institutions are eligible without regard for geographic location.
2. An institution will be awarded a maximum of one gift per RFP, regardless of the number of proposals submitted from the institution. However, collaborative proposals embracing multiple groups across the organization are encouraged.
3. Proposals that are incomplete, inaccurate, request funds in excess of the maximum award available, or are otherwise not responsive to the terms and conditions of this RFP will, at the sole discretion of Microsoft Research, be excluded from consideration.
4. Proposals from or on behalf of persons participating in the evaluation process for this RFP will not be considered.
5. Proposals should evidence a commitment to make any results arising from a funded project (including all intellectual property in those results) broadly available by either: (i) dedicating such results to the public domain; or (ii) making the results available  under a non-restrictive license that allows modification and redistribution without any significant restrictions or conditions, such as the BSD license. Proposals should further evidence willingness to contribute any resulting curriculum material to the MSDN Academic Alliance Repository.
6. Authors (including co-investigators) of winning proposals will be required to grant Microsoft permission to use their name, image, institutional affiliation and related professional information, as well as details of the winning project, in press releases or other forums.
7. All awards are contingent upon the acceptance by the academic institution that this unrestricted gift of Microsoft funds will not incur the overhead charges typically associated with grant funding.
8. If funded, the Principal Investigator or their designate should present the project at the 2007 Microsoft eScience Workshop (location and date to be determined) or similar event. Funds for travel and accommodation for this event should be included as a budget line item in the RFP proposal.

Submission Process
Proposals will be accepted in electronic form only at http://microsoft.redwhale.com. Proposals submitted to Microsoft will not be returned. Microsoft cannot assume responsibility for the confidentiality of information in submitted proposals. Therefore, proposals should not contain information that is confidential, restricted or sensitive. Microsoft reserves the right to make public proposals that receive awards, except those portions containing budgetary or personally identifiable information.

The submission process includes two parts.

1. Brief summary and contact information. Applicants must provide full contact information for principal investigators, amount requested and a brief abstract. This information will be submitted through a web form as part of the submission process.
2. Complete proposal containing full detail on the proposed project. 7 pages maximum, 10pt. font or larger, double-spaced, in either Microsoft Word or PDF format.

Proposals should address each of the items listed below under separate numbered headings.

1. Problem Statement: What is the problem addressed by the proposal and why is it important? What is the potential contribution to the field of the project if successful? Cite relevant work in the field as appropriate.
2. Expected outcomes: What tangible assets, if any, will be created as a result of the proposed project? Examples include scientific papers and other publications, students trained, software or datasets generated, etc.
3. Schedule: When is the project to be completed? What milestones will be used to measure progress of the project and when will they be completed? (If the project described is part of a larger ongoing research program, estimate the time for completion of this project only).
4. Use of Funds: Provide a high-level budget ($US) describing how the award will be used, including purchases of hardware or software, salaries, and other costs. Please note that, because awards are made as unrestricted gifts, Microsoft policy prohibits the payment of indirect cost (“overhead”).
5. Dissemination and Evaluation: How will the results of this project be evaluated and how will they be disseminated to others? Under what general license terms will the results be made available?
6. Other Support: Please list other contributions to this project (cash, goods or services), if any, but not including such things as use of university facilities otherwise provided on an ongoing basis. Please note: authors of winning proposals will be required to submit an original letter on department letterhead certifying the commitment of any additional or matching support described in the proposal.
7. Qualifications of Principal Investigator: Include a brief description of any relevant prior research, teaching, publication or other professional experience. A detailed vita or list of publications is not required.

Selection Process and Criteria
All proposals received will be reviewed by Microsoft Research and eligible proposals will be evaluated by a panel of subject-matter experts chosen by Microsoft Research. Based on evaluations by the review panel, Microsoft Research will select the most worthy proposals for funding. Microsoft Research reserves the right to fund winning proposals at an amount greater or less than the amount requested, up to the stated maximum amount for individual awards. Due to the volume of submissions, Microsoft Research cannot provide individual feedback on proposals that are not funded.

All proposals will be evaluated based upon the following criteria:

1. Well-defined goals and objectives that, if achieved, have the potential to have a significant impact on the field of synthetic biology as defined in the Goals and Objectives section above. These goals must be achievable within the one-year timescale of the gift, and where appropriate placed into the context of milestones in a larger or longer-running project.
2. Potential for wide dissemination and use of intellectual property created, including specific plans for publications, conference presentations, distance learning, etc., as well as plans to distribute content in multiple formats or languages.
3. Ability to complete the project including the adequacy of resources available, reasonableness of timelines, and number and qualifications of identified contributors.
4. Qualifications of principal investigator, including previous history of work in the area, successful completion of previous funded projects, teaching awards, books and papers published, etc.
5. Use of Microsoft tools and technologies: proposals should clearly indicate the Microsoft tools and technologies to be used in the project, or if no such technologies can be used, a clear statement should be made why this is the case.
6. Leveraging of other resources: preferential consideration will be given to proposals utilizing additional sources of funding to build larger or longer-running projects or connecting with existing resources such as the MIT BioBricks repository of standard biological parts.

Schedule and Deadlines

Announcement:	Saturday, September 4, 2006
First date for submission of proposals:	Monday, November 13, 2006
Last date for submission of proposals:	Friday, January 5, 2007, 12:00 P.M. PST (-8 UTC/GMT)
Notification of Awards:	Monday, March 5, 2007

Additional Resources

• Registry of Standard Biological Parts (http://parts.mit.edu)
   
• Arkin AP and Fletcher DA (2006) “Fast, cheap and somewhat in control” Genome Biology 7:114
   
• Endy D (2005) “Foundations for Engineering Biology” Nature 438:449-453
   
• Rothemund PWK (2006) “Folding DNA to Create Nanoscale Shapes and Patterns” Nature 440: 297-302
   
• Seeman NC. (2003) “At the Crossroads of Chemistry, Biology, and Materials: Structural DNA Nanotechnology” Chemical Biology 10:1151-1159
  
  

Please address any questions to erpinq@microsoft.com. Please put “Computational Challenges in Synthetic Biology” in the subject line of your e-mail message to ensure a prompt and proper response.

 

Microsoft Word version of this document