KOSEN 한인과학기술자네트워크

Bio-Computing (BIO-COMP) Primary Sponsor: Department of Defense Deadline: 5/3/2001 KEYWORDS "The Department of Defense encourages the participation of Minority Institutions (MIs)." COMMERCE BUSINESS DAILY ISSUE OF FEBRUARY 8,2001 PSA#2784 SOL BAA 01-26 DUE 050301 POC Dr. Sri Kumar, DARPA/ITO; Fax: (703) 522-7161 PROGRAM GOALS: The Bio-Computation program is aimed at exploring and developing computational methods and models at the bio-molecular and cellular levels. The program is directed towards achieving both powerful, synthetic computations that can be implemented in bio-substrates, as well as modeling and analytical tools for prediction and control of cellular internal processes and systems of living cells, for application in a variety of contexts of interest to DOD. Specifically, the program goals are twofold. First, the program aims to develop scalable DNA and related nucleotide manipulation techniques for realizing powerful computational methods for solving highly complex problems, for designing ultra-high density information storage, and for developing programmable nano-structures of nucleotides for novel applications. Second, the program aims to develop computational models, techniques, and tools, for in-silico analysis, capable of predicting cellular processes and their spatio-temporal behavior, which can also assist in developing control strategies. These include rapid prediction of the impact of external agents and environmental factors, and quick identification of targets and design of intervention mechanisms. Additionally, the program aims to validate and demonstrate the effectiveness of these models through experimentation, such as those directed towards highly conserved mechanisms, potentially of high payoff to DOD. Research and development is sought in the following two technical areas: I. DNA Computing; II. Computational Models and Simulation of Intra-Cellular Processes and Systems. These areas are described next. I. DNA COMPUTING: This technical area seeks research in innovative techniques and systems for performing computation in bio-substrates. The specific focus is on methods of representing information in DNA fragments, and related nucleotides, and using nucleotide manipulation techniques to perform arbitrary and powerful computations. The program seeks techniques that can be viable and scalable mechanisms for DOD applications. Such applications include: i) solution of complex computational problems, ii) ultra-high density content addressable storage, and iii) programmable and self-assembled nano-structures of DNA useful in applications such as improved crystallography and molecular electronics layout. Topics of particular interest are: 1. Scalable DNA Computing; 2. Compact, content addressable storage; 3. Programmable, self-assembled 2-D and 3-D DNA nano-structures; 4. Implementing computational elements and circuits that use in-vitro transcription and/or translation, and application demonstrations; 5. Other related ideas with revolutionary promise. II. COMPUTATIONAL MODELS AND SIMULATION OF INTRA-CELLULAR PROCESSES AND SYSTEMS: In this BAA technical area, DARPA seeks research on powerful computational models of intra-cellular processes and systems as a basis for predicting and controlling the spatio-temporal cellular behavior. Based on these models, DARPA seeks open source development of an in-silico cellular analysis and evaluation tool, Bio-SPICE, a Simulation Program for Intra-Cell Evaluation. Bio-SPICE is intended be a user-friendly simulation tool, with embedded models and techniques that effectively capture the processes governed by the network of molecular interactions including gene-gene, gene-protein, and protein-protein interactions, and can be customized for use in a variety of applications. These applications include the design of well informed and high success rate experiments, discovery of functional modules in cellular systems, and rapid and precise identification of targets and design of intervention methods. Additionally, model refinement and validation, through cell experimentation's are sought. The experimentation realm includes characterization, prediction, and control of highly conserved mechanisms of interest to DOD. These include, but are not limited to, mechanisms related to pathogenic processes, their prediction and control; mechanisms that enable powerful computing methods that mimic natural in-vivo computation; and circadian rhythms, the control over which may lead to enhanced war fighter performance in stressed conditions. The program seeks to develop Bio-SPICE, in an open source framework. The approach is to develop a model library or a kernel of relevant biochemical processes and analytical tools. This kernel will be integrated into a simulation environment that provides the necessary links to relevant databases. Additionally, user interface and data visualization tools that facilitate easy use by experimenters will be developed. The models will be tested, refined, and validated using experiments on conserved mechanisms. Research is sought on the following four topic areas: 1. Model Kernel; 2. Experimental Validation; 3. Simulation Environment; 4. Software Integration. PROGRAM SCOPE: DARPA anticipates the Bio-Comp program to be five years in duration. Proposals for all areas and topics, except the integration task, should have duration of no more than 36 months of base funding, and may include additional one or two year options. Proposals on integration can range from 36 to 60 months, with options, but cannot exceed 60 months. Cost sharing, as well as sharing of data and other relevant intellectual property, is encouraged. Proposals may involve other research groups or industrial cooperation. Proposed research should investigate innovative approaches and techniques that lead to or enable revolutionary advances in the state-of-the-art. Proposals are not limited to the specific strategies listed above, and alternative visions will be considered. Specifically excluded is research that primarily results in evolutionary improvement to the existing state of practice or focuses on a specific system or solution. PROPOSER INFORMATION AND TEAM FORMING MEETING: DARPA will hold a proposer information meeting on Bio-Computation. This meeting is also intended to facilitate team forming, in addition to the team forming web site indicated in the next section. This meeting will be held March 1, 2001, at the Greenbelt Marriott Hotel in Greenbelt, MD. Attendance at this meeting is OPTIONAL, but is recommended for potential bidders. Access the Bio-Comp website for the meeting details including registration at: http://www.dsic-web.net/ito/meetings/biocomp2001feb/index.html. TEAM FORMING WEB SITE: The formation of multi-disciplinary teams consisting of complementary areas of expertise is strongly encouraged. Teams may include experts from any type of organization. An interactive web site is established at the following URL where capability statements from those seeking teams can be posted: www.dsic-web.net/ito/solicitations/biocomp/teaming/login.html This site will remain active until May 3, 2001. Specific information content, communications, networking, and team formation are the sole responsibilities of the participants. Neither DARPA nor DoD endorses the destination web site or the information and organizations contained therein, nor does DARPA or DoD exercise any responsibility at the destination. GENERAL INFORMATION: The Defense Advanced Research Projects Agency/Information Technology Office (DARPA/ITO) requires completion of a Broad Agency Announcement (BAA) Cover Sheet Submission for each Proposal, by accessing the URL below: http://www.dyncorp-is.com/BAA/index.asp?BAAid=01-26. After finalizing the BAA Cover Sheet Submission, the proposer must submit the BAA Confirmation Sheet that will automatically appear on the web page. Each proposer is responsible for printing the BAA Confirmation Sheet and submitting it attached to the "original" and each designated number of copies. The Confirmation Sheet should be the first page of your Proposal. Failure to comply with these submission procedures may result in the submission not being evaluated. Detailed information and instructions are outlined within the Proposer Information Pamphlet (PIP). ABSTRACT FORMAT: To minimize unnecessary effort in proposal preparation, proposers are strongly encouraged to submit brief proposal abstracts in advance of full proposals. An original and 4 copies of the proposal abstract and 6 electronic copies (i.e., 6 separate disks) of the abstract (in Microsoft Word '97 for IBM-compatible, PDF, Postscript, or ASCII format on one 3.5-inch floppy disk or one 100 MB Iomega Zip disk). Each disk must be clearly labeled with BAA 01-26, proposer organization, proposal title (short title recommended) and Copy (Number) of 6. The proposal abstract (original and designated number of hard and electronic copies) must be submitted to DARPA/ITO, ATTN: BAA 01-26, 3701 N. Fairfax Drive, Arlington, VA 22203-1714, in time to reach DARPA by 4:00 PM (ET) Thursday, March 22, 2001, to guarantee review. Upon review, DARPA will make a recommendation to offerors either encouraging or discouraging submission of full proposals. PROPOSAL FORMAT: Proposers must submit an original and 4 copies of the full proposal and 10 electronic copies (i.e., 10 separate disks) of the full proposal (in Microsoft Word '97 for IBM-compatible, PDF, Postscript, or ASCII format on one 3.5-inch floppy disk or one 100 MB Iomega Zip disk). Each disk must be clearly labeled with BAA 01-26, proposer organization, proposal title (short title recommended) and Copy (Number) of 10. The full proposal (original and designated number of hard and electronic copies) must be submitted in time to reach DARPA by 4:00 PM (ET) Thursday, May 3, 2001, in order to be considered. Proposers must obtain the BAA 01-26 Proposer Information Pamphlet (PIP), which provides further information on the areas of interest, submission, evaluation, funding processes, proposal abstracts, and full proposal formats. This pamphlet may be obtained by fax, electronic mail, mail request to the administrative contact address given below. Proposals not meeting the format described in the pamphlet may not be reviewed. This Commerce Business Daily (CBD) notice, in conjunction with the BAA 01-26 PIP and all references, constitutes the total BAA. No additional information is available, nor will a formal RFP or other solicitation regarding this announcement be issued. Requests for same will be disregarded. The Government reserves the right to select for award all, some, or none of the proposals received. 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) and Minority Institutions (MIs) are encouraged to submit proposals. However, no portion of this BAA will be set aside for HBCU and MI participation due to the impracticality of reserving discrete or several areas of this research for exclusive competition among these entities. Evaluation of proposals will be accomplished through a scientific review of each proposal, using the following criteria which are explained in detail in the PIP and listed below in descending order of relative importance: (1) Overall Scientific and Technical Merit; (2) Innovative Technical Solution to the Problem; (3) Potential Contribution and Relevance to DARPA Mission; (4) Offeror's Capabilities and Related Experience; (5) Plans and Capability to Accomplish Technology Transition; (6) Cost Realism. All administrative correspondence and questions on this solicitation, including requests for information on how to submit a proposal abstract or proposal to this BAA, must be received at one of the administrative addresses below by 4:00 PM (ET) Thursday, April 26, 2001; e-mail or fax is preferred. DARPA intends to use electronic mail and fax for some of the correspondence regarding BAA 01-26. Proposals and proposal abstracts MUST NOT be submitted by fax or e-mail; any so sent will be disregarded. The administrative addresses for this BAA are: Fax: 703-522-7161; Addressed to: DARPA/ITO, BAA 01-26; Electronic Mail: baa01-26@darpa.mil; Electronic File Retrieval: http://www.darpa.mil/ito/Solicitations.html; Mail to:DARPA/ITO, ATTN: BAA 01-26, 3701 N. Fairfax Drive, Arlington, VA 22203-1714. Interested proposers must obtain and respond to ALL requirements in the Bio-Comp Proposer Information Pamphlet (PIP), available at: http://www.darpa.mil/ito/Solicitations/PIP_01-26.html.