SOLICITATION NOTICE
L -- Training NIH Scientists in the use and development of processing & analysis software to NMR data
- Notice Date
- 8/10/2006
- Notice Type
- Solicitation Notice
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, Nat'l Institute of Diabetes, Digestive, & Kidney Diseases, 2 Democracy Plaza, Suite 700W 6707 Democracy Blvd., MSC 5455, Bethesda, MD, 20892-5455
- ZIP Code
- 20892-5455
- Solicitation Number
- NIH-NIDDK-06-939
- Response Due
- 8/25/2006
- Archive Date
- 9/9/2006
- Description
- This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate written solicitation will not be issued. This solicitation number is NIH-NIDDK-06-939, and is issued as a Request for Quotation (RFQ). The solicitation/contract will include all applicable provisions and clauses in effect through Federal Acquisition Circular 2001-27. The North American Industry Classification (NAICS) Code is 541690 and the business size standard is 500 Employees. This acquisition is being conducted using Simplified Acquisition Procedures in accordance with FAR Part 13. It is the intent of the National Institutes of Health (NIH), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), to purchase professional services from Dr. Frank Delaglio. Dr. Delaglio will be training NIH scientists in the use and development of processing and analysis software related to nuclear magnetic resonance (NMR) data of proteins and nucleic acids, specifically the NIH packages NMRPipe, NMRDraw, DYNAMO, and TALOS, and oversee the development of appropriate documentation software for these packages by a third party contract. The goal of the training and documentation is to ensure continued utility of the vast amount of previously developed software, so that it can remain of maximum advantage to the Section on Biophysical NMR (LCP-NIDDK), all other NMR researchers at NIH, and the NMR community at large. Background Research in the Biophysical NMR Spectroscopy Section of the Laboratory of Chemical Physics (LCP) includes the planning and execution of studies in selected areas of chemistry, physics and biology involving the relationship between molecular structure and function on a wide range of systems of biological interest. Within the LCP there is considerable emphasis on development of new and improved methods for multi-dimensional nuclear magnetic resonance spectroscopy (NMR) and its application to the study of biomolecular structure and dynamics, development of theory for interpreting NMR data, and specific applications in biomolecular structure determination. In particular, novel experimental NMR approaches employing weakly aligned media are a key focus, as these experiments provide long range orientational information which is a powerful complement to the short range distance and torsion information used in conventional NMR structural studies. In addition, as more high-resolution structures are made available, database mining approaches to structural analysis become increasingly useful and effective, and this also has been a theme of computational efforts in LCP NMR. In addition, many NMR methods that are now widely applied to proteins are currently also being adapted in the LCP for precise NMR studies of nucleic acid structure and dynamics, an area which previously has been proven to be problematic. Recently, the LCP NMR lab has begun investigation on the promising possible advantages of joint use of NMR structural data with overall molecular shape information obtained from solution-state small-angle X-ray and neutron scattering. Advancement and application of all these NMR methods has depended critically on the development of specialized software with a variety of capabilities, including multidimensional Fourier reconstruction, signal enhancement, multidimensional peak analysis and quantification, analysis and simulation of NMR parameters based on structure, and NMR database-driven homology methods. Because of the striking volume and diversity of information involved in a typical NMR structural application, there is also a critical graphical design component to this work. Software facilities must present large amounts of multivariate and multidimensional data graphically, using suitable strategies so that analysis steps which require interactive decision making can be performed quickly and effectively, and meaningful relationships in the data can be revealed clearly. For the last 15 years, the lab has been involved in the development of an evolving software framework to support all the research efforts of the lab. On the one hand, this software has served as a platform for rapid proof-of-concept applications in support of new methods. On the other, this software system has also served as a platform for providing stable, easy to use facilities for application of new NMR methods as they become standardized and more widespread. The collection of software created in the Biophysical NMR Spectroscopy Section, LCP-NIDDK, over the past 15 years is a component of virtually every project performed in the laboratory. It is routinely used in all the NIH intramural biomolecular NMR laboratories, and it has become a standard tool for NMR structural biology across the world. A substantial amount of development effort has been directed at implementing new facilities within the framework of the TCL scripting language. The scripting language allows new and customized applications to be developed more quickly and flexibly by recombining existing functions. This has been an effective approach for our own software development in support of specific research goals, including novel methods for protein NMR structure determination without the use of NMR-derived distances. The current software system includes roughly 60 programs, mostly written in C++ language, with well over on thousand options and settings. An in-house version of the TCL script interpreter, NMRWish, has been augmented with over 160 commands having ca 500 options and settings, and a library of more than 200 script files. The scope of the software covers a substantial fraction of all capabilities needed for biomolecular structure determination by NMR. However, many of these facilities cannot be broadly used, because they were created as part of a particular research-based application, and as such not described in detail for general use. As the original developer of this software, Dr. Delaglio is uniquely suited to train NIH employees in the design, architecture, and further development of this system, thereby ensuring its long term continued benefit to the government. Duties and Responsibilities The purpose of this contract is to obtain continuity in the maintenance, development, and dissemination of the above described software system along three lines: support of the lab?s new experimental methods, implementation of the lab?s new computational methods, and further progress towards a comprehensive software environment for all major aspects of biomolecular structure calculation and analysis by NMR. Because this software is a key component in the plans and research continuity for LCP NMR, it is critical that support and development of the software continues without interruption. The contractor?s primary responsibility is the training and coaching of scientists in the Biophysical NMR Spectroscopy Section, LCP, in the support and further development of the lab?s NMR software system. The system is implemented in the C programming language using a bottom-up design, with a combination of stand-alone modules, modules implemented using a UNIX filter paradigm, and extensions implemented in a customized version of the TCL/Tk interpreter. High-level applications in the system are constructed and coordinated using shell scripts and TCL scripts. Graphics facilities are implemented in X11, and hard copy output by direct generation of PostScript. The current version of the software includes over 60 programs and more than 160 script-based applications. The core signal processing module provides 50 filter-based functions for multidimensional spectral visualization, signal quantification, statistics, optimization, and matrix decomposition, NMR parameter calculation, database manipulation, and molecular structure calculation by simulated annealing. Principal training and support tasks include the points below: Training to allow continuation of ongoing software projects in application of dipolar coupling data and NMR homology approaches to structure calculation, including extension of these methods to nucleic acids. Training to allow continuation of ongoing software projects in sequential assignment, including a multispectral interactive system integrated with a computer-assisted approach based on combinatorial optimization via genetic algorithm and simulated annealing. Training to allow continuation of ongoing development of improved methods for database-mining approaches to protein backbone chemical shift analysis and prediction, and extend existing chemical shift database methods to protein side-chain analysis. Training to allow continuation of ongoing projects in signal enhancement, including use of Filter Diagonalization Methods (FDM), enhanced approaches to Linear Predication (LP) and Maximum Entropy Method (MEM), Multi-way Spectral Decomposition, reconstruction of spectra data with non-conventional sampling schemes (non-linear sampling, projection reconstruction). Training to allow continuation of ongoing computational developments for joint use of NMR and small-angle scattering data. Training to allow continuation of general support, maintenance, and dissemination of existing software, including adaptation for new computer hardware, parallel processing facilities, and operating systems, and new spectrometer data formats. Training to allow continuation of ongoing general refinements of existing software, including tools for simplified/automated use of processing and analysis protocols that have become routine. Training to allow continuation of ongoing support of lab facilities for use of the software, including configuration of computers and peripherals, user accounts, etc. Training to allow continuation of ongoing support resources for dissemination and exchange of software, data, and documentation, including management of the lab?s web server and lab?s web pages describing the system. Oversee the further development of documentation of the software package, carried out by an outside contract. The position requires a unique combination of mastery in scientific software design and development, expertise in numerical methods, and a thorough knowledge of the biomolecular NMR processing and analysis system currently in use in the Biophysical NMR Spectroscopy Section, LCP. This notice of intent is not a request for competitive quotations. However, all responses received, within 15 days from the date of publication of this synopsis will be considered by the Government. A determination by the Government not to compete this proposed acquisition is based upon responses to this notice and is solely for the purpose of determining whether to conduct a competitive acquisition. The offeror must include a completed copy of the provision of FAR Clause 52.212-3, Offeror Representations and Certifications ? Commercial Items with its offer. The provisions of FAR Clause 52.212-4, Contract Terms and Conditions ? Commercial Items, applies to this acquisition. The addenda to the clause reads as follows: The offeror must include in their quotation, the unit price, the list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. The FAR Clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders ? Commercial Items ? Deviation for Simplified Acquisitions, applies to this acquisition. The clauses are available in full text at http://www.arnet.gov/far. Interested vendors capable of furnishing the government with the item specified in this synopsis should submit their quotation to the below address. Quotations will be due fifteen (15) calendar days from the publication date of this synopsis or August 25, 2006. The quotation must reference ?Solicitation number? NIH-NIDDK-06-939. All responsible sources may submit a quotation, which if timely received, shall be considered by the agency. Quotations must be submitted in writing to the National Institute of Diabetes and Digestive and Kidney Diseases 6707 Democracy Blvd., Room 775, Bethesda, Maryland 20817, Attention: Patricia Haun. Faxed copies will not be accepted.
- Record
- SN01111280-W 20060812/060810220403 (fbodaily.com)
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