SOLICITATION NOTICE
D -- NMR Software Documentation
- Notice Date
- 8/16/2004
- Notice Type
- Solicitation Notice
- NAICS
- 541512
— Computer Systems Design 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-04-284
- Response Due
- 9/10/2004
- Archive Date
- 9/25/2004
- Point of Contact
- Diana Ly, Contract Specialist, Phone 301594-7730, Fax 301-480-8261,
- E-Mail Address
-
LyD@extra.niddk.nih.gov
- Description
- 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. Gabriel Cornilescu. Dr. Gabriel Cornilescu will be developing documentation for a software system previously developed for processing and analyzing multi-dimensional multinuclear NMR spectra. The goal of this documentation project is to create a comprehensive on-line description of the software and its uses, so that all software facilities can be of maximum advantage to the Section on Biophysical NMR (LCP-NIDDK), all other NMR researchers at NIH, and the NMR community at large. Dr. Gabriel Cornilescu?s documentation shall include: 1) Introduction. Introduce the purpose and scope of the software, and describe the prerequisites for using the software. Key UNIX commands and concepts will also be listed. 2) Installation and Getting Started Tutorial. Describes how to install the software, and how to test the installation. It also describes in step-by-step detail examples of basic 2D and 3D processing, including format conversion, Graphical inspection of raw data, interactive phase correction, creation of processing scripts, listing spectral parameters, viewing processed data, rephrasing, and simple peak detection. 3) Spectral Processing and Viewing. Covers the practical rules and details of Fourier processing, such as first-point scaling and phase correction, zero fill, appropriate use of solvent filters and baseline correction, reconstructing imaginary data, Linear Prediction, and Maximum Entropy Reconstruction. Special processing schemes for interleaved data will be discussed. The section will also cover details of using the graphical programs to display spectra, estimate noise levels, and adjust contour levels. Use of scripts for displaying overlays, forming projections, strip viewing, and hard copy will be presented. 4) Peak Analysis and Quantification. Covers peak detection settings and noise discrimination, interactive adjustment of peak tables. Also, spectral series analysis by Fourier interpolation (series Tab) and special fitting (autoFit), and general fitting (modelX/Y). Includes discussion of methods to estimate errors in model parameters. 5) Chemical Shifts and Dipolar Couplings. Format of chemical shift table. Using TALOS to predict protein backbone angles. Using tools to predict and view shifts based on protein backbone angles. Format and meaning of Dipolar Coupling Table. Fitting dipolar couplings to structure by SVD. Displaying couplings and their statistics. Fitting dipolar couplings to an existing structure with tensor restraints. Cross-validation, evaluation with structural noise and coupling measurement noise. Fitting couplings to an ensemble. Displaying tensor parameters with a PDB file. Using MFR to estimate protein tensor parameters (below). 6) TCL Script Writing. Basic TCL introduction. Commands for manipulating tables (gdb database command). Commands for reading and drawing spectral regions (ROI commands). Combining database and ROI commands to build applications. Mathematical operations on spectral regions. Simple X/Y model fitting applications. Reading PDB structures and NMR parameters. Probing and manipulating PDB coordinates and angles. Coordinate alignment of structures. Simulating NMR parameters (J-couplings, dipolar couplings, backbone chemical shifts). 7) NMR Homology and Molecular Fragment Replacement. Introduction. Preparing working structure and input tables. Conducting the MFR search. Viewing MFR fragment phi/psi trajectories. Creating angle-average structures or angular restraints. Refining fragments. Fragment assembly. 8) Structure Calculation with the DYNAMO System. Introduction to DYNAMO. Description of table-based specification of molecular structure and restraints. Specifying sequences interactively or from existing files. Building an extended structure. Importing a structure. Preparation or conversion of restraint tables. Annealing schemes. Special options for dipolar coupling data. Ranking and evaluating structures. Finding and displaying coordinate alignment and statistics. Preparing and refining an average structure. Definition of new residue types and molecules. 9) Program Reference Guide. This provides a list of all the programs in the NMRPipe system. Each program will have a description of its purpose, a summary of its command-line options, and one or more examples of its use. 10) NMRPipe Reference Guide. This provides a list of all of the processing functions in the ?nmrPipe? processing program. Each function will have a description of its purpose, a summary of its command-line options, and one or more examples of its use within a processing scheme. 11) NMRWish Reference Guide. This provides a list of all of the special commands which have been added to the ?NMRWish? TCL interpreter. 12) Script Reference Guide. This provides a list of all of the applications implemented as stand-alone scripts. The Institute intends to procure these services by other than full and open competition from Dr. Gabriel Cornilescu. To the best of the Government?s knowledge he is the only source that will provide NIDDK with these services. Interested vendors may identify in writing their interest with a capability statement to the Contracting Office prior to the closing date of this notice. This notice of intent is not a request for competitive proposals, however, all responses received, before the closing date, of this announcement 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 within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. It is anticipated that Request for Quotation (RFQ) NIH-NIDDK-04-284 will be available fifteen (15) days after the publication date of this synopsis. This Request for Quote (RFQ) will be issued on September 1, 2004. Receipt of quotations will be due ten (10) days after the release of the RFQ. The anticipated award date is September 13, 2004. Request for copies of the RFQ must be in writing and may be FAXED to 301-480-8261. Quotations must be submitted in writing to the National Institute of Diabetes and Digestive and Kidney Diseases, 6707 Democracy Blvd., Room 773, Bethesda, MD 20817, Attention: Diana Ly. FAXED quotations must contain offerors names, address, telephone number and fax number and should document the following: 1) extensive prior experience with the NMRPipe software system; 2) experience developing NMR applications using the NMRWish TCL interpreter; 3) basic knowledge of the C programming language. FAXED quotations will only be accepted if dated and signed by an authorized company representative.
- Place of Performance
- Address: 9000 Rockville Pike, Bethesda, MD
- Zip Code: 20892
- Country: USA
- Zip Code: 20892
- Record
- SN00644463-W 20040818/040816211816 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
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