National Institutes of Health, NIAID, Rocky Mountain Laboratories, 903 South 4th Street, Hamilton, MT 59840

99 -- SCIENTIFIC SOFTWARE SOL RML-RFQ-009 DUE 061900 POC Lynda Kieres, Purchasing Agent (406) 363-9210 / Rebecca Guenthner, Contracting Officer (301) 402-2284 17. This notice is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation, proposals are being requested and a written solicitation will not be issued. This solicitation is being issued as a request for quotations (RML-RFQ-009). The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 97-17 (through 4/25/2000). This acquisition will be processed under Simplified Acquisition Procedures (SAP) and is a Small Business Set-Aside. The associated Standards Industrial Classification Code (SIC) for this procurement is 7372 and the size standard is $18.0. SCHEDULE: The Rocky Mountain Laboratories, Laboratory of Human Bacterial Pathogenesis (LHBP) proposes to procure Geospiza Software Package 20000319-1 from Geospiza Inc., 2442 NW Market St. PMB 344, Seattle, WA 98107. The LHBP utilizes PE Biosystems 3700 DNA sequencers that generate 675,000 sequence bases of information per day. In order to keep track of this high through-put sequence data, state-of-the-art software is required to process bioinformatics algorithms with relational database technology, integrating sequencing, quality control, and accounting functions that can make sequencing data readily available to researchers. FOB Point shall be Destination, Hamilton, MT. Inside delivery shall be no more than 30 days after receipt of order (ARO). Delivery location is Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT. It is mandatory that the software has the following capabilities: 1) the software must be compatible with the existing SunMicro Systems SRVR E450 computer and must operate with 4 processors (400MHZ) set in parallel allowing for rapid computer processing of sequencing data; 2) the software must run Phred/Phrap parallel written software (Southwest Software); 3) the software must access OPT Memory cards which allow for high speed RAM access functions, a necessary component of high speed data processing coupled with the parallel interfaced processors; 4) the software must interface with An Opt int (18.2 GB) hard drive for software storage and short-term data storage; 5) the software must provide on-line data entry for sequencing requests and it must automate sample tracking; 6) web-based interfaces must be used to submit sequencing requests and enter sample information; 7) sample information must be automatically linked to the appropriate chromatogram files so that sample status can be easily monitored; 8) the software must operate so that Sequencing requests can be used to prepare cost accounting reports and custom reports can be created using Structured Query Language (SQL) queries; 9) the software should automatically organize chromatogram files with their supporting documentation; 10) run files must be automatically created for the ABI PRISM 373 DNA Sequencer, 377 DNA Sequencer, and 3700 DNA Analyzer as well as the Amersham Pharmacia Biotech MegaBACETM 1000 DNA Sequencing Systems; 11) instrument maintenance information must be recorded and stored by the software centrally; 12) instrument maintenance and status must be recorded instantaneously in a database, thereby streamlining instrument monitoring and cost tracking; 13) the program also must perform automatic central storage of instrument data and information; 14) data from automated DNA sequencers should be stored in a relational database management system (RDBMS), which is compatible with the following instruments, ABI PRISM 310 Genetic Analyzer, 373 DNA Sequencer, 377 DNA Sequencer, and 3700 DNA Analyzer, as well as the Amersham Pharmacia Biotech MegaBACETM; 15) the software must be compatible with file formats including ABI, SCF and ESD; 16) chromatogram files must be processed through the phred base-calling algorithm, to provide sequences, quality values, and quality control data; 17) sequence contaminants must be identified using the cross-match similarity analysis algorithm (P. Green, unpublished); 18) custom reports need to be created with Structured Query Language (SQL) queries; 19)the software must provide for automated Screening for vector, E. coli, and other contaminating sequences; 20) analysis capabilities must be able to be extended to automate assembly and contig reports using the phrap algorithm (P.Green, unpublished); 21) the software should be able to compare query sequences to a set of subject sequences and provide data in a variety of linked reports (to be specified); 22) databases containing protein or nucleotide sequences must be able to be searched with the NCBI BLAST 2.0 gapped alignment search algorithm; 23) the software should support viewing through widely available web-browser applications for submitted Sequence data and search results; 24) the software must support programs from the NCBI tool kit that are used to filter low complexity sequences prior to database searching; 25) the software must allow multiple sequences to be searchedconcurrently; 26) the software must present data in well-organized tables with sortable fields; 27) automatic verification of file format, program choice, and search database must be performed by the software in order to reduce time lost to nonfunctional searches; 28) concurrent searches and summaries should be performed with this one software for multiple sequences; 29) the software must allow Data transfer from remote and local sites by FTP; 30) multiple databases generated through total genome sequencing or comparative genomics sequencing projects should be maintained and accessed by the software; 31) the software must be able to export and transmit readable, processed data to Linux-based Dell computing finishing stations that run Consed.; 32) the software manufacturers must provide a minimum of 3 days of on-site training; 33) consultation services involving problem solving upgrades, training, help with Structured Query Language (SQL) queries, future expansion or incorporation of linked or novel software packages must be available and not merely limited to over-the-phone discussion, but inclusive of on-site visits. These consultation services must be available on a cost per need basis, reasonable and inline with previous training and installation costs and services;34) off site online access for repair or uploading of program updates including access for trouble shooting and software repair must be available and performed when requested; 35) the vendor must be responsible for installation, start-up and analysis of efficient operation: The following FAR provisions and clauses apply to this acquisition: 52.212-1 Instructions to Offerors Commercial; Offerors must include with their offer a completed copy of the provisions at FAR 52.212-3 Offerors Representations and Certifications Commercial Items. FAR 52.212-2 Evaluation Commercial Items; FAR 52-212-4 Contract Terms and Conditions Commercial Items; FAR 52-212-5 Contract Terms and Conditions Required to Implement Statues or Executive Orders Commercial Items applies to this acquisition. The proposal will be evaluated based on the technical information provided as to how the above specifications will be met. The clauses of subpart (b), which apply, are 6 and 10. Copies of the above-referenced clauses are available upon request, either by telephone or fax. This is not a solicitation for competitive proposals. However, if any other interested party believes that it can meet the requirements it may submit a statement of capabilities to the POC indicated above (Fax -- 406-363-9288). Capability statements and related materials must be received in this office no later than 4:30 PM (MDST) 06/19/00. See Numbered Note 22. Posted 05/31/00 (W-SN460235). (0152)

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