SOLICITATION NOTICE
D -- GENOME DATA - ASSESSMENT AND ANALYSIS
- Notice Date
- 4/21/2004
- Notice Type
- Solicitation Notice
- NAICS
- 541710
— Research and Development in the Physical, Engineering, and Life Sciences
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy & Infectious Diseases/AMOB, 10401 Fernwood Drive, Suite 2NE70, MSC 4811, Bethesda, MD, 20817
- ZIP Code
- 20817
- Solicitation Number
- Reference-Number-RML-RFQ-4026
- Response Due
- 5/6/2004
- Archive Date
- 5/21/2004
- Point of Contact
- Julienne Keiser, Purchasing Agent, Phone 406-363-9370, Fax 406-363-9376, - Rebecca Guenthner, Chief Contracting Officer, Phone 301-402-2284, Fax 301-480-3695,
- E-Mail Address
-
Jkeiser@niaid.nih.gov, rguenthner@niaid.nih.gov
- Small Business Set-Aside
- Total Small Business
- Description
- 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; quotes are being requested and a written solicitation will not be issued. This procurement is being issued as a request for quotation. Submit offers on RML-RFQ # 4026. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2001-22 dated 4/5/04. This acquisition will be processed under Simplified Acquisition Procedures (SAP) and is a Total Small Business Set-Aside. The North American Industry Classification System (NAICS) code for this procurement is 541710 and the small business size is 500. The Rocky Mountain Laboratories(RML), Laboratory of Human Bacterial Pathogenesis (LHBP), has been charged with performing basic research contributing to the development of diagnostic reagents, therapeutics and vaccines against human bacterial pathogens. The sequencing of bacterial genomes is paramount to those diagnostic and vaccine based discoveries. The contractor shall provide to LHBP services taking the 1.9MB RML genome raw data and materials at 13.5X, and perform library construction and finishing reactions to take the genome to total completion for publication by the LHBP. This service will be accomplished in the following manner: Contractor scientists shall 1) Assess the data provided from the LHBP; 2) Perform closure of the genome to 20 contigs/Mb; 3) Perform closure to one(1) contig or single ungapped genome; 4) Perform validation and final completion genome to publication quality. The contractor shall keep all RML-derived data secure and will not release or maintain any of the data beyond this contract effort. If Internet connectivity is needed in order to perform the work, or transfer deliverables, contractor computers will be secure and in compliance with RML IT security procedures and policies. The LHBP will provide biological reagents consisting of PCR fragments from clone libraries, a detailed description of how the libraries were constructed (including vector sequences, cloning sites used, naming schema, etc.) as well as up-to-date assembly files in ace format with all supporting chromatogram files. Step 1: Receipt of materials from RML/LHBP. Assembly, analysis of assembly and QC of LHBP materials: From date of receipt of materials, total twenty(20) days. The contractor shall provide to RML confirmation that the contractor has all of the necessary materials to proceed effectively and that successful data conversion has occurred. A brief report shall also be provided outlining any areas of potential difficulty. Step 2: Closure to 20 contigs/MB. The following shall be performed: 1). Fosmid library construction and sequencing. (~1000 RxNs performed); 2) Primer walking reactions; 3) Delivery of assembly and trace data by FTP; 4) Update of RML ERGO database; 5) Automated ORFs called and functionally annotated; 6) One round of manual analysis of annotation; 7) Analysis of gene conservation; 8) Identification of phage regions; 9) Delivery of analysis data; 10) Online update of RML ERGO server. Duration: Four(4) months from end of receipt of materials (Step 1) to delivery of update onto RML ERGO. Trace data for all primer-walking/finishing reactions, in SCF format, shall be available for ftp download, including a list of primers and their sequences. Contigs in flat file format shall be delivered on a CD. Gene annotation and pathway information shall be delivered by flat file (EMBL format) on a CD. A list of unique and conserved ORFs and DNAs for the M12 genome, as compared to all existing genomes available to the contractor, shall be provided in flat file format on a CD. A written report on the number, location, positional information, including images and text, and annotation of phage-like regions in the M12 genome shall be provided. An update to the RML ERGO server shall be performed with the primary sequence information and results of genome analysis. Step 3: Closure to ungapped genome. The following shall be performed: 1) Primer walking to ungapped assembly; 2) Delivery of ungapped assembly and additional trace data by ftp access; 3) Update of ungapped data in ERGO database; 4) Automated analysis of ungapped genome for ORF calling and functional analysis; 5) Second round of manual analysis for annotation purposes; 6) Analysis of gene conservation; 7) Identification of phage regions; 8) Delivery of conservation/unique data analysis in flat file format on CD; 9) online update of RML ERGO server. Duration: four(4) months from end of Step 2 to delivery of update onto RML ERGO. Trace data for all primer-walking/finishing reactions, in SCF format, shall be available for ftp download, including a list of primers and their sequences. A preliminary draft of the single contig/chromosome assembled where 90% of bases are at Q40 average or higher shall be delivered in flat file format on a CD. A preliminary final genome annotation and pathway identification shall be provided in flat file format on CD. A preliminary final list of unique and conserved ORFS and DNAs for the M12 genome compared to all other genomes available to the contractor shall be provided in flat file format on a CD. A written report on the number, location, and positional information, in the ungapped genome including images and text, and annotation of phage-like regions in the M12 genome shall be provided. An update to the RML ERGO server shall be performed with the primary sequence information and results of the ungapped genome analysis. Step 4: Genome validation and completion: 1) Validation of final genome assembly based on universal and specific primers; 2) Delivery of validation data and biological reagents; 3) Identification of low quality regions and frame shifts; 4) Sequence quality score improvement; 5) Delivery of assembly and additional trace data; 6) Update of data in ERGO server database; 7) Automated annotation and pathway identification for M12; 8) A final round of manual annotation; 9) Manual pathway identification; 10) Functional reconstruction of genome; 11) Detailed analysis of conserved and unique genes; 12) Analysis of conserved and unique pathways; 13) Identification of horizontally transferred regions; 14) Final analysis of genes in main chromosome; 15) Generation of linear map; 16) Generation of circular map; 17) Online update of RML ERGO server; 18) Submission of completed sequence to GenBank. Duration: Five(5) months from end of Step 3 to submission of completed sequence to GenBank. The contractor shall deliver a set of ordered validation primers in 96-well format for the genome, with full written description. Ordered PCR fragments corresponding to the total genome validation effort shall be delivered. A report on PCR validation/confirmation results containing gel images of PCR fragments in html and excel format shall be provided on a CD or via interactive web site. The final sequence of the genome shall be provided on a CD. Trace data for all quality improvement reactions shall be available via ftp. Final, verified sequence for the genome shall be provided in flat file format on a CD. A report on regions of the genome that the contractor was unable to improve quality shall be provided. Final manual gene annotation and pathway identification shall be provided in flat file format on a CD. A final list of all unique and conserved ORFS and DNAs for the M12 genome compared to all other genomes available to the contractor shall be provided in a detailed report format with images and sequence similarity values. An excel spread sheet containing all genes in the M12 genome with ERGO database Ids and Spy number gene aliases, along with the functional annotation for each gene shall be delivered by electronic mail. A detailed written report on horizontally transferred regions of DNA in the M12 genome, containing figures and text shall be delivered. A linear contig map of the M12 genome in PostScript format, containing all orfs coded by functional annotation shall be delivered via electronic mail. Update of the RML ERGO server with primary sequence and genome annotation information shall be performed. Production and submission of a full genome GenBank genome submission file shall be performed. FOB Point shall be Destination, Hamilton, MT. Delivery location is Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT. The following FAR provisions and clauses apply to this acquisition: 52.212-1 Instructions to Offerors?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; FAR52.246-2 Inspection of Supplies-Fixed Price; FAR52.227-14 Rights In Data ? General; HHSAR 352.224.70 (b)(f) Confidentiality of Information Clause. Offerors must include with their offer a completed copy of the provisions at FAR 52.212-3 Offerors Representations and Certifications?Commercial Items. The contractor shall be required to complete on-line Security Training to insure compliance with RML-IT security procedures and policies. By submission of an offer, the offeror acknowledges the requirement that a prospective awardee shall be registered in the CCR database prior to award, during performance, and through final payment of any contract, basic agreement, basic ordering agreement, or blanket purchasing agreement resulting from this solicitation. Offers may be mailed or faxed to the POC indicated above (Fax - 406-363-9376). Offers must be submitted not later than 4:30 PM (MDST) 5/6/04. Copies of the above-referenced clauses are available upon request, either by telephone or fax. All responsible sources may submit an offer that will be considered by this Agency.
- Place of Performance
- Address: Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT
- Zip Code: 59840
- Country: USA
- Zip Code: 59840
- Record
- SN00570023-W 20040423/040421211814 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
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