SOLICITATION NOTICE
D -- Acetobacter-like Genome Sequencing Project
- Notice Date
- 8/16/2004
- Notice Type
- Solicitation Notice
- NAICS
- 325414
— Biological Product (except Diagnostic) Manufacturing
- 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-4061
- Response Due
- 8/31/2004
- Archive Date
- 9/15/2004
- 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 # 4061. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2001- 24 ? dated 06/18/04. 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 325414 and the small business size is 500. The National Institute of Allergy and Infectious Disease (NIAID), Laboratory of Host Defenses (LHD), 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. SCHEDULE: The NIAID has a need to sequence an Acetobacter-like genome that is estimated to be approximately three(3) MB in size, to total completion. The contractor shall provide to the NIAID services to perform library construction, shotgun sequencing, sequence assembly, annotation, and finishing reactions to take the genome to total completion for publication by the NIAID. The contractor shall provide all personnel for the work effort. Personnel shall include at a minimum, one(1) genome analyst, two(2) computational biologists, one(1) project manager, two(2) technical scientists, and two(2) bioinformatisists. The contractor shall keep all NIAID-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 NIAID/RML IT security procedures and policies. The NIAID will provide purified bacterial genomic DNA and a written protocol describing the purification method. The NIAID will also be available for annotation expertise and guidance related to genome finishing issues. The contractor shall accomplish all requirements and deliverables through the following steps: Step 1: Written notification of receipt of materials from RML/LHD. Duration for Step 1: From date of receipt of materials -Total thirty(30) days. Deliverables for Step 1: The contractor shall provide to RML confirmation that the contractor has all of the necessary materials to proceed. A brief report shall also be provided outlining any areas of potential difficulty. Step: 2: Library construction, shotgun sequencing, assembly, and delivery of data. The following shall be performed: 1) Two genomic libraries shall be constructed by random, mechanical shearing. One library shall contain inserts of 2-3kb, the other up to 40kb. Libraries shall be non-amplified, quality control tested for ligation, size distribution of fragments, clone integrity, and quality of paired-end sequencing. 2) Clones shall be picked for template purification and freezer storage by robotic colony picking robots. 3) Templates shall be isolated by alkaline lysis and sequenced by PCR using the di-deoxy method of Sanger and vector?specific primers. 4) Shotgun sequencing shall be performed to 7X, based on predicted size of the genome from first two thousand(2000) reads. No other project or sequencing effort shall interfere or intermingle with the continuous shotgun genome effort described for this genome. 5) Two(2) to three (3) rounds of auto finishing shall be performed. 6) Genome assemblies shall rely on proven contractor-based assemblers or publicly available assembler software. Duration for Step 2: Two (2) months from end of receipt of materials (Step 1) to delivery of 7X data. Deliverables for Step 2: Trace data for all primer-walking/finishing reactions, in SCF format, shall be available for ftp download. Contigs in flat file format shall be delivered on CD. Gene annotation and pathway information shall be delivered by flat file (EMBL format) on CD. A list of unique and conserved ORFs and DNAs for the genome, as compared to all existing related genomes, shall be provided in flat file format on CD. Data upload to the RML\NIAID ERGO server shall be performed. Internet connectivity to Contractor?s graphics-based genome data analysis and data interpretation interface shall be provided. Step 3: Closure 20 contigs/MB genome. The following shall be performed: 1) Primer walking to ungapped assembly. 2) Manual editing of read and contig sequences, and manipulation of the layout. 3) Orf calling and automated annotation. Duration for Step 3: Two (2) months from end of receipt of materials (Step 2) to delivery of 20contigs/MB data. Deliverables for Step 3: Trace data for all primer-walking/finishing reactions, in SCF format, shall be available for ftp download. Contigs in flat file format shall be delivered on CD. Gene annotation and functional and pathway information shall be delivered by flat file (EMBL format) on CD. A list of unique and conserved ORFs and DNAs for the genome, as compared to all existing related genomes, shall be provided in flat file format on CD. Data upload to the RML\NIAID ERGO server shall be performed. Internet connectivity to Contractor?s graphics-based genome data analysis and data interpretation interface shall be provided. Step 4: Ungapped assembly, Annotation of the completed genome. The following shall be performed: 1) Multiple rounds of primer walking to reach ungapped assembly. 2) Manual editing of read and contig sequences, and manipulation of the layout to reach ungapped assembly. 3) For the finished ungapped genome, a first round automated analysis for ORF calling and functional analysis using BLAST, motif searches, gene context, SignalPtRNAScan or other proven and appropriate software. 4) A second round of manual analysis for annotation purposes focusing on related annotated genomes for comparative purposes. 5) Analysis of gene conservation. 6) Delivery of conservation/unique data analysis in flat file format on CD.Duration for Step 4: Four(4) months from end of Step 3 to delivery of update onto RML\NIAID ERGO server. Deliverables for Step 4: Trace data for all primer-walking/finishing reactions, in SCF format, shall be available for ftp download. A preliminary draft of the single contig/chromosome assembled where the total genome is at Q40 or higher (no more than one error per 10,000 bases) shall be delivered in flat file format on CD. Final genome annotation and pathway identification shall be provided in flat file format on CD. A final list of unique and conserved ORFS and DNAs for the new genome compared to all other closely related publicly available genomes shall be done. Data upload to the RML\NIAID ERGO server 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) 8/31/04. 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
- SN00644467-W 20040818/040816211818 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
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