SOLICITATION NOTICE
68 -- Genome Sequencing & Finishing
- Notice Date
- 2/20/2003
- Notice Type
- Solicitation Notice
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy & Infectious Diseases/AMOB, 10401 Fernwood Drive MSC 4811 Room 2NE70-A, Bethesda, MD, 20817
- ZIP Code
- 20817
- Solicitation Number
- RML-RFQ-3015
- Archive Date
- 3/18/2003
- 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 format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes being requested & a written solicitation will not be issued. This procurement is being issued as a request for quotation. Submit offers on RML-RFQ-3015. Solicitation documents and incorporated provisions & clauses are those in effect through Federal Acquisition Circular 2001-12 dated 1/27/03. This acquisition will be processed under Simplified Acquisition Procedures (SAP) and is a Small Business Set-Aside. The North American Industry Classification System (NAICS) code for this procurement is 325414 & the small business size is 500. SCHEDULE: Purpose and objectives of NIAID,RML,LHBP for this acquisition are as follows: Independently, and not as an agent for the government, the contractor shall provide to LHBP services from qualified & experienced personnel to produce and complete five steps described here-in. The five requirements are as follows; 1)Focused effort & analysis of targeted regions. 2)Design and synthesis of primer pairs for PCR. 3)(SNP) analysis. 4)Streamlining genome integration process into the RML ERGO server. 5)Genome updates into RML ERGO server. This is a one time work effort. The data & files must be compatible, transferable to and readable by current RML computing systems, PC, MAC and Unix/Linux-based. The Contractor shall perform the following steps as specified. Step#1: Focused effort and analysis of targeted regions. A Ph.D.-level scientist shall oversee production of seven genomes.The Scientist shall be in direct contact with all RML/LHBP project managers, supervisors & technical staff and shall be responsible for analysis of and reports on the following: Macrolide resistance regions, Prophage regions, Critical virulence gene determinant regions, Multi-genome comparative analysis, 25KB flanking regions, Figures and/or written sections of potential manuscripts, Data mining reports, Status/progress reports. The RML Project Officer will request a report and the contractor scientist shall construct reports not less than 2 pages nor more than 50 pages, but which shall include, but are not limited to, single/multiple graphics DNA sequence(s), charts, figures, tables, or text as requested. Significant amounts of work may be broken into several reports upon agreement with the Project Officer. Step#2: Design & synthesis of primer pairs for PCR. The Contractor shall design & synthesize PCR primers for analysis of target regions selected by the Project Officer. The Contractor shall test primers producing gel images demonstrating their effectiveness. The primers shall be purchasable in 96 well microtiter plate format. Written protocol describing PCR reagents & conditions shall be provided to LHBP. Step#3:(SNP)analysis. The Contractor shall provide detailed analysis on single nucleotide polymorphisms (SNP) for a targeted genome. SNPs shall be identified as synonymous or non- synonymous in all regions but not limited to ORF or intergenic regions. Contractor shall perform this analysis for incomplete genomes & provide probability values for all SNPs. Non-synonymous SNPs shall be cataloged according to virulent, metabolic & regulatory subsystems. Reports shall be in Microsoft Excel or Word format. Delivery & installation of SNP data shall be on CD-ROM & incorporatable into RML ERGO server (Step #5). Step#4: Streamlining genome integration process into RML ERGO server. RML ERGO server shall be modified so new genome data can be easily uploaded into the server. Contractor shall work with RML/LHBP in order to facilitate this process. All installation software or scripts shall be written in Perl & run under current Perl modules in ERGO. New genome data shall be transferable by secure tunnel transmission onto server. Configuration shall occur so that bi-weekly genome updates will be compatible & integratable with RML ERGO server. Server shall be capable of receiving updates of single or multiple genomes from contractor via Step 5. Streamlining effort shall not affect normal operation of server & existing support contracts. Step#5: Genome updates into RML ERGO server. LHBP requires new genomes to be loaded into the RML ERGO server. Data files for ORF calling & determination of protein and RNA encoding regions shall be made by the contractor for unannotated genomes. ERGO-specific analytical data for similarities, bi-directional best hits, pairs of close bi-directional best hits, along with pinned regions, fusion clustering, protein family clustering & functional coupling shall be performed. Genome SNP data shall be importable in this context. Manual annotation shall be performed, but not limited to unannotated genomes. Automated functional assignments of protein encoding regions & manual genome annotation shall be performed. All Streptococcus genome ORFs shall have SPY aliases. Genome updates shall involve but not be limited to synchronized & unsynchronized delivery. All genome updates shall be performed via secure tunnel. CD-Rom disks of genome update data shall also be provided. The following are reporting requirements and deliverables: 1)Deliverables: Contractor scientist shall provide a report to RML Project Officer within one week of a request by e-mail. Duration: Approximately 40 weeks. Reports shall not number more than 50 total. 2)Deliverables: The contractor shall provide PCR primers in 96-well format per target region & shipped on dry ice. A detailed report on results (gel images), conditions & reagents shall be provided. Primer sequences in a tab-delimited format shall be provided. Duration: Not exceed 2.5 weeks for each request. 3) Deliverables: SNP data shall be in ASCII text files or tab-delimited format sent via CD-ROM. SNP Data shall be installable on RML ERGO server as requested by Project Officer via Step 5. Duration: Not to exceed 7 days following request for comparison studies to be performed. 4)Deliverables: Streamlining of RML ERGO server to support rapid genome data updates & transfers from contractor or other sources, or via Step 5 orders, including Data packaging Tools, Data Installation Tools, & Data Validation Tools. Duration: Not to extend two months from start of streamlining process to completion.5) Deliverables: Non-synchronized genome updates: shall involve creating necessary data files, determining coding regions, calculation of analytical data, functional assignments & manual genome annotation. Genome data shall be delivered via secure tunnel into RML ERGO server. Formats compatible with contractors interface. Requests shall be considered RUSH requests. Synchronized genome updates: Bi-weekly internal contractor updates shall be made available upon request. Contractor update Calendar shall be provided. Duration: requests for genome updates following completion of Step 4 shall not exceed 7 days or 14 days where manual annotation is requested. Requests for Genome updates shall not exceed 30 days where Step 4 is not completed. FOB Point shall be Destination, Hamilton, MT. Delivery as annotated above. Following FAR provisions & clauses apply to this acquisition: FAR52.212-1 Instructions to Offerors-Commercial; FAR52.212-2 Evaluation-Commercial Items; FAR52.212-4 Contract Terms&Conditions-Commercial Items; FAR52.212-5 Contract terms & 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. Offerors must include along with their offer a completed copy of provisions at FAR52.212-3 Offerors Representations & Certifications-Commercial Items. Award will be based on capability to meet above stated salient characteristics, delivery, price & past performance. Offers may be mailed or faxed to POC indicated above(Fax-406-363-9376). Offers must be submitted not later than 4:30 PM(MDST) 3/3/03. Copies of 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
- SN00262049-W 20030222/030220213246 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
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