SOLICITATION NOTICE
A -- Bioinformatics Processing
- Notice Date
- 9/20/2006
- 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-NOI-RML-6053
- Response Due
- 9/26/2006
- Archive Date
- 10/11/2006
- Small Business Set-Aside
- Veteran-Owned Small Business
- Description
- This notice is a combined synopsis/solicitation, Notice of Intent. The Government intends to negotiate on a sole source basis with Integrated Genomics, Inc. for bioinformatics processing of 3 complete genomes and 2 incomplete genomes, 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 not being requested and a written solicitation will not be issued. Submit offers on NOI-RML #6004. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-12 dated 8/4/2006. 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 541710 and the small business size is 500. The National Institute of Allergy and Infectious Disease (NIAID), Rocky Mountain Laboratories, has a need for a contractor to take 3 genomes that are complete and 2 genomes that are incomplete, sequenced by Nimblegen and in Nimblegen data format and upload the data into the RML ERGO server (Integrated Genomics). The upload shall be in accord with NIAID IT security measures and the upload shall not impinge or sacrifice the current service and support contract in place with the ERGO server. Following data upload the genomes shall be annotated according the the annotation currently in place for the published and publicly available Chlamydia trachomatis Serovar HAR genome. Annotation of the 5 genomes shall be in accord with the sequential numbering and open reading frame (orf) calls of the Chlamydia trachomatis Serovar HAR genome.Genome aliases shall be provided by the government. Novel or unique orfs relative to the Chlamydia trachomatis Serovar HAR genome shall be sequentially numbered as with Chlamydia trachomatis Serovar HAR genome but will also contain a letter code identifying the uniqueness of the ORF relative to the published genome. The contractor shall re-orient the origin of replication based upon the Project Officer's analysis and direction.Annotation shall be at a level compatible with and in accord with NCBI submission requirements. Following complete and full annotation of the 5 genomes, the data shall be reloaded into the RML ERGO server. Once the 5 genomes are completely annotated and in RML ERGO the contractor shall perform pair wise comparisons using HAR strain as the reference strain and the newly annotated 5 genomes as the queries. The Contractor shall produce detailed reports with excel spreadsheets and other accompanying data and graphs regarding a full and complete polymorphism analysis. Polymorphisms shall be analyzed at the SNP level, encompassing Synonymous vs.Non-synonymous, transitions versus transversions, Orf to SNP frequency, Non-orf coding regions to SNP frequency, Insertions and deletions (InDels) ranging in size from 1 base InDels up to 5 kb or larger InDels. Results shall be presented in graphical format. Data shall be resented in Excel format with extensive detail on base positions, changes relative to reference strain, InDel length, etc... A 6-way comparison shall also be performed for the same data output. Finally, a truncated orf survey shall be performed where all orfs showing truncation or premature stops will be identified. All of this work shall not infringe or draw into question proprietary access or privileges to the RML ERGO database and server system. The contractor will 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. Inspection Criteria: All work will be inspected and approved by the project officer or his designee via the weekly reports and communications. Acceptance Criteria: will be based upon decisions made by the RML and the Project Officer. 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; FAR52.227-14 Rights In Data ? General; HHSAR 352.224.70 (b)(f) Confidentiality of Information Clause. By submission of an offer, the offeror acknowledges the requirement that a prospective awardee shall have posted their FAR 52.212-3 Offerors Representations and Certifications Commercial Items at website http://orca.bpn.gov. 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, e-mailed or faxed to the POC indicated above; (Fax - 406-363-9288), (E-Mail/ horrellb@niaid.nih.gov). Offers must be submitted not later than 4:30 PM (MDST) 9/26/2006. Copies of the above-referenced clauses are available from http://www.regulations.gov or, 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 St, Hamilton, MT
- Zip Code: 59840
- Country: UNITED STATES
- Zip Code: 59840
- Record
- SN01149205-W 20060922/060920220230 (fbodaily.com)
- Source
-
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