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FBO DAILY ISSUE OF DECEMBER 16, 2005 FBO #1481
SOLICITATION NOTICE

D -- MULTI GENOME COMPOSITE CONSTRUCTION

Notice Date

12/14/2005
 

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-6004
 

Response Due

12/27/2005
 

Archive Date

1/11/2006
 

Small Business Set-Aside

Total 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 13(thirteen) 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 2005-06 dated 10/31/05. 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 Rocky Mountain Laboratories(RML), has been charged with performing basic research contributing to the development of diagnostic reagents, therapeutics and vaccines against human bacterial pathogens. Construction of a custom microarray chip containing oligonucleotide sequences representing the open reading frames of 13(thirteen) bacterial pathogen genomes, condensed into composite, and or single genomes will contribute towards achieving those goals. The contractor shall provide to RML services to construct and provide sequence and annotation files for bacterial genomes that shall conform to specifications defined by Affymetrix in the GeneChip? CustomExpress? Array Design Guide and approved in advance by the Affymetrix Chip Design Team. Labor categories may be suggested by the vendor and approved in advance by the Project Officer. This is a 10(ten) week, one time work effort, where the final product shall be the production of flat files, 2(two) per composite or single genome. RML has a need for the contractor to use URLs and RML data, some of which is incorporated into the RML ERGO server to construct final files for each of the genomes discussed below. These final files will be Fasta files of ORFs and annotation files for those ORFs in tab-delimited format with column headers. 2(two) files total, per composite, or single genome effort shall be constructed, one in fasta format and the other in annotation format. Unique identifiers specific to ERGO annotations for all orfs present in the RML ERGO server shall be incorporated into the annotation files. The final Fasta and annotation files shall match the format Affymetrix requests. The final Fasta and annotation files shall meet Project Officer specifications. During the production of the files the contractor shall communicate with Affymetrix and the Project Officer in order to make sure that compliance with Affymetrix design requirements in the form of these files is occurring. A final Conference call will occur with the RML Project Officer and Affymetrix and the contractor to make sure that all of Affymetrix file requirements have been met at the end of the contract. The following genomes, shall be included in this effort: A. Burkholderia sp. genomes: 1. Burkholderia cenocepacia J231. 2. Burkholderia mallei. 3. Burkholderia strain 383. 4. Burkholderia vietnamensis strain G4. 5. Burkholderia pseudomallei 1026b. 6. Burkholderia pseudomallei K96243. B. Mycobacterium sp. genomes: 1. Mycobacterium leprae. 2. Mycobacterium marinum M. 3. Mycobacterium smegmati. 4. Mycobacterium avium strain avium. 5. Mycobacterium avium strain pseudotuberculosis. 6. Mycobacterium tuberculosis strain CDC155. 7. Mycobacterium tuberculosis strain H37Rv. 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 RML will provide genomic data in the form of flat files and up-to-date assembly files in ace format with all supporting chromatogram files if needed. All genomes shall undergo intra- and inter-comparative analysis in order to identify regions of duplication and uniqueness. For composite genome construction, one genome shall be designated as the backbone genome and shall be represented in the orf and annotation flat files in its near entirety (absent homologous repetitive sequences at a 97% DNA identity or higher). Subsequent genomes that are within the same genus, but that will make up the composite aspects of the genome will only be represented at the level of unique sequences not present in the backbone genome (at 96% DNA identity or less). Annotation must reflect this origin of sequence and the connection to the backbone genome. Decisions regarding whether to perform composite construction versus individual genome representation shall be based upon the contractor running test analyses, which may or may not involve BLAST searches/comparisons at different levels of DNA identity or similarity stringencies. If genomes are syntenous, composite construction can work, if they are nonsyntenous, demonstrating many genomic changes and differences, then independent representation might be the best option. Final decisions on composite versus single or independent representation shall be made following discussion and approval with the Project Officer. Final annotation and flat files shall have unique orf identifiers connected to the ERGO server and compatible with the ERGO server. The Contractor must have access, experience and proprietary rights for interacting with the ERGO server such that interactions will not void or cancel existing service and support contracts for the ERGO SERVER. Affymetrix shall be the sole source for probe pair design, synthesis and manufacturing of the chip. Sequence and annotation files shall be submitted to Affymetrix by the contractor following review and approval by the RML project Officer. Step 1: Receipt of all genomic materials Duration: From date of receipt of materials, Total 10(ten) days. Deliverables: The contractor shall provide to RML confirmation that for each genome category effort, the contractor has all of the necessary materials to proceed effectively. A brief report shall also be provided outlining any areas of potential difficulty. The contractor may begin work on flat file construction when all of the genomic data for that effort has been received or has been made available. Step 2: Sequence scanning and analysis of all genomes. Duration: 1-2 months total from end of receipt of materials (Step 1) for all composite, and single genomes to delivery of flat files to Affymetrix. Deliverables: Two flat files for each composite and single genome effort, consisting of a sequence flat file and an annotation file shall be delivered by email, ftp or on CD to the project officer for review and forwarded onto Affymetrix. Flat files delivered to Affymetrix for each genome effort shall be 100% compatible with Affymetrix design criteria as defined by Affymetrix. Composite and single genome flat file sets, including, but not limited to fasta orf files and annotation files may be delivered individually per group and invoiced as such, following acceptable review by the project officer. Inspection Criteria: All work for all composite genomes will be inspected and approved by the project officer or his designee via the reports and flat files submitted. Acceptance Criteria: will be based upon decisions made by 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; FAR52.246-2 Inspection of Supplies-Fixed Price; 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 - 406-363-9376), (E-Mail/ Jkeiser@niaid.nih.gov). Offers must be submitted not later than 4:30 PM (MDST) 12/27/05. 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
 

Record

SN00951989-W 20051216/051214211854 (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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