SOLICITATION NOTICE
68 -- BIOINFORMATICS PROCESSING 16(SIXTEEN) BACTERIAL PATHOGENS
- Notice Date
- 9/8/2005
- 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-NOI-RML-5031
- Response Due
- 9/19/2005
- Archive Date
- 10/4/2005
- 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 16(sixteen) bacterial pathogen 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 #5031. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-05B dated 8/26/05. 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 325414 and the small business size is 500. SCHEDULE: The National Institute of Allergy and Infectious Disease (NIAID), Rocky Mountain Laboratories, (RML), has a requirement to perform basic research contributing to the development of diagnostic reagents, therapeutics and vaccines against human bacterial pathogens. The sequencing of pathogen genomes is paramount to those diagnostic and vaccine based discoveries. The NIAID, RML has a need for construction of an Affymetrix microarray chip containing oligonucleotide sequences representing the open reading frames of 16(sixteen) bacterial pathogen genomes, condensed into composite, single and intergenic coverage genomes to contribute towards achieving those goals. The contractor shall provide the following: 1) 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. 2) This shall be a 10(ten) week, one time work effort, where the final product shall be the production of flat files, 2(two) per composite, single and intergenic genome. 3) The files shall be compatible with Affymetrix design criteria for custom chip synthesis. 4) The contractor shall 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 shall be Fasta files of ORFs and annotation files for those ORFs in tab delimited format with column headers. 5) 2(two) files total, per composite, single and intergenic genome effort shall be constructed, one in fasta format and the other in annotation format. Unique identifiers 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. 6) During the production of the files the contractor shall communicate with Affymetrix and the project officer in order to confirm that compliance with Affymetrix design requirements in the form of these files is occurring. (7 A final conference call shall occur with the RML project officer, Affymetrix, and the contractor to confirm that all of Affymetrix file requirements have been met at the end of the contract. 8) The following genomes, labeled by grouping, shall be included in this effort: A. Single Genomes: 1) Acetobacter; 2) Norcardia; 3. Staphylococcus aureus MW2; 4) Staphylococcus haemolyticus JCSC1435. B. Multi-Genome Composites: 1) Staphylococcus epidermidis, strain RP62A and strain ATCC12228; 2) Coxiella burnetti, strain TIGR, strain Graves, strain Kearns; 3) Chlamydia trachomatis, strain HAR, strain D, strain L2, strain MoPn; 4) Chlamydiophila caviae GPIC, and Chlamydiophila pneumoniae AR39; C. Intergenic Region Genomes: 1) Borrelia burgdorferi. The contractor shall provide all personnel for the work effort. The contractor shall keep all RML derived data secure and shall 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 NIAID/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. REPORTING REQUIREMENTS AND DELIVERABLES: All genomes shall undergo intra and inter comparative analysis in order to identify regions of duplication and uniqueness. For composite genome construction, 1(one) genome shall be designated as the backbone genome and shall be represented in the orf and annotation flat files in it?s near entirety (absent homologous repetitive sequences at a 97% DNA identity or higher). Subsequent genomes that are within the same genus, but that shall make up the composite aspects of the genome shall 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. Intergenic genomes shall involve 2(two) aspects of the genome; 1) Intergenic/non-coding regions and 2) Opposite strand coding regions. The reason for the latter being that the chip shall be used to analyze signal RNAs, coded for in intergenic regions or opposite strands of coding regions. Intergenic regions and opposite strand coding regions shall contain appropriate annotation for each, to be discussed and decided upon by the contractor and project officer. Affymetrix shall be the sole source for probe pair design, synthesis and manufacturing of the chip. Sequences shall be submitted to Affymetrix by the contractor following review and approval by the NIAID/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 NIAID/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(one-two) months total from end of receipt of materials (Step 1) for all composite, single and intergenic genomes to delivery of flat files to Affymetrix. Deliverables: 2(two) flat files for each composite, single and intergenic 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 to Affymetrix. Flat files delivered to Affymetrix for each genome effort shall be 100% compatible with Affymetrix design criteria as defined by Affymetrix. Composite, single and intergenic 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 AND ACCEPTANCE: Inspection Criteria: All work for all composite genomes will be inspected and approved by the NIAID/RML project officer or his designee via the reports and flat files submitted. Acceptance Criteria: will be based upon decisions made by the NIAID/RML project officer. FOB Point shall be Destination, Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT. The following FAR provisions and clauses apply to this acquisition: (B)(1) 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; FAR 52.212-1 Instructions to Offerors Commercial; FAR52.212-2 Evaluation Commercial Items; FAR 52.212-4 Contract Terms and Conditions-Commercial Items; FAR 52-212.5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders-Commercial Items. FAR 52.246-2 Inspection of Supplies-Fixed Price. 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. FAR52.227-14 Rights In Data General; HHSAR 352.224.70 (b)(f) Confidentiality of Information Clause. Award will be based on the capability of the item offered to meet the above stated salient characteristics, including technical evaluation, delivery, price, and past performance. Offers may be mailed or faxed to the POC indicated above (Fax - 406-363-9288). Offers must be submitted not later than 4:30 PM (MDST), 9/19/05. 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
- Zip Code: 59840
- Record
- SN00889928-W 20050910/050908211935 (fbodaily.com)
- Source
-
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