SOLICITATION NOTICE
68 -- GIARDIA LIBRARY CONSTRUCTION AND GENOME ASSEMBLY
- Notice Date
- 8/9/2005
- 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-RML-RFQ-5034
- Response Due
- 8/24/2005
- Archive Date
- 9/8/2005
- 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 & a written solicitation will not be issued. Submit offers on RML-RFQ-5034. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-05 dated 7/27/05. 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 pathogens. The sequencing of pathogen genomes is paramount to those diagnostic and vaccine based discoveries. The NIAID, RML has a need to sequence a Giardia genome to 1X coverage that is estimated to be approximately 13 MB in size, with upload to the NIAID, RML ERGO Server. The contractor shall provide to the NIAID, RML, services to perform library construction, shotgun sequencing, sequence assembly, annotation, and finishing reactions to take the genome to 1X completion for upload to the NIAID, RML, ERGO server. The Contractor shall be required to complete: 1) Random small fragment (~2kb) and large fragment (~40kb) genome library construction 2) Shotgun sequencing, 3) Assembly 4) Genome analysis and 5) Updating the NIAID, RML ERGO Server. The contractor shall provide all personnel for the work effort. The contractor shall keep all NIAID, 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 NIAID,RML IT security procedures and policies. The NIAID, RML, will provide purified inactivated trophozoite pellets for DNA isolation and a written protocol describing suggested purification methods. The NIAID, RML will also be available for annotation expertise and guidance related to genome finishing issues. Reporting Requirements and Deliverables: Step 1: Written notification of receipt of materials from NIAID, RML. Duration for Step 1: From date of receipt of materials. Total 10(ten) days. Deliverables for Step 1: The contractor shall provide to NIAID, RML confirmation that the contractor has all of the necessary materials to proceed effectively. 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: 2(Two) genomic libraries shall be constructed by random, mechanical shearing. 1(One) library shall contain inserts of 2-3kb, the other fragments approximately 40kb in size. Libraries shall be non-amplified, Quality Control tested for ligation, size distribution of fragments, randomness, clone integrity and quality of paired-end sequencing. Clones shall be picked for template purification and freezer storage by robotic colony picking robots. Templates shall be isolated by alkaline lysis and sequenced by PCR using the di-deoxy method of Sanger and vector?specific primers. Shotgun sequencing shall be performed to 1X, based on predicted size of the genome from first 2000(two thousand) reads. No other project or sequencing effort shall interfere or intermingle with the continuous shotgun genome effort described for this genome. Sequence data shall be vector and quality screened. Whole genome assembly shall be performed using the Paracel Genome Assembler, Arachne, or another equivalent software package. Duration for Step 2: 2(two) 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. Data upload to the NIAID RML ERGO Server shall be performed. Internet connectivity to Contractor?s graphics-based genome data analysis and data interpretation interface shall be provided. Step 3: Orf calling, automated annotation and completion of 1X project: Orf calling and functional assignment data. Direct update of the NIAID RML ERGO Server with the 1X assembled and annotated genome. Duration for Step 3: 2(two) months from the end of receipt of materials (Step 2) to delivery of data into NIAID RML ERGO Server. Deliverables for Step 3: Data upload to the NIAID RML ERGO server shall be performed. Graphical presentation of the data shall mimic data already available for other genomes in the NIAID RML ERGO Server. Internet connectivity to Contractor?s graphics-based genome data analysis and data interpretation interface shall be provided. Inspection and Acceptance: 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 NIAID RML, and the 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. 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 (MDT), 8/24/05. 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
- SN00865951-W 20050811/050809211852 (fbodaily.com)
- Source
-
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