This Combined Synopsis/Solicitation opportunity was posted on June 18, 2008. The submission period has ended. Browse the details below for market research, or find similar active opportunities.

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Custom Genome Sequencing

Awarded

NOI-RML-8022Federal

Submission Closed07/03/2008, 11:30:00 PM UTC

Contract Overview

Solicitation details, issuing organization, response deadlines, documents, and interested companies for this government contract opportunity.

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NAICS: 541711

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AI Contract Overview

The National Institute of Allergy and Infectious Diseases Rocky Mountain Laboratories intends to negotiate a sole source, small business set-aside contract with Integrated Genomics for custom genome sequencing. The project requires high throughput paired read DNA sequencing of two bacterial species pathogens using 454 GSFLx pyrosequencing technology to achieve 20X coverage. The contractor is responsible for integrating this new data with existing Sanger-generated assemblies to close contig numbers, performing gene identification and annotation using tools such as CRITICA, Glimmer, and ProkPeg, and uploading the final assemblies into the RML ERGO server. Strict data security and quality standards are mandated, requiring the contractor to comply with RML IT security policies and ensure no cross species contamination occurs. Deliverables include SCF-formatted trace data, FASTA formatted contigs, and EMBL-formatted ASCII files provided via CD-ROM. This acquisition is processed under Simplified Acquisition Procedures with a delivery destination of Hamilton, Montana. Offers must be submitted by July 3, 2008, and will be evaluated based on technical capability, delivery, price, past performance, and overall best value to the government.

General Info

Agency

N/A

Contract Value

$54,000

NAICS

541711 - Research and Development in Biotechnology

Place of Performance

ROCKY MOUNTAIN LABS 903 S 4TH STREET, HAMILTON, MT, 59840, USA

Set-Aside

SBA

Awardee

INTEGRATED GENOMICS, INC

Award Issued Date

07/07/2008, 12:00:00 AM UTC

Documents

No documents available

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Timeline

PhaseAwarded

PostedJun 18

Combined Synopsis

AwardedJul 7

Contract was awarded

Submission Closed

07/03/2008, 11:30:00 PM UTC

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Organization & Contact Information

AgencyN/A

Contacts2 people available

OfficeN/A

Organization / Agency

N/A

Office AddressN/A

Contacts

Julienne KeiserPurchasing Agent

contact@example.gov

+1 (555) 000-0000

Lynda KieresContracting Officer

contact@example.gov

+1 (555) 000-0000

Full Description

This notice is a combined synopsis/solicitation, Notice of Intent. The Government intends to negotiate on a sole source basis with Integrated Genomics for custom genome sequencing, in accordance with the format in Subpart 12.6, in conjunction with FAR 13.5, as applicable, and 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-8022. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-26 dated 6/12/08. 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 541711 and the small business size is 500. The National Institute of Allergy and Infectious Diseases (NIAID), 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. The sequencing of two Bacterial species pathogens will contribute towards these goals. SCHEDULE: The RML has a need to run paired read chemistry on two Bacterial species to 20X coverage with assembly with a prior Sanger-generated assembly of each genome, gene identification, annotation and upload into the RML ERGO server. The contractor shall perform high throughput paired read DNA sequencing of a bacterial pathogen genome, the coordination of that data with an existing, unfinished assembled version of each genome with the final product being a new assembly uploaded into the ERGO server. These two new genome assemblies and their accompanying data shall be annotated and uploaded into the RML ERGO server. 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. High Throughput paired read DNA sequencing shall be performed by pyrosequencing technology using a 454 GSFLx sequencing machine. The bead-based library construction and operation of the 454 technology shall be performed at the highest levels of quality possible. Quality sequence and no cross species contamination shall occur and be ensured and maintained throughout the work effort. The whole genome paired read data shall be assembled with the current, unfinished versions of both genomes currently residing in ERGO. The goal of this project is to close more fully or completely the total contig number for each genome. Assembly can use the 454 Newbler Assembler that is compatible with the 454 GSFLx. Following the total, complete assembly of all data for both genomes (previously existing and paired read) the contractor shall use public and proprietary gene identification tools and technologies to identify open reading frames (ORFs) in the newly assembled sequence. Widely known and used Bioinformatics algorithms such as CRITICA and Glimmer and other well-known tools such as ProkPeg shall be used. Protein encoding regions and coding RNAs shall be identified. SCF-formatted trace data and the assembled contigs in FASTA format shall be available for download by FTP. The Trace data shall be readable by standard sequencing reading and editable software. Genomic data shall be uploaded into the RML ERGO server. Data shall be compatible with ERGO naming conventions and upload requirements. At no time shall the interface or upload of genomic data affect the service and support contract currently in place for the RML ERGO server. The contractor shall provide EMBL-formatted ASCII files containing all contig, protein sequence and annotation information by CD-ROM for data storage at RML. The highest level of quality and attention to detail shall be performed throughout all stages of the project for both genome efforts. 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: (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; 52.212-1 Instructions to Offerors Commercial Items; 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; 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. Award will be based on the capability of the item offered to meet the above stated salient characteristics, delivery, price, past performance, and the best value to the government. Offers may be mailed to Julienne Keiser at Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, Mt 59840, faxed to the POC indicated above (Fax - +1 (555) 000-0000), or e-mailed at (contact@example.gov). Offers must be submitted not later than 4:30 PM (MST) 7/3/08. Copies of the above-referenced clauses are available from http://www.arnet.gov/far/current/html/52_000_107.html or upon request, either by telephone or fax. All responsible sources may submit an offer that will be considered by this Agency.