This 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; proposals are being requested and a written solicitation will not be issued.

This is a Request for Quote (RFQ). This procurement is conducted unrestricted with full and open competition, open to both large and small businesses. The associated North American Industry Classification System (NAICS) code for the procurement is 541380 and the Small Business size standard is $12.0 Million. The US Army Corps of Engineers, Engineer Research and Development Center Contracting Office, has a requirement for contractor support to assess the chemical stress effects of munitions constituents (MCs) and intensive munitions (IMs) on global gene expression networks in highly sensitive Leopard Frog tadpoles of the species Rana pipien.

The following are needed to deliver the sequenced and annotated transcriptome required for the successful execution of the ERDC EL's research effort:
a. >500bp nucleic acid sequence average read lengths (GS-FLX+ Sequencer is the only machine to achieve required read lengths in a high-throughput format (see requirement b)).
b. 1.4 billion bases total read coverage (2 full plate runs on GS-FLX).
c. Quality filtering of raw nucleic acid sequence data.
d. Nucleic acid sequence clustering.
e. Nucleic acid sequence assembly into contiguous sequences
f. Contiguous sequence matched against GenBank nucleic acid sequence database.
g. Sequences translated to amino acid code and matched to protein orthologs.
h. Functional annotation including gene ontology (GO) associations and Kyoto Encyclopedia of Genes and Genomes (KEGG) database matches to canonical pathways.
i. Prompt, on-demand bioinformatics support for one year

FAR Provision 52.212-1, Instructions to Offerors - Commercial Items, applies to this acquisition. Award shall be made to the responsible offeror whose proposal is determined to be Lowest Price Technically Acceptable in accordance with Clause 52.212-2 Evaluation -Commercial Items. Technical data is required to verify technically acceptable. The Clause 52.212-4, Contract Terms and Condition - Commercial Items, applies to this acquisition. The Clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items, applies to this acquisition. The clauses cited within the clause as indicated below are applicable:
FAR clauses 52.209-6, 52.219-6, 52.219-28, 52.222-3, 52.222-19, 52.222-21, 52.222-26, 52.222-35, 52.222-36, 52.222-37, 52.225-1, 52.225-5, 52.225-13, and 52.232-33. The clause at DFARS 252.212-7001, Contract Terms and Conditions Required to Implement Statutes or Executive Orders Applicable to Defense Acquisitions of Commercial Items, DFARS 252.232-7003, Electronic Submission of Payment Requests and Receiving Reports, and DFARS 252.232-7010, Levies on Contract Payments applies to this acquisition.

All interested firms must be registered in SAM. The Government will award a contract resulting from this synopsis/solicitation to the responsible lowest price offeror whose offer meets and/or exceeds the specifications herein. If you are not registered in the (SAM) System for Award Management (formerly CCR, ORCA, and EPLS), an award cannot be made to your company. You may register electronically at https://www.sam.gov/. Registering electronically will expedite the registration process acquisition.

All quotes should be emailed to: [email protected] no later than 11:00 am CST 18 September 2012. Point of Contact: Amanda Andrews, Contract Specialist, 601-634-5249.

Questions/Answers

1) The solicitation mentions "nucleic acid". Is this genomic DNA, mRNA or cDNA?

cDNA


2) How many biological samples have to be analyzed?

Ultimately, there is one sample to be analyzed, a normalized cDNA library.


3) What is the nature of the requested bioinformatics support? Does this include additional analysis or only interpretation of original data? How many hours of support per year does the government estimate for this project?

Bioinformatics support: Adapter sequence trimming, raw read quality control, sequence clustering, contiguous sequence assembly, blast search for contigs & singletons, annotation with protein identity, GO ontology, KEGG pathway, InterPro and other tasks based on need.

There is no interpretive analysis needed per se.

Bioinformatics Support: This is difficult to guess. Above and beyond the tasks described above, the contractor should expect anywhere from 40-160 hours of additional support in response to project needs.

4) When you say it is "normalized cDNA library", does it mean that it is already prepped for 454 sequencing (i.e. adapter ligated etc.)?

Yes, the sample we will submit will have appropriate adapters incorporated for 454 sequencing.

Bid Protests Not Available