MODIFICATION
66 -- Genetic Analysis System
- Notice Date
- 7/10/2003
- Notice Type
- Modification
- Contracting Office
- Department of Agriculture, Agricultural Research Service, Mid South Area Office, 141 Experiment Station Road, Stoneville, MS, 38776
- ZIP Code
- 38776
- Solicitation Number
- IFB-2003-4431-021
- Response Due
- 8/20/2003
- Archive Date
- 9/4/2003
- Point of Contact
- Terry Krutz, Supervisory Contract Specialist, Phone 662-686-5361, Fax 662-686-5373,
- E-Mail Address
-
tkrutz@ars.usda.gov
- Description
- This modification is to include the below additional information required for the purchase of Genetic Analysis System for DNA and protein sequence analysis using sophisticated algorithms and accelerated computer hardware for fast and effective analysis. 3. Description of Supplies/Services. Said machine must be capable of analysis speeds using programs equivalent to the public domain programs blastx (using default settings found at NCBI), tblastx, and Smith-Waterman (equivalent to tswx) analysis using 1500 or 25 (for tswx) individual sequences with the average sequence size 600 bp or greater against the non-redundant GenBank database of speeds equal or better than 35 minutes, 17 hours, 19 hours (using 25 sequence) respectfully. Parameters for searchers are based on Paracel values and are as follows: blastx -i MatureStem.fasta.txt (provided dataset) -d moira/nr -e 1e-10 -v 200 -b 100 -o blastx.out.1 ?quiet; tblastx -i MatureStem.fasta.txt -d moira/NT -e 1e-10 -v 200 -b 100 -o tblastx.out.1 ?quiet; tswx query=MatureStem.1st25.fasta.txt db="NT.*.rframe" matrix=blosum62 evalue_threshold=1e-10 summaries=200 alignments=100 verbose=pq mhsp=data format=paracel > tswx.out. Hardware must be capable of containing the present entries of the GenBank databases and have enough capacity for anticipate expansion of the databases for the next calendar year. Analysis package should include the following or equivalent programs: Smith-Waterman Smith-Waterman with intron-sensitive double-affine algorithm Smith-Waterman Frame Smith-Waterman Reverse Frame Smith-Waterman Reverse Frame with intron-sensitive double-affine algorithm Smith-Waterman Double Frame Smith-Waterman Double Frame with intron-sensitive double-affine algorithm Needleman-Wunsch BLAST (blastn, blastp, blastx, tblastn, tblastx, phi-blast, megablast) Mass spec Blast Position-specific algorithms: Profile Profile Frame Hidden Markov Model (HMMER) HMM Frame Genomic HMM Frame GeneWise Psi-blast The system should have a user-friendly interface, a results viewer and a filtering package. The USDA, ARS, Mid South Area, Catfish Genetics Research Unit, Stoneville, Mississippi has a requirement for a Paracel GM Target Discovery GeneMatcher 2, Item No. 73100002000 and accessories or equal. This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotations are being requested and a written solicitation will not be issued. Solicitation No. IFB 2003-4431-021 is being issued as an Invitation for Bid. This solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 97-12. Offerors are to provide prices for the following: (1) 1 ea - GM-Target Discovery, Item No. 73100002000, GeneMatcher 2, 3072 processors (1 pipe) System, BlastMachine 2, 10 CPU, Xeon Cabinet, 19" rack, 25U Paracel Blast Software (10 Licenses) including first three year's support; (2) Upgrade to Manager Node, Dual 2.4 Ghz Xeon Processor, 4 ea. 200 GB Hard Drives, 3 Ware RAID Controller Card, 1 ea IDE 20 GB or better System Drive, 2GB RAM, 2U Chassis, CD ROM, LINUX pre-installed; (3) 1 ea., Node, Worker, Dual Xeon 2.4 Ghz, 2 Gb RAM, 60 Gb IDE, 1U chassis Item No. 62300401024; (4) Additional Pipe (3072 processors); (4) Software, 4 ea., Item No. 83100001000, Perpetual License, Paracel Blast, per CPU. Delivery of the equipment shall be made within 60 days after receipt of the contract order and will be delivered to USDA, ARS, CGRU, 141 Experiment Station Road, Stoneville, Mississippi 38776. Price should reflect FOB Destination. Price will include everything identified above. FAR 52.212-1, Instructions to Offerors - Commercial, FAR 52.212-2, Evaluation- Commercial Items; FAR 52.212-3, Offeror Representations and Certifications - 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 apply to this acquisition. These clauses maybe viewed at http://www.arnet.gov/far/ Quotations will be evaluated on price, past performance, and proof of experience with this kind of equipment. Offers should include a list of at least four references to include company name, point of contact, phone number and fax number. References should reflect similar type of work or equipment purchases. Offers to include a commercial warranty for equipment. Offer must include a 30 calendar day acceptance period. Offerors are to be received not later than Close o f Business (4:30 CST), July 21, 2003 at the USDA, ARS, MSA, Contracting Office, 141 Experiment Station Road, P. O. Box 225, 141 Experiment Station Road, Stoneville, MS 38776-0225. The POC for this project is Terry A. Krutz (662) 686-5361.
- Place of Performance
- Address: USDA, ARS, CGRU, 141 Experiment Station Road, Stoneville, MS
- Zip Code: 38776
- Country: USA
- Zip Code: 38776
- Record
- SN00368292-W 20030712/030710213310 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
(may not be valid after Archive Date)
| FSG Index | This Issue's Index | Today's FBO Daily Index Page |