MODIFICATION
70 -- Laboratory Information Management System
- Notice Date
- 7/14/2015
- Notice Type
- Modification/Amendment
- NAICS
- 334614
— Software and Other Prerecorded Compact Disc, Tape, and Record Reproducing
- Contracting Office
- Agricultural Research Service - Plains Area
- ZIP Code
- 00000
- Solicitation Number
- AG-6538-S-15-0051
- Archive Date
- 8/1/2015
- Point of Contact
- Donita J. Furman, Phone: 402-762-4145
- E-Mail Address
-
donita.furman@ars.usda.gov
(donita.furman@ars.usda.gov)
- Small Business Set-Aside
- Total Small Business
- Description
- The Agricultural Research Service, U.S. Meat Animal Research Center, is looking to replace our current Laboratory Information Management System (a heavily customized instance of MiniLims from BioTeam, Inc) as it is no longer supported and the large number of samples we produce has led to performance issues with this system. The replacement LIMS system should have similar flexibility in terms of ability for the system administrator to make minor customizations (e.g., changing the possible values for a restricted field) without requiring vendor support. Key features of the MiniLims installation include managing and integrating data and metadata (including sample provenance and output from bioanalytical instrumentation) associated with samples, semi-automated annotation of microbial genomes (currently MiniLims calls the DIYA annotation tool and runs it on user-defined assemblies) including production of GenBank-ready files, and open source components such that the code can be modified or enhanced by ARS (for example by API) without mandatory participation of the vendor. The procurement requests customization (if required) to extend our current capability by including output from the OmniLog bacterial phenotyping system from Biolog Inc., to include run definition for pre-defining instrument runs, and real-time monitoring of the instrument to record run data and associate it with the strains and metadata associated with those strains. Additional customization to support recording of samples for metabalomics and proteomics through existing UPLC/Mass Spec instruments is requested. The LIMS also needs to perform real-time monitoring of next-generation sequencing platforms (MiSeq, NextSeq, and RSII) to record completed runs and associate run data with sequencing libraries, the DNA samples from which the libraries were made, the biological material from which the DNA was derived, and metadata associated with that biological material (bacterial or animal tissue), using traceable parent-child relationships. The ability to record user-input Minimum Information about Genomic Sequence (MIGS), and Minimum Information about Metagenomic Sequence (MIMS) data is critical, with enforced syntax that conforms to international standards. The system will be able to handle sample types that are not necessarily slated for sequencing or bacterial phenotyping (e.g., samples to be run for Proximate Analysis will be entered into the system, with capability to note analyses performed and their performance dates; but monitoring of the equipment or generation of machine instructions is not required). The vendor will assume responsibility for installation of the system, customizing for activities specified here, porting the data currently in MiniLims, into the appropriate database structures of the new LIMS, and training staff to use the system, as part of this procurement. We desire the LIMS to be capable of generating instructions (runsheets for PacBio and OmniLog; samplesheets for illumina) to post directly to the instruments through the network infrastructure, so that sequencing runs are pre-entered into the LIMS with enforced consistency and there is no need to re-enter data on the instruments themselves. This procurement will be awarded in phases as funds become available. Funds are currently available for the beginning phases. As phases are completed, payment will be made to the contractor. Purchase orders for additional phases will be signed as the need arises and funding becomes available. Please note, however, the entire scope of the project will be used as the evaluation criteria for the award. Selection criteria will include 1) ease of: data input, small administrator-level customizations, tracing of samples from animal, cell culture, or environmental source through to sequence or OmniLog data, and query of the LIMS database to generate reports about samples, instruments, and instrument runs. 2) ability to handle large (hundreds of thousands) of samples 3) total cost of ownership (annual subscription versus ownership of software) SAM: Vendor must be registered in the System for Award Management prior to the award of the contract. You may register by going to www.sam.gov. You will need to your Tax ID, Duns Number, Bradstreet number and banking information. PAYMENT: Any award made under this solicitation is subject to 31 CFR Part 208 which requires all payments made by the government to be made by electronic funds transfer. Please note on your proposal if you will accept a government purchase (VISA) card. All sources wishing to provide a quotation must respond by 3:00 PM, July 17, 2015. Quotations should be addressed to USDA Agricultural Research Service, State Spur 18D Bldg 1, Clay Center, NE 68933. POC - Donita Furman, Contracting Officer, 402-762-4145. The quotations can be faxed to 402-762-4148 or emailed to donita.furman@ars.usda.gov. All responses will be evaluated to determine the company's capability to meet the above requirements. The Government shall award a contract resulting from this solicitation to the responsive/responsible offeror whose offer conforming to the solicitation will be most advantageous to the Government per FAR 13.106-2. Applicable Provisions: The following Federal Acquisition Regulation (FAR) and the Department of Agriculture Acquisition Regulation (AGAR) provisions and clauses apply to this acquisition: FAR 52.204-7 System for Award Management: AGAR 452.204-70 Inquiries; FAR 52.209-6 Protecting the Government's Interests when Subcontracting with Contractors Debarred, Suspended or Proposed for Debarment; FAR 52.212-1 Instructions to Offers-Commercial Items; FAR 52.212-2 Evaluation-Commercial Items (filled in as follows: Technical specifications/support, and price); FAR 52.212-4 Contract Terms and Conditions-Commercial Items; FAR 52.212-5 Contract Terms and Conditions Required to Implement Statutes of Executive Orders-Commercial Items; AGAR 452.219-70 Size Standard and NAICS Code Information; FAR 52.222-3 Convict Labor; FAR 52.222-19 Child Labor - Cooperation with Authorities and Remedies; FAR 52.222-21 Prohibition of Segregated Facilities; FAR 52.222-26, Equal Opportunity Employment; FAR 52.222-36 Affirmative Action for Workers with Disabilities; FAR 52.222-50 Combating Trafficking in Persons; FAR 52.223-18 Encouraging Contractor Policy to Ban Text Messaging While Driving; FAR 52.225-13 Restrictions on Certain Foreign Purchases; FAR 52.225-25 Prohibitions on Contracting with Entities Engaging in Certain Activities or Transactions Relating to Iran-Reps and Certs; FAR 52.232-33 Payment by Electronic Funds Transfer-Central Contractor Registration; FAR 52.233-3 Protest After Award; FAR 52.233-4 Applicable Law for Breach of Contract; FAR 52.252-1 Solicitations Provisions Incorporated by Reference; FAR 52.252-2 Clauses Incorporated by Reference. 52.232-18 -- Availability of Funds. Availability of Funds (Apr 1984) Funds are not presently available for this contract. The Government's obligation under this contract is contingent upon the availability of appropriated funds from which payment for contract purposes can be made. No legal liability on the part of the Government for any payment may arise until funds are made available to the Contracting Officer for this contract and until the Contractor receives notice of such availability, to be confirmed in writing by the Contracting Officer.
- Web Link
-
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- Place of Performance
- Address: State Spur 18D Bldg 1, Clay Center, Nebraska, 68933, United States
- Zip Code: 68933
- Zip Code: 68933
- Record
- SN03796093-W 20150716/150714235303-a4b69867c356321f38c6a03f1fdd2805 (fbodaily.com)
- Source
-
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