MODIFICATION
70 -- Integration of Ayrris Large Appliance and LIMS 24/7
- Notice Date
- 3/10/2014
- Notice Type
- Modification/Amendment
- NAICS
- 541511
— Custom Computer Programming Services
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- NIH-HHS-NHLBI-CSB-(HG)-2014-085-DLM
- Archive Date
- 3/27/2014
- Point of Contact
- Dorothy Maxwell, Phone: 301-435-0352
- E-Mail Address
-
maxwelld@mail.nih.gov
(maxwelld@mail.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- INTRODUCTION: The National Institute of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI) Office of Acquisition (OA) on behalf of the National Human Genome Research Institute, (NHGRI), intends to negotiate and award a purchase order on a noncompetitive sole source basis to Appistry Inc., 1141 South 7th Street, Suite 300, St. Louis, MO 63104 to procure the following: **CHANGES/CORRECTIONS HAVE BEEN MADE UNDER PROCUREMENT AND PERIOD OF PERFORMANCE. THIS IS A FOLLOW-ON REQUIREMENT IT SECURITY PROVISIONS AND 508 COMPLIANCE LANGUAGE IS ALREADY OBTAINED FROM PREVIOUS CONTRACT. Procurement : 1. Ayrris Large Appliance (software only) Annual contract; 2. Two-Year (24-Months) managed hosting of Ayrris on up to 512 Nodes; 3. UDP Pipeline Development and Integration of Pipeline with RURO LIMS 24/7. BACKGROUND : The National Institutes of Health (NIH) is the nation's leading medical research agency and the primary Federal agency conducting and supporting medical discoveries that improve people's health and save lives. The National Human Genome Research Institute (NHGRI), National Institutes of Health Undiagnosed Disease Program (UDP) is a trans-National Institute of Health (NIH) initiative that focuses on the most puzzling medical cases referred to the NIH Clinical Center in Bethesda, MD. It was organized by the National Human Genome Research Institute (NHGRI), the NIH Office of Rare Diseases Research (ORDR) and the NIH Clinical Center. Many medical specialties from other NIH research centers and institutes contribute the expertise needed to conduct the program, including endocrinology, immunology, oncology, dermatology, dentistry, cardiology and genetics, among the dozens of participating senior attending physicians. A longstanding medical condition that eludes diagnosis by a referring physician can be considered undiagnosed and may be of interest to this clinical research program. identified new and rare diseases. Genomic DNA will be isolated from all admitted Undiagnosed Diseases patients and family members. Depending on the phenotype of the patient, these DNA samples will be sent for exome sequencing as the first step to obtain variant information that may determine the mechanism of the patients' disease. The Undiagnosed Diseases Laboratory will perform extensive analyses on the large amount of exome sequencing and variant data that is generated in a timely manner to facilitate genetic studies when combined with SNP analysis. This information will then be used to perform research experiments to discern the genetic and molecular basis of 4 the unique disease of the patient. OBJECTIVES: Appistry Ayrris has been integrated with the RURO LIMS 24/7 system that allows for a continuous pipeline that makes collecting, storing, managing and routing data simple, reliable and efficient. This has enabled the NIH UDP laboratory to establish and maintain a full change of custody for samples and associated data across the experimental life cycle, standardize physical and digital processes to achieve compliance with specific regulations, and create production-grade workflows necessary for the laboratory. They have executed the NIH UDP Diploid-Alignment Pipeline on Ayrris and integrated this pipeline within LIMS 24/7 that allows users to monitor the progress of the pipelines without requiring detailed knowledge of how the pipeline is executing. Appistry has currently developed this pipeline in collaboration with the NIH UDP and will continue to perform these analyses with the UDP next-generation data that is generated by sequencing UDP patient exomes. PERIOD OF PERFORMANCE : Twenty-Four (24) months from the date of award. JUSTIFICATION : In a previous contract award, Appistry integrated Ayrris and LIMs24/7 to allow the laboratory to turn workflows into a continuous pipeline that has made collecting, storing, managing, and routing data simple, reliable, and efficient. Integrating the LIMS with a robust big-data environment has enabled the UDP laboratory to establish and maintain a full chain of custody for samples and associated data across the experimental life cycle, standardize physical and digital processes to achieve compliance with regulations such as CLIA, HIPAA or Safe Harbor, and create production-grade workflows necessary for running defined lab workflows at scale. Additionally, Appistry has executed the NIH UDP Diploid-Alignment Pipeline on Ayrris and integrated it with the Ruro LIMS 24/7. Appistry has successfully tested running the Diploid-Alignment Pipeline on Ayrris in Appistry's St. Louis datacenter with execution times taking approximately 26 hours on 100 CPU-cores. This pipeline consists of two phases with the first phase run per individual, and the second phase run per trio or cohort. The Broad Institute GATK Best Practices are followed where appropriate along with extensive parallel executions of time-intensive steps such as alignment, base quality score recalibration, and variant calling. Appistry has also implemented the pipeline within LIMS24/7 by creating two subject workflows corresponding to the two phases of the pipeline. During their pipeline execution on Ayrris, the respective LIMS24/7 subjects are updated automatically through Ayrris-LIMS24/7 API calls to reflect their movement through the workflows. This enables a LIMS24/7 user to monitor the progress of the pipelines without requiring detailed knowledge of how the pipeline is executing. The current contract will allow the use of Appistry Ayrris to align, genotype, and annotate next generation sequencing short reads from 600 individuals consented to the NIH UDP research protocol. They will be doing this using the NIH UDP Diploid-Alignment pipeline that has been developed in collaboration with the NIH UDP. REGULATORY AUTHORITY: This acquisition is conducted under the authority of 41 U.S.C. 253(c) as set forth in FAR Part 6.302-1, only one responsible source and no other supplies or services will satisfy agency requirements. ADDITIONAL INFORMATION: Industry Classification (NAICS) Code is 541511, Custom Programming Services, small business size standard is $25.5M.. The acquisition is being conducted under FAR Part 13, simplified acquisition procedures, therefore the requirements of FAR Part 6 B Competitive Requirements are not applicable (FAR Part 6.001). The resultant Contract will include all applicable provisions and clauses in effect through the Federal Acquisition Circular (FAC) 05-72 (January 30, 2014). This synopsis is not a request for competitive proposals. However, interested parties may identify their interest and capability to respond to this notice. Responses to this notice shall contain sufficient information to establish the interested parties' bona-fide capabilities for fulfilling the requirement and include: unit price, list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov." A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. The information received will normally be considered solely for the purposes of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement. All responses must be received by March 12, 2014 and must reference synopsis number HHS-NIH- NHLBI-CSB-(HG)-2014-085-DLM, may be submitted to the National, Heart, Lung and Blood Institute, Office of Acquisition, COAC Services Branch, 6701 Rockledge Drive, Suite 6149, Bethesda, Maryland 20892-7902, Attention: Dorothy Maxwell. Response may be submitted electronically to maxwelld@mail.nih.gov. Faxes will not be accepted. Responses will only be accepted if dated and signed by an authorized company representative. "All responsible sources may submit a bid, proposal, or quotation which shall be considered by the agency."
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NHLBI/NIH-HHS-NHLBI-CSB-(HG)-2014-085-DLM/listing.html)
- Place of Performance
- Address: NIH, Building 50, Rockville, Maryland, 20852, United States
- Zip Code: 20852
- Zip Code: 20852
- Record
- SN03306846-W 20140312/140310235229-0150ae2a9e4460d24febb10d59f60a45 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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