SPECIAL NOTICE
66 -- Notice of Intent to Sole Source NGS Computer Workstation
- Notice Date
- 1/18/2017
- Notice Type
- Special Notice
- NAICS
- 541512
— Computer Systems Design Services
- Contracting Office
- Department of the Army, U.S. Army Medical Research Acquisition Activity, U.S. Army Medical Research Acquisition Activity, Attn: MCMR-AAA, 820 Chandler Street, Frederick, MD 21702-5014, Maryland, 21702-5014, United States
- ZIP Code
- 21702-5014
- Solicitation Number
- W81XWH-17-T-0080
- Archive Date
- 2/18/2017
- Point of Contact
- Wanda D. King, Phone: 3016192376
- E-Mail Address
-
wanda.d.king.civ@mail.mil
(wanda.d.king.civ@mail.mil)
- Small Business Set-Aside
- N/A
- Description
- NOTICE OF INTENT TO SOLE SOURCE 1. Solicitation Number: W81XWH-17-T-0080 2. Sole Source Title: Computer Workstation for next generation sequencing (NGS) data and genomic sequences associated bioinformatics tasks Certified: Puget Peak Quad Xeon Tower. 3. Agency: U.S. Army Medical U.S Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 4. Contracting Office: U.S. Army Medical Research Acquisition Activity (USAMRAA), Fort Detrick, Frederick, MD 5. Location: Fort Detrick, Frederick, MD 6. Description: The U.S. Army Medical Research Acquisition Activity (USAMRAA) intends to award a sole source Firm-Fixed Price supply contract to Puget Sound Systems, Inc. located at 2707 W. Valley Highway N., Auburn, WA 98001-1614 including DUNS 128267585 and CAGE Code 31YA3. The statutory authority permitting the acquisition of this requirement by other than full and open competition is 41 U.S.C. 1901. The Federal Acquisition Regulation (FAR) citation is 13.106-1(b)(1)(i), and the FAR citation title is "Only one source reasonably available" to include brand name. 7. Background: The U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) has an outstanding national reputation to protect both the Military personnel and civilians from the threat of infectious diseases. USAMRIID plays a vital role in the status of the country's preparedness for biological terrorism and biological warfare and is known the birthplace of medical biodefense operating containment laboratories with extensive training and consultation to other agencies in establishing their own facilities. The requirement is for a Computer Workstation for NGS as a requirement for the purpose of intent to sole source under one requirement. The Computer Workstation for NGS is specifically the system must be able to process large volumes of next generation sequencing data and genomic sequences, as well as myriad associated bioinformatics tasks and will include a three (3) year hardware and /or parts warranty. 8. Scope and Purpose: This requirement is combined with Supermicro X10QBL-4CT, 4 x Intel Xeon E7-8867 V4 2.4 GHz Eighteen Core 45MB 165W, 32 x Samsung DDR4-24-32GB ECC Reg., EVGA FeForce GRTX 950 2GB Sc, Silverstone USB 3.0 PCI-Express Card, Western Digital RE 2TB SATA 6Gb/s, Asus 24 x DVD-RW SATA (Black), Rosewill Blackhawk Ultra, EVGA SuperNOVA 1600W P2 Power supply, 4 x Corsair Hydro Series H60 CPU Cooler (Rev. 2), Peak Quad E7 Xeon Quiet cooling Package, Ubuntu 16.04 LTA with Unity Desktop Installation (64-bit) Limited Support, and Warranty Lifetime labor and Tech Support, 3 Year Parts. Included to have the following Minimum Essential characteristics that are essential to the requirement for USAMRIID: Minimum Essential Characteristics (MECS) For Puget Peak Quad Xeon Tower DSD requires a computer workstation for computationally intensive bioinformatics tasks. Specifically, the system must be able to process large volumes of next generation sequencing (NGS) data and genomic sequences, as well as myriad associated bioinformatics tasks. NGS allows for the sequencing of billions of base pairs (bp) by massively parallel short or long read strategies and technologies. The minimum characteristics of a system to process such information include: -Must have at least 72 64-bit instruction set CPU cores with a minimum base frequency of 2.3GHz per core on a single motherboard. -Must have at least 1TB total DDR4 RDIMM RAM with a minimum clock speed of 2133 MHz -Must have three 2TB hard drives (HDDs) with a disk speed of at least 7.2K RPM. -Must have at least one RJ45 port with 10Gbps networking capability. -Must have an internal SATA DVD+/-RW optical drive. -Must have internal cooling capability. -Must have a 3-year hardware and/or parts warranty. Supporting Information The system described is designed to accomplish computationally intensive bioinformatics tasks. Software that currently requires this hardware includes: - Kraken: a whole-genome NGS read metagenomics classifier that uses a hash table of genome sequence k-mers to classify query sequences by taxon. Building and indexing a k-mer hash table requires significant RAM size proportional to the size of the sequence database it is built from. After the database is preloaded into RAM, requiring sufficient RAM size and clock speed to accommodate the database, the Kraken classification procedure also requires as many parallel CPU cores to classify millions of NGS reads. The standard Kraken database (bacteria, archaea, and viruses) requires 75GB of RAM, however, including other essential database subsets (fungi, human, non-human primate, mouse, and other mammalian model organisms) can easily achieve a database >250GB. Functional testing of building a large database from publicly-available genome sequences on a cloud server with 244GB of RAM fails to meet the minimum RAM requirements for the build, necessitating designated hardware. In addition, genome sequences for building the database are typically gathered from NCBI's RefSeq database, but larger and more comprehensive collections, such as NCBI's GenBank, are necessary for diagnostic and exploratory purposes. As more genome sequences become publicly available, the computational requirements to run Kraken will increase as well. For more details, see the Kraken user manual at http://ccb.jhu.edu/software/kraken/MANUAL.html#system-requirements. -BWA/Bowtie/Bowtie2/etc.: NGS read mappers that build an FM-index of reference sequences from which to align query sequences. Like Kraken, building an index/database for BWA/Bowtie requires RAM space proportional to the size of genome sequences provided. In addition, the BWA/Bowtie index must also be loaded into RAM during mapping. These NGS read mappers are used for single genomes as well as metagenomes, the latter of which has similar requirements to other extremely computationally intensive metagenomics classifiers. -SPAdes/IDBA_UD/SSAKE/etc.: de novo genome and metagenome assembly software. Although no index, database, or reference is required to build, de novo assembly involved the creation of large and complex de Bruijn graphs or large k-mer hash tables in order to construct contigs from NGS reads. Without predefined databases, the RAM requirements depend greatly on the information complexity of the sample. Metagenomes are many fold more complex than single genomes, requiring tens to hundreds of gigabytes of RAM to complete assembly. In light of these software requirements and additional operating requirements, each characteristic is justified for the following reasons: A. Must have at least 72 64-bit instruction set CPU cores with a minimum base frequency of 2.3GHz per core on a single motherboard: Parallelization of bioinformatics algorithms is essential to ensuring that tasks complete in a timely manner. Typically, the data being processed is large, the task is computationally complex, or both of these factors are compounded. Without the totality of CPU cores designated to a single process, said process can take hours to days to complete, in turn significantly slowing down a pipeline with many components and numerous samples in queue. The CPU cores must share the same motherboard to ensure optimal task distribution and speed of processing. A system that is unable to maintain normal CPU operating temperatures (typically controlled by internal cooling hardware) specified by the CPU manufacturer under full load (all cores) does not fulfill this requirement. B. Must have at least 1TB total DDR4 RDIMM RAM with a minimum clock speed of 2133 MHz: The NGS and metagenomics software described above operate in memory. Not only is size of available RAM an issue, but RAM speed is essential as data is written and rewritten within memory and between memory and the disk. 1TB or greater total RAM ensures that no planned computational experiments will be unable to complete due to insufficient RAM, while current DDR4 RAM technology ensures that information is moved and stored in short term at rates that support reasonable speed of execution of RAM-intensive bioinformatics software. C. Must have three 2TB hard drives (HDDs) with a disk speed of at least 7.2K RPM: NGS data files typically range in the hundreds of megabytes to tens of gigabytes, the system's physical storage must be capable of holding all of the files being processed. In addition, NGS read mappers and metagenomics classifiers build databases/indexes ranging into the hundreds of gigabytes. - Must have at least one RJ45 port with 10Gbps networking capability: Large files or batches of files exceeding hundreds of gigabytes in size, such as NGS data files and genome sequence databases, will need to be transferred to the workstation, requiring a high-speed link between the source and workstation. - Must have an internal SATA DVD+/-RW optical drive: Initial operating system (OS) installation and subsequent troubleshooting is most easily achieved via a DVD containing the installation packages to fix a broken OS. - Must have internal cooling capability: The system must be able to handle high thermal output with internal cooling hardware during computation using all CPU cores. This can include fan/heatsink or fan/liquid-cooling combination units that sit atop each CPU in order to maintain CPU temperature under full load to within the CPU manufacturer's operating guidelines. - Must have a 3-year hardware/parts warranty: Computationally-intense bioinformatics put physical strain on a system's hardware. A hardware/parts warranty within the minimum relevant lifespan of the system is necessary to ensure that its components are protected in the event that they fail under normal operation. 9. North American Industry Classification System (NAICS) Code: The NAICS code for this requirement is 541512 size standard $27.5M, Computer Systems Design Services. 10. Anticipated Period of Performance: The anticipated period of performance is delivery plus a 36-month standard warranty. 11. Information to Industry: This Notice of Intent to Sole Source is for informational purposes only in accordance with (IAW) Federal Acquisition Regulation (FAR) 5.201 and not a request for competitive proposals. Therefore, no solicitation document exists for this requirement. Interested parties should submit a Capability Statement and pricing information for this requirement within fifteen (15) days of public notice to be considered by the Government. A determination to compete the proposed contract based upon responses to this notice is solely within the discretion of the Government. Responses received will be considered solely for the purpose of determining whether to conduct a competitive requirement. 12. Response Due Date: Interested vendors should submit the Capability Statement in response to this Notice of Intent to Sole Source electronically by 10:00 A.M. (EST) 03 Feb 2017 via e-mail to the Contract Specialist, Ms. Wanda King, at wanda.d.king.civ@mail.mil. No phone calls will be accepted. 13. Notice Closes: This Notice of Intent to Sole Source closes on 03 February 2017 at 10:00 A.M. (EST). 14. Questions Closing Date: Questions to address this requirement shall be in no later than 27 January 2017 at 10:00 A.M. (EST). 15. Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in response to this notice. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s). I attest that the aforementioned details are complete, accurate and this Notice of Intent is prepared to the best of my ability. //Signed// Wanda King Contract Specialist
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/USA/USAMRAA/DAMD17/W81XWH-17-T-0080/listing.html)
- Place of Performance
- Address: USAMARIID, 1425 Porter Street, Fort Detrick, Maryland, 21702, United States
- Zip Code: 21702
- Zip Code: 21702
- Record
- SN04373782-W 20170120/170118234157-e5929cf9e8df4718a32a89f4c2a1f1d9 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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