Attachment 1 - Statement of Work - Customized Computer Workstations.pdf

Statement of Need and Purpose:

The purpose of this acquisition is to purchase five (5) custom-configured, enterprise-class scientific computer workstations that will be used with a new multispectral light sheet microscope, a new confocal imaging cytometer system, and a new epifluorescence slide scanner. The workstations need to be custom configured to support CUDA-optimized acquisition, processing and analysis of multi-TB size fluorescence image datasets.

Background Information and Objective:

NINDS Flow and Imaging Cytometry Core Facility (FICCF) has a need to provide routine use of multispectral 2D and 3D imaging technology to support over 250 basic and clinical research projects in 45 NINDS and other NIH intramural programs. These ongoing research projects rely on the functionality of the customized workstation infrastructure and the software programs that run on the system. Any disruptions to current research workflow would be unacceptable and potentially devastating to ongoing research efforts.

The custom workstations must be compatible with multispectral light sheet, confocal, and epifluorescence slide scanning microscopy systems. The custom-configured scientific computer workstations must be designed to seamlessly integrate with the existing scientific imaging platforms and data acquisition, processing and analysis infrastructure at the NINDS FICCF.

SCOPE OF WORK:

General Requirements:

Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work herein.

Specific Requirements:

System:

Five (5) enterprise-class scientific computer workstations must each include all hardware and software components listed below and the systems must be fully assembled, configured, tested and validated by the vendor. Validation shall include a continuous (i.e.

error-free) 72-hour burn-in onsite at the Core Facility. All five workstations will be clones of each other and shall be able to effectively be used as a mini-cluster for optimally processing multispectral 2D/3D and very large imaging datasets (>100TB), with no

Statement of Work Custom Developed

Scientific Workstations constraints on data bandwidth. The workstations should be configured for the multi-user lab space environment (i.e., small footprint, low noise, low heat, easy storage expansion, user-friendly, and desktop compatible) and not as a rack/server room system. The workstations must have the capability for: (1) processing extremely large (>100 TB) image datasets for collaborative multiplex immunohistology projects allowing optimal transfer, post-acquisition image processing and quantitative image analysis using the scientific computers equipped with optimal CPU/GPU/RAM/SSD/NAS/RAID/CUDA/NAS Machine Learning/Deep Learning hardware and software configuration and custom built to meet the requirement for complex computation; (2) digital slide format processing;

(3) multi-channel fluorescence acquisition; (4) multispectral data, processing, analysis and visualization; and (5) seamless multi-user support.

Seamless Integration:

There is currently an existing infrastructure comprised of 11 customized high-end scientific workstations that support the specialized NIH equipment and research environment. NINDS requires five new enterprise-class scientific workstations, which will increase the capacity and support a new multispectral light sheet microscope, a confocal imaging cytometer, and an epifluorescence slide scanning system. The five new workstations must be custom developed to seamlessly integrate into the existing infrastructure at the Core Facility. The workstations shall efficiently increase the bandwidth in order to effectively accommodate the anticipated increased workload, while still maintaining optimal performance and productivity at the Core Facility. The five workstations must be custom configured to seamlessly integrate with the existing NINDS multiplex immunohistology imaging platform, image acquisition, and data analysis pipeline at the Core Facility. The custom workstations must be fully compatible with multispectral light sheet, confocal, and epifluorescence slide scanning microscopy systems.

Required Hardware and Software Components for each Workstation:

o 1x Phanteks Enthoo 719 (PH-ES719LTG_DAG01) High Performance Full Tower Case o 4x Phanteks - Stackable 3.5" HDD Bracket Duo Pack Cases PH-HDDKT_03 o 7x Noctua Fan NF-A14 PWM 140x140x25mm 4Pin SSO2 Bearing A-Series Blade

Geometry Retail, 3 x Front Intake, 3 x Top Exhaust, 1 x Rear Exhaust o 1x EVGA SuperNOVA 1600 T2 Power Supply, ATX12V/EPS12V - 120 V AC, 230 V AC

Input Voltage - 3.3 V DC, 5 V DC, 12 V DC, 5 V DC, -12 V DC Output Voltage - Modular - 96%, Efficiency - 1600 W o 1x Supermicro H11DSI-NT Server Motherboard - AMD Chipset - Socket SP3 - 2 TB DDR4 SDRAM Maximum RAM - DIMM, RDIMM - 16 x Memory Slots - 2 x USB 3.0 Port - 10 x SATA Interfaces, Dual 10GBase-T LAN Ports, 2 PCI-E 3.0 x16, 3 PCI-E 3.0 x8, 2 USB 3.0 ports, 4 USB 2.0 ports o 1x Supermicro TPM 2.0 module with Infineon 9665, RoHS/REACH, PBF o 2x AMD EPYC 2nd Gen 7742 64-core/128-thread CPUs (a total of 128-core/256-thread dual AMD CPUs/system), 2.25 GHz Processor, 256 MB Cache o 2x Noctua NH-U12S TR4-SP3, Premium-Grade CPU Cooler for AMD sTRX4/TR4/SP3 o 2x Noctua NF-F12 PWM, Premium Quiet Fan, 4-Pin (120mm, Brown), Push Pull on

Coolers o 16x 128GB 8RX4 2666 DDR4 LRDIMM-3DS STD RAM (total of 2TB RAM/system) o 1x 48GB NVIDIA Quadro RTX800 GPU (primary graphics visualization card) o 1x 48GB NVIDIA Quadro RTX800 GPU (dedicated compute graphic card) o 1x 2TB NVMe SSD (Intel DC P4511 or equivalent) - M.2 22110 Internal - PCI Express

3.1 x4 (primary boot SSD) o 1x Intel Tri-Mode PCIe/SAS/SATA RAID Adapter (16 internal ports) 12Gb/s SAS, with Intel RAID Maintenance Free Backup (AXXRMFBU7) o 4x Internal 12G U.2 Cable (Mini SAS HD to U.2, SFF-8643 to SFF-8639) with SATA power, 0.7m, 2ft o 2x Supermicro 55cm OCuLink SFF-8611 (x4) to U.2 SF-8639 with 4 Pin Power Cable o 2x Supermicro Internal iPASS to 4 SATA 64/54/44/34cm with Sideband 64cm Cable o 6 x 15.36TB SSD NVMe (Micron 9300 PRO or equivalent) configured as 92TB RAW data RAID 0 NVMe internal drive (high performance 92TB NVME SSD RAID) o 4 x 32TB SSD SATA (3.5” Micron ExaDrive NL or equivalent) configured as 128TB

RAW data RAID 0 SATA internal drive (temp data storage 128TB SATA SSD RAID) o 1x 10GbE NAS UNIT - 160 TB RAW, Synology NAS DS3617xs 12Bay Xeon D-1527

16GB DDR4 USB3.0, Diskless NAS, Noise Level: 22.3 dB(A) o 2x 16GB Synology Memory Module DDR4 2666 MHZ ECC RAM 16GB o 1x Synology AC E10G18-T2 10GbE Ethernet Adapter 2 x RJ45 ports o 2x 960GB Intel SSD D3-S4610 2.5 SATA 6Gb/s 3D2 TLC (cache drives) o 10x Toshiba HD MG08ACA16TE 3.5 16TB SATA ES 72 256M 6Gb/s 512E Enterprise

Drives (install, configure & test as RAID 6 128TB NAS with 32TB for data protection) o 2x Tripp Lite USB 3.0 Hub SuperSpeed 10-Port USB-A Compact 20kV ESD Industrial o 1x 32-inch 8K monitor o 1x wired backlit keyboard o 1x wireless mouse o 1x Windows 10 Enterprise 64-bit, installed and validated

Configurations of internal SSD and external NAS drives:

The above listed SSD and NAS drives are to be installed and configured as follows:

o 1x 2TB SSD NVMe to be connected to the M.2 (JMD1): DC P4511 2 TB SSD (primary boot SSD) o 4 x 15.36TB SSD NVMe to be connected to the Tri-Mode RAID card: 4 x 15.36TB

NVME SSD (utilizing all ports on the RAID controller) o 2 x 15.36TB SSD NVMe to be connected to the onboard oculink ports P2-NVME1 and P2_NVME0 (utilizing all onboard NVME ports) o 4 x 32TB SSD SATA to be connected to the onboard SATA ports CPU1-SATA0-3 (with 6 additional SATA ports available: CPU2-SATA0-3, P2-SATA0 and P2-SATA1) o All 6 x 15.36TB NVMe SSDs are to be software configured as one internal RAID 0 NVMe high performance data processing drive with 92TB storage capacity.

o All 4 x 32TB SATA SSDs are to be software configured as a separate internal RAID 0 SATA temp data drive with 128TB storage capacity.

o 1x 10GbE NAS UNIT - 160TB RAW to be installed into Synology NAS DS3617xs 10GbE disk array external unit consisting of 10x 16TB Toshiba MG08ACA16TE 3.5 SATA HDDs (main storage drives) and 2x Intel SSD D3-S4610 960GB 2.5 SATA 6Gb/s 3D2 TLC (cache drives) and connected to the custom workstation as configured above using 10GbE LAN. After configuring the NAS as RAID 6 disk array, 128TB usable space will be dedicated for data storage and 32TB space for data protection

Workstation System Software Compatibility:

Each system must be compatible with Windows 10 Enterprise 64-bit OS and be optimally configured to support custom development of complex CUDA-enabled machine learning and deep learning algorithms to allow high-end processing, analysis and visualization of very large (>100TB) 2D/3D image datasets using the following scientific software:

• Adobe Creative Cloud Software (https://www.adobe.com/creativecloud.html)

• Aivia (https://www.drvtechnologies.com/aivia)

• Arivis Vision4D (https://www.arivis.com/en/imaging-science/arivis-vision4d)

• Bitplane Imaris (https://imaris.oxinst.com/applications/fluorescence-microscopy)

• FIJI/ImageJ (https://en.wikipedia.org/wiki/Fiji_(software))

• Indica Labs Halo (https://indicalab.com/halo/)

• Matlab (https://www.mathworks.com/products/matlab.html)

• MBF Bioscience (https://www.mbfbioscience.com/products)

• Microvolution (https://www.microvolution.com/)

• syGlass (https://www.syglass.io/)

• Zeiss ZEN (https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html)

• ThermoFisher HCS Studio (https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/hcs-studio-2.html)

Image file formats that need to be fully supported on this system must include BigTIFF, JP- 2000, DICOM, CZI and Adobe PSB with no restriction on input image channels or image size.

https://www.adobe.com/creativecloud.html https://www.drvtechnologies.com/aivia https://www.arivis.com/en/imaging-science/arivis-vision4d https://imaris.oxinst.com/applications/fluorescence-microscopy https://en.wikipedia.org/wiki/Fiji_(software) https://indicalab.com/halo/ https://www.mathworks.com/products/matlab.html https://www.mbfbioscience.com/products https://www.microvolution.com/ https://www.syglass.io/ https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/hcs-studio-2.html https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/hcs-studio-2.html

Delivery:

The 5 Workstations shall be delivered within 30-60 days ARO. The workstations must be fully assembled, tested and validated (including a minimum burn-in time for 72 hours to verify the systems are working) within 10 days from delivery.

Delivery must be Freight on Board (FOB) destination, include inside delivery, and be coordinated with the Contracting Officer’s Representative (COR) prior to shipment. The equipment shall be delivered between the hours of 8:00am and 5:00pm, Bethesda, MD, local prevailing time, Monday through Friday. Delivered to Building 10, Room 5S241, Bethesda, MD 20892.

Payment Schedule:

Payment Deliverable 100% Configuration, Assembly, Delivery, and Validation (including 72-hour burn-in) for all 5 workstations

Warranty:

The contractor shall provide a 36-month warranty on each of the five workstations, including all parts and labor, which shall begin once the workstations are set up and the operating system and installed components have been tested and validated for a minimum of 72-hour successful burn-in at the Core Facility. Individual components may have varying manufacturer warranties; however, the contractor must provide a minimum 36-month warranty for each component. Contractor shall provide on-site services at the Core Facility for any required replacement components due to malfunctions, and warranty shall include all travel, parts and labor.