The Lab has licenses and capabilities to utilize the following computational software packages for research:
1. High Performance Computing:
A. AWS: Amazon Elastic Compute Cloud (EC2), allows users to have at their disposal a virtual cluster of computers, available all the time, through the Internet. AWS's virtual computers emulate most of the attributes of a real computer, including hardware central processing units (CPUs) and graphics processing units (GPUs) for processing; local/RAM memory; hard-disk/SSD storage; a choice of operating systems; networking; and pre-loaded application software such as web servers, databases, and customer relationship management (CRM). (https://aws.amazon.com/console/). [Yale University, New Haven, Connecticut, USA, Rothberg Fund (January 1, 2020), USA: Grant/award/project title: “CHEST-AI: AI tool for detection of lung diseases from chest X- ray data”: https://medium.com/tsai-city/kickstarting-healthcare-innovation-with-the-rothberg-catalyzer-prototype-fund-6f5a1f37c5c2 Poster Link, [*2023:1, 4, 9; 2021: 17, 23], [**21, 23, 29, 30], Github, Product.]
Microway Xeon + NVIDIA GPU OctoPuter (with up to 10 GPUs), NumberSmasher Intel Xeon + GPU 4U OctoPuter (Black) Four 2700W (2+2) Redundant Power Supplies, Titanium Level, Two 4th Gen Intel Xeon Scalable processors (LGA-4677 Socket E) Supports up to 350W TDP CPUs (Aircooled), Supports up to 350W TDP CPUs (Liquid Cooled)) * special considerations may be needed for frequency-optimized CPUs, Four Intel UPI interconnects between CPU sockets (up to 16 GT/s), Thirty-two slots for up to 8TB ECC DDR5 4800MHz memory, Dual Integrated Intel X710-AT2 10GbE ports (RJ-45), One slot for AIOM/OCP 3.0 Networking/Fabric Module (via CPU1), Integrated Intel C741 chipset, Integrated ASPEED AST2600 BMC with Graphics Controller, Supports Redfish & IPMI 2.0 w/ Virtual Media, KVM, and Dedicated LAN
Twelve PCI-E x16.0 5.0 slots (or ten double-width and one single-width) (24) Hot-Swap 2.5" drive bays support: Default: eight SATA 6Gbps (via PCH) and eight U.2 NVMe4 bays (four via CPU1; four via CPU2), Optional RAID controllers are , available to enable the remaining drive bays, Internal ports: two M.2 slots (PCIe 4.0 x4 NVMe via PCH), one serial COM header, one TPM header, Rear ports: AIOM-provided ports (optional), two 1G LAN, one IPMI LAN, one VGA, one serial, and two USB 3.0 ports, Front I/O: power button and reset button, Dimensions: 29" D x 7.0" H x 17.2" W, 100 lbs. Includes 25.6" to 33.05" Rackmount Rail Kit (29" chassis depth) (2) Intel Xeon 8480+ 'Sapphire Rapids-SP' 2.0 GHz 56-core CPU - 350W TDP (up to 2 CPU sockets), with two AVX-512 units per core, 105MB L3 Cache, up to 6TB DDR5-4800 memory, up to four 16GT/s UPI links, supports Hyper-Threading, and Turbo Boost up to 3.8 GHz (clock speeds with AVX-512 instructions: x.x - x.x GHz) *special thermal solutions may be required to cool this CPU - please inquire (16) 128GB DDR5 4800 MHz ECC/Registered Memory (2TB Total Memory @ 4800MHz) (2) Kioxia CD6 960GB 2.5" U.2 NVMe4 SSD (5-year ~1 DWPD) (15mm height) PCI-E x4 4.0 NVMExpress 1.4 Interface to System; Supports hot-swap with compatible NVMe backplane, Targeted Lifetime Endurance: ~1 Drive Writes Per Day, Power loss protection (PLP) and end-to-end data correction; Supports Sanitize Instant Erase, Sustained 128 KiB Sequential Read: 5,800 MB/s, Sustained 128 KiB Sequential Write: 1,300 MB/s, Sustained 4 KiB Random Read: 700,000 IOPS, Sustained 4 KiB Random Write: 30,000 IOPS, 2,500,000 hours MTTF (Linux Software RAID1 Mirror recommended) (8) NVIDIA "Hopper" H100 PCI-E+NVLink 80GB ECC Passive GPU Accelerator Card, Supports full-speed PCI-E 5.0 x16 link to host, 128GB/s, Pairs of cards support NVLink3 with 300GB/s in each direction, 600GB/s total (requires bridge kit), H100 GPU chip with NVIDIA passive heatsink (300W-350W TDP, 8-pin CPU connector), Independent INT32, FP32, FP64, and Tensor Cores, 4th-generation Tensor Cores support B1/INT4/INT8/FP16/BF16/TF32/FP64, 80GB High-Bandwidth HBM2e ECC Memory (2TB/s peak bandwidth), Base performance: 26 TFLOPS (FP64), 51 TFLOPS (FP32), TensorCore Performance: up to 51 TFLOPS (FP64), 756 (TF32), 1513 (FP16/BF16), 3026 (INT8), Supports Multi-Instance GPU (MIG) with up to 7 independent GPU instances @ 10GB each, Double PCI-E slot form factor, Compilers, libraries, and tools from NVIDIA HPC SDK: https://developer.nvidia.com/hpc-sdk, Pre-optimized application containers, models, and resources: https://ngc.nvidia.com/ Virtual GPU (vGPU) software support: NVIDIA AI Enterprise for VMware, NVIDIA Virtual Compute Server (12) NVIDIA NVLink Bridge for "Ampere" A40/ A100/A6000 PCI-E+NVLink GPU Accelerator, 2-slot, AIOM 1G Ethernet Dual-Port RJ45 Server Adapter with Intel i350 network controller, Includes Multi-Core Processor Support and Server Virtualization Optimization. Microway Dual Xeon 4th and 5th Gen 2U Server NumberSmasher Dual Intel Xeon 2U 12-bay Compute Server 1200W High-Efficiency "Titanium" Redundant 1+1 Power Supply Up to two 4th Gen Intel Xeon Scalable processors (Socket E, up to 350W) Four Intel UPI interconnects between CPU sockets (up to 16 GT/s) Sixteen slots for up to 4TB ECC DDR5-4800 memory (Up to 4TB Optane Persistent Memory 300 series supported) Networking through I/O Module Integrated Intel C741 chipset and ASpeed AST2600 Graphics Controller IPMI 2.0 w/ Virtual Media, KVM and Dedicated LAN Support PCI-Express expansion slots: Four PCI-E 5.0 x8 full height, helf length Note: pairs of vertically adjacent x8 slots two can be converted to x16 FHFL by deactivating one adjacent x8 slot. 1U heatsinks are required for accommodating FHFL double slot wide GPUs Two PCI-E 5.0 x16 full height, helf length Two PCI-E 5.0 x16 OCP 3.0 Mezzanine Note: some PCIe slots, when active, may disable NVMe capability on up to four drive bays Twelve hot-swap 3.5" NVMe5/SATA/SAS Drive Bays (optional SAS3) Two (optional) rear hot-swap 2.5" NVMe5/SATA/SAS Drive Bays Note: NVMe activation on rear drive bays will disable one PCIe x8 slot or two front NVMe drive bays Two M.2 Slots (PCIe 5.0 x4; form factor 2260/2280) Internal ports: TPM 2.0 header Rear ports: (LAN through I/O Module), one IPMI LAN, one VGA, two USB 3.0, one serial COM port Front I/O: power button, reset button, and UID button Includes 26.5" to 36.4" Rackmount Rail Kit (25.5" chassis depth) (2) Intel Xeon 4510 'Emerald Rapids-SP' 2.4 GHz 12-core CPU - 150W TDP (up to 2 CPU sockets) with two AVX-512 units per core, 30MB L3 Cache, up to 4TB DDR5-4400 memory, up to two 16GT/s UPI links supports Hyper-Threading, and Turbo Boost up to 4.1 GHz (16) 16GB DDR5 4800 MHz ECC/Registered Memory (256GB Total Memory @ 4400MHz) (2) 960GB Micron 7500 PRO 2.5" U.3 NVMe SSD (5-year ~1 DWPD) OCP 2.0 + Opal 2.01 PCI-e Gen4 NVMExpress Interface to System Supports hot-swap with compatible NVMe backplane 3D TLC NAND Internal Solid State Drive Targeted Lifetime Endurance: ~1 Drive Write Per Day, 1752 TBW Built in power-loss data protection Sequential Read: up to 6,800 MB/s Sequential Write: up to 1,400 MB/s Random Read IOPS: up to 1,000,000 Random Write IOPS: up to 145,000 Read Latency: 70µs Write Latency: 15µs 2,000,000 Hours MTBF. [The Department of Defense (DoD), Army Materiel Command (AMC), Grant/award/project title: “HBCU/MI Equipment/Instrumentation grant award" (May 1, 2024- August 31, 2025), Claflin University, Orangeburg, South Carolina, USA. Project officer: William A Creech. Total Award (Direct and indirect costs), Role: PI, Effort=100%, 1.35 person per month release, $410,596. Funding award number (FOA): W911NF23S0014, Grant Program (CFDA) 12.630: Basic, Applied, and Advanced Research in Science and Engineering: Intel Xeon NVIDIA GPU Server for Enhancing Computational Capabilities at Claflin University.]
B. Lenovo ThinkSystem SR250 rack servers:
Base Configuration: 1 × ThinkSystem SR250/SR150 3.5"x4 Chassis 1 × Operating mode selection for: "Efficiency - Favoring Performance Mode", 1 × Intel Celeron G4900 2C+1 54W 3.1GHz Processor, Memory 1 × ThinkSystem 8GB TruDDR4 2666MHz (1Rx8, 1.2V) UDIMM, Storage: 1 × Select Storage devices - no configured RAID, 1 × On Board SATA AHCI Mode, PCI 1 × ThinkSystem SR250/SR150 x8/x8 PCIe Riser, Power ThinkSystem SR250/SR150 Fixed 300W PSU, 1 × 2.8m, 10A/100-250V, C13 to IEC 320-C14 Rack Power Cable ThinkSystem SR250 Refresh Motherboard, ThinkSystem SR250/SR150/SR250 V2 Front VGA Connector Kit v2, ThinkSystem Toolless Friction Rail v2, ThinkSystem EIA Plate with Lenovo Logo, ThinkSystem 1P CPU Entry Heatsink, ThinkSystem SR250/150 Package, ThinkSystem 1x1 3.5" HDD Filler, ThinkSystem SR250 Fan Module, Lenovo Label and ThinkSystem SR250 3.5" Model Number Label, ThinkSystem SR250 Service Label LI, ThinkSystem Intel Label - Celeron Processor (2015), ThinkSystem SR250/SR150 Fixed 300W PSU Kit, ThinkSystem 300W Fixed PSU Caution Label, ThinkSystem SR250 4x3.5" SS BP BKT Kit v2, ThinkSystem SR250 System Label GBM w/o Energy Star, XCC Network Access Label, Feature Enable TPM on MB, ThinkSystem SR250 WW Doc. Security: Enable TPM 2.0 Disable IPMI-over-LAN. [Institutional Development Award (IDeA) Networks of Biomedical Research Excellence (INBRE), Research Education of Teachers SC INRE South Carolina Established Program for Stem Cooperative Research South Carolina Established Program for Stem Cooperative Research (SC EPSCoR), Research Experience for Teachers (RET) ,program (May 1, 2022- August 31, 2022): https://www.furman.edu/integrative-research/education-outreach/research-experience-for-teachers-program/ (******Ms. Etha, Bamberg Ehrhardt High School). Award utilized for configuring computing infrastructure (Lenovo ThinkSystem SR250 rack servers) in the Department of Computer Science for machine learning applications. (Direct costs, Effort=100%), Github, Github]
C. Microsoft Azure:
Microsoft Azure has multiple capabilities such as software as a service (SaaS), platform as a service (PaaS) and infrastructure as a service (IaaS) and supports many different programming languages, tools, and frameworks, including both Microsoft-specific and third-party software and systems. [Microsoft for Startups Founders Hub Azure Credits (May 1, 2022) $25,000 (https://www.microsoft.com/en-us/startups): Grant/award/project title: “CHEST-AI:AI toolfordetectionoflungdiseases from chest X-data”.]
2. Database Installations:
MongoDB: MongoDB is a source-available cross-platform document-oriented database program. Classified as a NoSQL database program, MongoDB uses JSON-like documents with optional schemas. MongoDB is developed by MongoDB Inc. and licensed under the Server Side Public License. (https://www.mongodb.com/)
MySQL: MySQL is an relational database management system. Its name is a combination of "My", the name of co-founder Michael Widenius's daughter, and "SQL", the abbreviation for Structured Query Language. (https://www.mysql.com/)
3. Simulation Studies:
DEVSJava: DEVSJava is a tool set for discrete event modeling and simulation of complex systems. The DEVS (Discrete-Event System Specification) formalism provides an engine for advanced M&S technology to support “virtual build and test.” This formalism has been applied to solving complex problems for over 20 years. DEVSJava provides a powerful environment for the analysis of complex systems. This environment incorporates the information of system structure as well as component behavior in an integration platform. The result is a high flexibility platform to realize hierarchical M&S with various abstraction levels. Capability to implement different system abstractions, and to control problem complexity, gives DEVSJava the power to execute analyses ranging from simple to highly sophisticated. (http://www.ms4systems.com/pages/devsjava.php)
4. Structure analysis:
AutoDock: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Over the years, it has been modified and improved to add new functionalities, and multiple engines have been developed. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. More recently, we developed AutoDock-GPU, an accelerated version of AutoDock4 that is hundreds of times faster than the original single-CPU docking code. (https://autodock.scripps.edu/)
Coot: Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more. (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/)
PyMOL: PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. (https://pymol.org/2/)
MGLTools: Thew MGLTools software suite was developed in the Sanner lab at the Center for Computational Structural Biology (CCRB) formerly known as the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. Navigation portlet on the left has links to downloads, screenshots, documentation section of this website where you can find more information about MGLTools. (https://ccsb.scripps.edu/mgltools/)
Cytoscape: Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store. (https://cytoscape.org/what_is_cytoscape.html)
5. Sequence analysis:
MACS2: A commonly used tool for identifying transcription factor binding sites is named Model-based Analysis of ChIP-seq (MACS). The MACS algorithm captures the influence of genome complexity to evaluate the significance of enriched ChIP regions. Although it was developed for the detection of transcription factor binding sites it is also suited for larger regions. MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used either for the ChIP sample alone, or along with a control sample which increases specificity of the peak calls. (https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html)
GeneMania: GeneMania helps predict functions of genes and gene sets (https://genemania.org/)
QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA): Quickly visualize and understand complex ‘omics data and perform insightful data analysis and interpretation by placing your experimental results within the context of biological systems. (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/)
Geneious: Geneious Prime puts industry-leading bioinformatics and molecular biology tools directly into researchers hands, streamlining sequence analysis and insights. (https://www.geneious.com/)
GeneSpring GX: Agilent's GeneSpring provides powerful, accessible statistical tools for intuitive data analysis and visualization. Designed specifically for the needs of biologists, GeneSpring offers an interactive environment that promotes investigation and enables understanding of Transcriptomics, Genomics, Metabolomics, Proteomics and NGS data within a biological context. (https://www.agilent.com/en/product/software-informatics/genomics-software-informatics/gene-expression/genespring-gx)
Galaxy is a web-based platform for data intensive biomedical research. You can install your own Galaxy by following the tutorial and choose from thousands of tools from the Tool Shed. (https://usegalaxy.org/)
QIAGEN IPA: visualize and understand complex ‘omics data and perform insightful data analysis and interpretation by placing your experimental results within the context of biological systems.
GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis.
Taverna is a domain-independent suite of tools used to design and execute data-driven workflows.
JBrowse: The next generation genome browser. The mission of the JBrowse Consortium is to develop a comprehensive, pluggable, open-source computational platform for visualizing and integrating biological data. (https://jbrowse.org/jb2/)
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AWS Academy Learner Lab: Services available are AWS Academy courses, Amazon SageMaker, Amazon EC2, etc.
