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/)
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
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
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/)
Grow with Google GwG digital skills: Skillshop is a one-stop shop training center for everyone who uses Google professional tools and solutions. Skillshop provides training and education through comprehensive courses to help you shine in your job, transform your business, or land your next big opportunity. The Grow with Google HBCU Career Readiness Program hosts content on Skillshop and features five unique learning paths for students to choose from.
AWS Academy Learner Lab: Services available are AWS Academy courses, Amazon SageMaker, Amazon EC2, etc.
