Available Scientific Software

The following list is the supported software on GSU’s HPC resources.  Additionally, some of the licensed software may be downloaded on individual PC/Mac.  For a list of licensed software that is available to faculty/staff/student, visit IS&T Software page.

Abinit is a computing program that allows users to calculate properties of systems made of electrons and nuclei, including total energy, charge density, and electronic structure. Using various molecular theories, Abinit can also perform molecular dynamics simulations, generate dynamical matrices, compute excited states, and more. Abinit is a collaboration focused tool, and allows for the modification of coding and programing to suit your needs and the needs of your project.

Abinit is available on the following HPC resources: VELA

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.

Software used on the following HPC resources: CARINA

AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multiple method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP.

Software used on the following HPC resources: VELA and CARINA

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Software used on the following HPC resources: VELA

DOCK addresses the problem of "docking" molecules to each other. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes. Historically, the DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years.

Software used on the following HPC resources: VELA

EnginFrame is the most advanced, commercially supported Grid Portal in the industry, and has a proven track record of successful production deployments within corporate networks and research Grids. EnginFrame enables efficient Inter-/Intranet access to Grid-enabled infrastructures. HPC clusters, data, licenses, batch & interactive applications can be accessed by any client using a standard browser.

Software used on the following HPC resources: CARINA

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are:
•  Import of data from BAM, SAM or FastQ files (any variant)
•  Providing a quick overview to tell you in which areas there may be problems
•  Summary graphs and tables to quickly assess your data
•  Export of results to an HTML based permanent report
•  Offline operation allows automated report generation without running the interactive application

Software used on the following HPC resources: VELA

Gaussian is an electronic structure program, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).

Software used on the following HPC resources: CARINA and VELA

Gromacs is a high performance program used to compute molecular dynamics. Gromacs focuses on calculating biochemical molecules like proteins, lipids, and nucleic acids that contain complicated bonded interactions. However, Gromacs’ efficient and speedy calculations also lend well to non-biochemical molecules.

Gromacs is available on the following HPC resources: VELA

Application for technical computing and model-based design. Core products are MATLAB® for mathematical calculations, analyzing and visualizing data, and writing applications; and Simulink® for modeling and simulating complex dynamic systems.

Georgia State has negotiated with The MathWorks, Inc. for a Total Academic Headcount (TAH) Campus License Agreement. The TAH Campus License provides access to MATLAB standard configurations and a set of additional products available to any faculty, staff and student of Georgia State. More information on how to start using the campus-wide MATLAB license.

Matlab on Linux high-performance research cluster, MATLAB and MATLAB Distributed Computing Server

Software used on the following HPC resources: VELA

Tivoli Workload Scheduler LoadLeveler is a parallel job scheduling system that allows users to run more jobs in less time by matching each job’s processing needs and priority with the available resources, thereby maximizing resource utilization. LoadLeveler also provides a single point of control for effective workload management and supports high availability configurations. In addition, it offers detailed accounting of system utilization for tracking or chargeback.

Software used on the following HPC resources: CARINA

Platform LSF is the most powerful workload manager for demanding, distributed and mission-critical high performance computing environments. It provides a complete set of workload management capabilities; all designed to work together to address your high performance computing needs.

Software used on the following HPC resources: VELA

Almost any workflow involves computing results, and that’s what Mathematica does—from building a hedge fund trading website or publishing interactive engineering textbooks to developing embedded image recognition algorithms or teaching calculus.

Mathematica is renowned as the world’s ultimate application for computations. But it’s much more—it’s the only development platform fully integrating computation into complete workflows, moving you seamlessly from initial ideas all the way to deployed individual or enterprise solutions.

Software used on the following HPC resources: VELA

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Software can be found on the following HPC resources: CARINA

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

NWChem software can handle:
•  Biomolecules, nanostructures, and solid-state
•  From quantum to classical, and all combinations
•  Gaussian basis functions or plane-waves
•  Scaling from one to thousands of processors
•  Properties and relativity

Software used on the following HPC resources: VELA

BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. The user specifies a statistical model, of (almost) arbitrary complexity, by simply stating the relationships between related variables. The software includes an ‘expert system’, which determines an appropriate MCMC (Markov chain Monte Carlo) scheme (based on the Gibbs sampler) for analysing the specified model. The user then controls the execution of the scheme and is free to choose from a wide range of output types.

Software used on the following HPC resources: VELA

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

Software used on the following HPC resources: VELA

SAS helps solve next-generation business problems with market-leading business analytics solutions. Through advancements in high-performance computing, improvements in environment management, enhancements in data management, and expanded analytics capabilities to better manage and process “big data,” SAS software’s “big analytics” technologies are embedded in a framework that supports the entire decision-making process.

Software can be found on the following HPC resources: VELA and CARINA

Stata statistical software is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. Stata is not sold in modules, which means you get everything you need in one package.

Software used on the following HPC resources: VELA

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, etc.) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

Software used on the following HPC resources: VELA

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

Software used on the following HPC resources: VELA

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range.

Software used on the following HPC resources: VELA