Life Sciences Software Packages

F
FileGator
FileGator is a free, open-source, self-hosted web application for managing files and folders. You can manage files inside your local repository folder (on your server's hard drive) or connect to other storage adapters.
APPLICATION
P
PyMol
PyMOL is an open-source molecular visualization system, maintained and distributed by Schrödinger.
VISUALIZATIONOPEN_SOURCE
S
Scipion
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM).
VISUALIZATIONOPEN_SOURCE
I
IGV
The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data.
VISUALIZATIONOPEN_SOURCE
F
FastQC-GUI
FastQc GUI is a graphical user interface for FastQC.
MODELVISUALIZATIONOPEN_SOURCE
V
VisIt
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
VISUALIZATIONOPEN_SOURCE
Dd
Dx Desktop
DX Desktop is a cloud-based version of the popular Ubuntu MATE desktop environment, designed to run entirely in the cloud.
TOOL
E
Ensembl-VEP
VEP (Variant Effect Predictor) is a versatile and widely used bioinformatics tool developed by the Ensembl project.
MODELOPEN_SOURCEGENOMIC_VARIANTS
S
Samtools
A versatile suite of tools for processing and analyzing genomic data, particularly optimized for high-throughput sequencing data in SAM, BAM, and CRAM formats.
MODELOPEN_SOURCESEQUENCING_DATA_ANALYSIS
P
Pangolin
Pangolin (Phylogenetic Assignment of Named Global Outbreak LINeages) is an open-source bioinformatics tool specifically developed for classifying SARS-CoV-2 virus samples into specific lineages.
MODELOPEN_SOURCEVIRAL_GENOMIC_CLASSIFICATION
L
LAMMPS
LAMMPS is an open-source software package designed for molecular dynamics simulations. It implements multi-machine parallel computing using MPI and provides empirical potential functions for atoms in the periodic table.
MODELOPEN_SOURCEMOLECULAR_DYNAMICS_SIMULATION
I
iVar
A cutting-edge bioinformatics tool specifically designed for the analysis and visualization of viral genomic data.
MODELOPEN_SOURCEVIRAL_GENOMIC_ANALYSIS
G
GROMACS
Renowned for efficiently simulating biomolecules such as proteins, lipids, and nucleic acids, GROMACS is an indispensable tool in fields like biophysics, pharmacology, and biochemistry.
MODELOPEN_SOURCEMOLECULAR_DYNAMICS
F
FastQC-CLI
FastQC is a program designed to spot potential problems in high throughput sequencing datasets. This is the Command Line Interface (CLI) version of FastQC
MODELOPEN_SOURCESEQUENCING_DATA_ANALYSIS
C
Cutadapt
Cutadapt is a powerful and flexible library available through Conda, designed for the preprocessing of high-throughput sequencing data.
MODELOPEN_SOURCEADAPTER_TRIMMING
B
BLAST
BLAST (Basic Local Alignment Search Tool) is a pivotal tool in bioinformatics, facilitating fast and accurate comparison of query sequences against extensive databases of known sequences.
MODELBIOMOLECULAR_DYNAMICSFORCE_FIELD_SIMULATION
B
BWA
BWA (Burrows-Wheeler Aligner) is a widely used and efficient open-source software tool designed for the alignment of high-throughput sequencing reads to a reference genome.
OPEN_SOURCEBIOINFORMATICSGENOMICS
C
CDK
The Chemistry Development Kit (CDK) is a Java library for cheminformatics and bioinformatics, developed at the University of Notre Dame.
MODELOPEN_SOURCE
Jl
Jupyter Lab
Jupyter Lab is an open-source web-based interactive development environment (IDE) for data scientists and researchers. It provides a flexible and powerful environment for working with code, data, and visualizations.
NOTEBOOKOPEN_SOURCE
A
AmberMD
AmberMD is a molecular dynamics software suite for biomolecular simulations, using force fields originally created for the AMBER force field.
MODELOPEN_SOURCEBIOMOLECULAR_DYNAMICS
P
ParaView
ParaView is an open-source, multi-platform data analysis and visualization application. It allows users to interactively visualize and analyze large datasets using a distributed computing architecture.
VISUALIZATIONOPEN_SOURCECOMPUTATIONAL_FLUID_DYNAMICS
Vc
VS Code
VS Code is a web-based version of the popular code editor, Visual Studio Code (VS Code), designed to run entirely in the cloud.
NOTEBOOKOPEN_SOURCE

Computational Fluid Dynamics Software Packages

F
FileGator
FileGator is a free, open-source, self-hosted web application for managing files and folders. You can manage files inside your local repository folder (on your server's hard drive) or connect to other storage adapters.
APPLICATION
U
Uintah-Wasatch
Wasatch is an advanced multi-physics simulation software that provides high-fidelity solutions for fluid dynamics and reactive transport processes across various engineering and scientific applications.
MODEOPEN_SOURCECFD
O
ODT
The One-Dimensional Turbulence (ODT) model is a computationally efficient simulation approach that simplifies turbulent flow dynamics to one dimension using stochastic triplet maps, enabling detailed insights into turbulent energy transfer and dissipat...
MODELOPEN_SOURCECFD
V
VisIt
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
VISUALIZATIONOPEN_SOURCE
Dd
Dx Desktop
DX Desktop is a cloud-based version of the popular Ubuntu MATE desktop environment, designed to run entirely in the cloud.
TOOL
S
SU2
A robust open-source CFD code, is primarily developed for aerospace and other engineering applications. Renowned for its flexibility, it caters to a broad spectrum of flow problems.
MODELOPEN_SOURCEMULTI_PHYSICS
Jl
Jupyter Lab
Jupyter Lab is an open-source web-based interactive development environment (IDE) for data scientists and researchers. It provides a flexible and powerful environment for working with code, data, and visualizations.
NOTEBOOKOPEN_SOURCE
O
OpenFOAM
OpenFOAM is a leading open-source software for computational fluid dynamics (CFD), known for its extensive capabilities and flexibility.
MODELCOMPUTATIONAL_FLUID_DYNAMICSMULTIPHYSICS_SIMULATION
P
ParaView
ParaView is an open-source, multi-platform data analysis and visualization application. It allows users to interactively visualize and analyze large datasets using a distributed computing architecture.
VISUALIZATIONOPEN_SOURCECOMPUTATIONAL_FLUID_DYNAMICS
Vc
VS Code
VS Code is a web-based version of the popular code editor, Visual Studio Code (VS Code), designed to run entirely in the cloud.
NOTEBOOKOPEN_SOURCE

Data Science Software Packages

F
FileGator
FileGator is a free, open-source, self-hosted web application for managing files and folders. You can manage files inside your local repository folder (on your server's hard drive) or connect to other storage adapters.
APPLICATION
P
PyMol
PyMOL is an open-source molecular visualization system, maintained and distributed by Schrödinger.
VISUALIZATIONOPEN_SOURCE
S
Scipion
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM).
VISUALIZATIONOPEN_SOURCE
I
IGV
The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data.
VISUALIZATIONOPEN_SOURCE
F
FastQC-GUI
FastQc GUI is a graphical user interface for FastQC.
MODELVISUALIZATIONOPEN_SOURCE
V
VisIt
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
VISUALIZATIONOPEN_SOURCE
Dd
Dx Desktop
DX Desktop is a cloud-based version of the popular Ubuntu MATE desktop environment, designed to run entirely in the cloud.
TOOL
E
Ensembl-VEP
VEP (Variant Effect Predictor) is a versatile and widely used bioinformatics tool developed by the Ensembl project.
MODELOPEN_SOURCEGENOMIC_VARIANTS
S
SU2
A robust open-source CFD code, is primarily developed for aerospace and other engineering applications. Renowned for its flexibility, it caters to a broad spectrum of flow problems.
MODELOPEN_SOURCEMULTI_PHYSICS
S
Samtools
A versatile suite of tools for processing and analyzing genomic data, particularly optimized for high-throughput sequencing data in SAM, BAM, and CRAM formats.
MODELOPEN_SOURCESEQUENCING_DATA_ANALYSIS
P
Pangolin
Pangolin (Phylogenetic Assignment of Named Global Outbreak LINeages) is an open-source bioinformatics tool specifically developed for classifying SARS-CoV-2 virus samples into specific lineages.
MODELOPEN_SOURCEVIRAL_GENOMIC_CLASSIFICATION
L
LAMMPS
LAMMPS is an open-source software package designed for molecular dynamics simulations. It implements multi-machine parallel computing using MPI and provides empirical potential functions for atoms in the periodic table.
MODELOPEN_SOURCEMOLECULAR_DYNAMICS_SIMULATION
I
iVar
A cutting-edge bioinformatics tool specifically designed for the analysis and visualization of viral genomic data.
MODELOPEN_SOURCEVIRAL_GENOMIC_ANALYSIS
G
GROMACS
Renowned for efficiently simulating biomolecules such as proteins, lipids, and nucleic acids, GROMACS is an indispensable tool in fields like biophysics, pharmacology, and biochemistry.
MODELOPEN_SOURCEMOLECULAR_DYNAMICS
F
FastQC-CLI
FastQC is a program designed to spot potential problems in high throughput sequencing datasets. This is the Command Line Interface (CLI) version of FastQC
MODELOPEN_SOURCESEQUENCING_DATA_ANALYSIS
C
Cutadapt
Cutadapt is a powerful and flexible library available through Conda, designed for the preprocessing of high-throughput sequencing data.
MODELOPEN_SOURCEADAPTER_TRIMMING
B
BLAST
BLAST (Basic Local Alignment Search Tool) is a pivotal tool in bioinformatics, facilitating fast and accurate comparison of query sequences against extensive databases of known sequences.
MODELBIOMOLECULAR_DYNAMICSFORCE_FIELD_SIMULATION
B
BWA
BWA (Burrows-Wheeler Aligner) is a widely used and efficient open-source software tool designed for the alignment of high-throughput sequencing reads to a reference genome.
OPEN_SOURCEBIOINFORMATICSGENOMICS
C
CDK
The Chemistry Development Kit (CDK) is a Java library for cheminformatics and bioinformatics, developed at the University of Notre Dame.
MODELOPEN_SOURCE
Jl
Jupyter Lab
Jupyter Lab is an open-source web-based interactive development environment (IDE) for data scientists and researchers. It provides a flexible and powerful environment for working with code, data, and visualizations.
NOTEBOOKOPEN_SOURCE
O
OpenFOAM
OpenFOAM is a leading open-source software for computational fluid dynamics (CFD), known for its extensive capabilities and flexibility.
MODELCOMPUTATIONAL_FLUID_DYNAMICSMULTIPHYSICS_SIMULATION
A
AmberMD
AmberMD is a molecular dynamics software suite for biomolecular simulations, using force fields originally created for the AMBER force field.
MODELOPEN_SOURCEBIOMOLECULAR_DYNAMICS
P
ParaView
ParaView is an open-source, multi-platform data analysis and visualization application. It allows users to interactively visualize and analyze large datasets using a distributed computing architecture.
VISUALIZATIONOPEN_SOURCECOMPUTATIONAL_FLUID_DYNAMICS
Vc
VS Code
VS Code is a web-based version of the popular code editor, Visual Studio Code (VS Code), designed to run entirely in the cloud.
NOTEBOOKOPEN_SOURCE

Development Software Packages

F
FileGator
FileGator is a free, open-source, self-hosted web application for managing files and folders. You can manage files inside your local repository folder (on your server's hard drive) or connect to other storage adapters.
APPLICATION
U
Ubuntu
Ubuntu is a popular Linux distribution that is widely used for desktop and server applications. It is known for its ease of use, stability, and large software repository.
OPEN_SOURCETOOL
N
Nginx
Nginx is a web server to serve static files and reverse proxy to other services. It is a lightweight and high-performance web server.
SERVEROPEN_SOURCE
Dd
Dx Desktop
DX Desktop is a cloud-based version of the popular Ubuntu MATE desktop environment, designed to run entirely in the cloud.
TOOL
Jl
Jupyter Lab
Jupyter Lab is an open-source web-based interactive development environment (IDE) for data scientists and researchers. It provides a flexible and powerful environment for working with code, data, and visualizations.
NOTEBOOKOPEN_SOURCE
Vc
VS Code
VS Code is a web-based version of the popular code editor, Visual Studio Code (VS Code), designed to run entirely in the cloud.
NOTEBOOKOPEN_SOURCE
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