https://github.com/lammps/lammps

Public development project of the LAMMPS MD software package

kokkos lammps molecular-dynamics simulation

Last synced: 04 Feb 2026

https://github.com/biolab/orange3

🍊 :bar_chart: :bulb: Orange: Interactive data analysis

classification clustering data-mining data-science data-visualization decision-trees machine-learning numpy orange orange3 pandas plotting python random-forest regression scikit-learn scipy visual-programming visualization

Last synced: 04 Feb 2026

https://github.com/neuronsimulator/nrn

NEURON Simulator

high-performance-computing neuron neuroscience simulation

Last synced: 04 Feb 2026

https://gitlab.kitware.com/vtk/vtk

Visualization Toolkit

Last synced: 05 Feb 2026

https://github.com/nextflow-io/nextflow

A DSL for data-driven computational pipelines

aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine

Last synced: 04 Feb 2026

https://github.com/imagej/ImageJ

Public domain software for processing and analyzing scientific images

computer-vision image-processing

Last synced: 05 Feb 2026

https://gitlab.com/gromacs/gromacs

The GROMACS molecular simulation toolkit.

molecular dynamics simulation

Last synced: 05 Feb 2026

https://github.com/GenericMappingTools/gmt

The Generic Mapping Tools

c earth-science generic-mapping-tools geophysics geospatial mapping

Last synced: 05 Feb 2026

https://github.com/broadinstitute/gatk

Official code repository for GATK versions 4 and up

bioinformatics dna gatk genome genomics ngs science sequencing spark

Last synced: 04 Feb 2026

https://github.com/samtools/samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

Last synced: 05 Feb 2026

https://github.com/knime/knime-core

KNIME Analytics Platform

database integration machine-learning open-source tool-blending workflow

Last synced: 05 Feb 2026

https://gitlab.kitware.com/paraview/paraview

Parallel Data Analysis and Visualization Application based on VTK.

paraview

Last synced: 05 Feb 2026

https://github.com/afni/afni

Official AFNI source and documentation

anatomical-mri dwi fmri fmri-analysis fmri-data-analysis mri quality-control statistical-inference statistics visualization

Last synced: 05 Feb 2026

https://github.com/rachis-org/rachis

Source for the QIIME 2 Framework (Q2F).

hacktoberfest

Last synced: 05 Feb 2026

https://github.com/cytoscape/cytoscape

Cytoscape: an open source platform for network analysis and visualization

Last synced: 05 Feb 2026

https://github.com/ESCOMP/CESM

The Community Earth System Model

climate climate-model ncar

Last synced: 05 Feb 2026

https://github.com/BenLangmead/bowtie

An ultrafast memory-efficient short read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 05 Feb 2026

https://github.com/Slicer/Slicer

Multi-platform, free open source software for visualization and image computing.

3d-printing 3d-slicer c-plus-plus computed-tomography image-guided-therapy image-processing itk kitware medical-image-computing medical-imaging national-institutes-of-health neuroimaging nih python qt registration segmentation tcia-dac tractography vtk

Last synced: 04 Feb 2026

https://github.com/visit-dav/visit

VisIt - Visualization and Data Analysis for Mesh-based Scientific Data

data-analysis data-viz hpc python radiuss scientific-computing scientific-visualization visualization

Last synced: 04 Feb 2026

https://github.com/trinityrnaseq/trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

Last synced: 05 Feb 2026