Open-source scientific software for researchers
A curated, filterable directory across genomics, structural biology, chemistry, microscopy, neuroscience, medical imaging, astronomy, climate, and physics. Pick a domain, or search by name.
3D Slicer↗
Extensible platform for medical image visualization, segmentation, and IGT.
AFNI↗
Analysis of Functional NeuroImages — interactive FMRI processing.
AI2 ScholarQA↗
Long-form scientific question answering grounded in the research literature.
Aivia↗
AI-powered commercial microscopy image analysis and visualization.
Aladin↗
Sky atlas for visualizing images and catalogues over the whole sky.
Alevin-fry↗
Fast, memory-frugal single-cell and single-nucleus quantification.
Allen Brain Atlas↗
Gene expression, connectivity, and cell-type atlases of mouse and human brain.
AllenSDK↗
Access to Allen Institute datasets and reference atlases — mouse brain atlas, cell types, connectivity.
AlphaFold↗
Deep-learning protein-structure prediction that reshaped structural biology.
AlphaFold DB↗
Predicted protein structures for hundreds of millions of sequences.
AlphaPept↗
Modular Python framework for fast shotgun proteomics.
Alyx↗
Web-based electronic lab notebook and colony/experiment database for multi-lab collaborations.
AMBER↗
Molecular mechanics and MD suite with the Amber force fields.
anipose↗
Robust 3D pose via multi-camera triangulation, sitting downstream of DeepLabCut.
ANTs↗
Advanced Normalization Tools — high-quality image registration and segmentation for MRI/brain pipelines.
Apptainer↗
Container platform built for HPC (formerly Singularity) — reproducible, rootless environments on clusters.
Arbor↗
Modern multi-compartment simulation library that maps morphological networks onto GPUs and multicore CPUs.
ArchR↗
Full analysis suite for single-cell ATAC-seq.
AREPO↗
Moving-mesh magnetohydrodynamics code for cosmological simulations.
Arivis Vision4D↗
Commercial 3D/4D visualization and analysis for large microscopy volumes.
Astropy↗
Core Python library for astronomy: coordinates, FITS, units, tables, cosmology.
astroquery↗
Query astronomical databases and archives from Python.
AutoDock Vina↗
Widely used open-source molecular docking and virtual screening engine.
Avogadro↗
Free molecular editor and visualizer for building inputs and inspecting geometries.
B-SOiD↗
Unsupervised discovery of behavioral clusters from pose data, then a fast frame-wise classifier.
BayesSpace↗
Bayesian clustering and enhancement for spatial transcriptomics.
BBKNN↗
Batch-balanced kNN graphs for integrating single-cell datasets in Scanpy.
bcftools↗
Variant calling and VCF/BCF manipulation sitting next to samtools.
bedtools↗
Swiss-army knife for genomic interval arithmetic on BED, GFF, VCF and BAM.
Benchling↗
Cloud R&D platform: ELN, molecular biology, and sample tracking.
BIDS↗
Community standard for organizing neuroimaging and ephys datasets in a machine-readable layout.
BigStitcher↗
Fiji plugin for aligning and fusing terabyte-scale multi-view light-sheet data.
Bika LIMS↗
Open-source laboratory information management system on Plone.
Bio-Formats↗
Reads and writes hundreds of proprietary microscopy formats into a common model.
Bioconductor↗
Open project for R packages in genomics, flow cytometry, and computational biology.
BioContainers↗
Container registry of bioinformatics tools for reproducible pipelines.
BioGRID↗
Curated genetic and protein interaction data.
Biopython↗
Tools for computational molecular biology: sequence parsing, alignment, structure and database access.
BLAST↗
The standard local sequence similarity search against nucleotide and protein DBs.
BluePyOpt↗
Data-driven optimization of neuron model parameters using evolutionary algorithms.
Boltz↗
Open biomolecular structure prediction for proteins, ligands, and complexes.
Bowtie2↗
Fast, memory-efficient short-read aligner for DNA sequencing.
BrainGlobe Atlas API↗
One programmatic interface to many reference atlases across species — the backbone of BrainGlobe.
brainreg↗
Automated 3D whole-brain registration to a reference atlas, with an optional napari plugin.
brainrender↗
3D rendering of anatomically registered neuroanatomical data, driven by the BrainGlobe Atlas API.
Brainstorm↗
GUI-first application for MEG/EEG/iEEG analysis and source imaging.
Brian2↗
Equation-oriented simulator for spiking networks — define models in plain math and run them fast.
BWA↗
Burrows–Wheeler aligner for mapping DNA sequences against a large reference.
CaImAn↗
End-to-end calcium imaging: motion correction, source extraction, deconvolution and cross-session registration.
CalculiX↗
Open 3D structural finite-element solver with Abaqus-like input.
CAMERA↗
Annotation of isotopes, adducts, and fragments on XCMS peak lists.
CARE↗
Content-aware image restoration for denoising and isotropic reconstruction.
CARTA↗
Cube Analysis and Rendering Tool for Astronomy — large radio cubes.
Cartopy↗
Cartographic projections and geospatial plotting for Matplotlib.
CASA↗
Common Astronomy Software Applications for radio interferometry.
CDK↗
Java library for cheminformatics, rendering, and QSAR descriptors.
CDO↗
Climate Data Operators — command-line processing of GRIB and NetCDF.
CEBRA↗
Contrastive learning of consistent low-dimensional embeddings from joint neural and behavioral time series.
Cell Ranger↗
Official 10x pipeline from FASTQ to count matrices for Chromium assays.
cell2location↗
Bayesian mapping of cell types onto spatial transcriptomics spots.
CellChat↗
Inference of cell–cell communication from single-cell expression.
cellfinder↗
Detects and atlas-maps cells across whole-brain microscopy volumes with detection plus a deep classifier.
CellPhoneDB↗
Ligand–receptor database and inference of cell–cell communication.
Cellpose↗
Generalist deep-learning cell segmentation with a human-in-the-loop GUI. Works in 2D and 3D.
CellProfiler↗
Modular, repeatable pipelines for segmentation and high-content feature extraction, runnable headless.
CESM↗
Community Earth System Model — coupled atmosphere, ocean, land, ice.
CHARMM↗
Chemistry at HARvard Macromolecular Mechanics — simulation and force fields.
ChEBI↗
Chemical Entities of Biological Interest — ontology of small molecules.
ChemAxon↗
Commercial cheminformatics platform for drawing, naming, and chemical search.
ChemBERTa↗
Transformer language models pretrained on SMILES for molecular property prediction.
ChEMBL↗
Bioactive molecules with drug-like properties and bioactivity data.
Chemprop↗
Message-passing neural networks for molecular property prediction.
ChemSpider↗
Royal Society of Chemistry structure search across hundreds of sources.
Cicero↗
Predicts cis-regulatory DNA interactions from single-cell chromatin.
CloudVolume↗
Serverless client for reading and writing Neuroglancer Precomputed volumes, meshes and skeletons at petascale.
Clustal Omega↗
Scalable multiple sequence alignment for large protein families.
Code_Aster↗
EDF's open structural mechanics and thermomechanics FEM code.
Code_Saturne↗
EDF's general-purpose CFD software for incompressible and low-Mach flow.
ColabFold↗
Accessible AlphaFold2 / AF2-multimer predictions via MMseqs2 MSAs.
Comet↗
Open tandem mass spectrometry sequence database search tool.
COMSOL↗
Commercial multiphysics finite-element simulation platform.
Consensus↗
Search engine that answers research questions with findings from papers.
CP2K↗
Atomistic and molecular simulations with DFT and mixed Gaussian/plane-wave methods.
Cufflinks↗
Classic transcript assembly and differential expression from RNA-seq.
CWL↗
Common Workflow Language — portable descriptions of data analysis workflows.
DALI↗
Distance-matrix protein structure comparison, a classic of fold matching.
DANDI↗
CLI and archive for publishing, versioning and sharing NWB and BIDS datasets on the DANDI cloud.
DANNCE↗
Direct 3D pose estimation for freely moving rodents from synchronized multi-camera video.
Dask↗
Parallel computing that scales NumPy, pandas and scikit-learn from a laptop to a cluster.
DataJoint↗
Relational data-pipeline framework that automates neuroscience data collection and computation.
DataLad↗
Distributed data version control on Git and git-annex, tracking large files and full provenance.
dcm4che↗
Open-source DICOM toolkit and archive used in PACS integrations.
DCMTK↗
OFFIS DICOM toolkit — convert, send, and inspect DICOM objects.
deal.II↗
C++ finite-element library for adaptive, high-order PDE solvers.
DeepCell↗
Deep learning for cell segmentation and tracking in live-cell imaging.
DeepChem↗
Deep-learning toolkit for molecules, materials, and biology datasets.
DeepEthogram↗
Supervised behavior classification straight from raw video pixels — no pose step — producing full ethograms.
DeepImageJ↗
Fiji/ImageJ plugin to run trained deep-learning models on microscopy images.
DeepLabCut↗
Markerless 2D/3D pose estimation for any animal or human via transfer learning — the field's most-used tracker.
DeepMedic↗
3D CNN for brain-lesion segmentation, originally for tumor MRI.
DESeq2↗
Differential gene expression from count data with shrinkage estimators.
DestVI↗
Multi-resolution deconvolution of spatial transcriptomics with scvi-tools.
DGL-LifeSci↗
Graph neural networks for molecules and proteins on DGL.
DIA-NN↗
Neural-network engine for data-independent acquisition proteomics.
DiffDock↗
Diffusion-based molecular docking that samples ligand poses without a pocket prior.
DIPY↗
Diffusion imaging in Python — reconstruction, tractography, and microstructural models.
Dockstore↗
Registry of Docker-based tools and workflows (CWL, WDL, Nextflow).
DoubletFinder↗
Doublet detection for scRNA-seq in Seurat workflows.
DrugBank↗
Drug and drug-target database used throughout pharmacology.
DrugCentral↗
Drug information resource covering active ingredients and indications.
DVC↗
Git for data and models — versioning, reproducible pipelines and experiment tracking.
Dynamax↗
State-space models in JAX — the modern successor to ssm, with GPU-friendly inference.
EBRAINS↗
European research infrastructure for brain data, atlases, and simulation.
edgeR↗
Empirical Bayes RNA-seq differential expression for designed experiments.
EEGLAB↗
The classic EEG analysis environment with ICA, time-frequency tools and a huge plugin ecosystem.
eLabFTW↗
Free open-source electronic lab notebook for research teams.
Elephant↗
Analysis toolkit for spike trains and signals: correlation, spectral and Granger analysis, SPADE, CSD.
Elicit↗
AI research assistant that finds papers, extracts evidence, and synthesizes findings.
Elmer↗
Open finite-element multiphysics simulation software.
EncyclopeDIA↗
Chromatogram-library DIA search and quantification.
Ensembl↗
Genome browser and annotations for vertebrates and other eukaryotes.
ESA PolSARpro↗
Polarimetric SAR data processing and educational toolbox.
ESM↗
Evolutionary Scale Modeling — protein language models for structure and function.
ESMFold↗
Single-sequence protein structure prediction from ESM language models.
ESMValTool↗
Community diagnostics and performance metrics for Earth system models.
Evo↗
DNA foundation model at genome scale for sequence generation and prediction.
ExoTransmit↗
Radiative-transfer code for exoplanet transmission spectra.
EXTRACT↗
Robust automated cell extraction that suppresses contamination and crosstalk in calcium movies.
facemap↗
Tracks mouse orofacial movements and predicts neural activity from behavior via SVD of face video.
FEniCS↗
Automated finite-element solver for PDEs with a Python/C++ interface.
FeynCalc↗
Mathematica package for symbolic semi-automatic high-energy calculations.
FieldTrip↗
Comprehensive toolbox for advanced MEG, EEG and invasive electrophysiology analysis.
Fiji / ImageJ↗
The public-domain workhorse of scientific image processing, with a vast ecosystem of plugins.
FiPy↗
Finite-volume PDE solver written in Python.
fMRIPrep↗
Robust, BIDS-app fMRI preprocessing that replaces lab-specific pipelines.
Foldseek↗
Ultrafast protein structure search in 3Di space, including AlphaFold DB.
FragPipe↗
GUI workflow around MSFragger, Philosopher, and IonQuant.
FreeBayes↗
Haplotype-based Bayesian variant detector for small variants from BAM.
FreeCAD↗
Open-source parametric 3D CAD/CAE modeler.
FreeSurfer↗
Cortical reconstruction, parcellation, and morphometry from structural MRI.
FreeView↗
FreeSurfer's 3D viewer for volumes, surfaces, and labels.
FSL↗
FMRIB Software Library — MRI analysis from BET to FEAT and TBSS.
FutureHouse↗
AI-scientist platform (PaperQA, Crow, Falcon) for literature and experimental design.
GADGET↗
N-body / SPH code for cosmological structure formation.
Gaia Archive↗
ESA Gaia catalogue of billion-star astrometry and photometry.
Galaxy↗
Web platform that makes reproducible bioinformatics accessible without writing code.
GAMESS↗
General Atomic and Molecular Electronic Structure System — open ab initio code.
Gammapy↗
Python package for gamma-ray astronomy data analysis.
GATK↗
Genome Analysis Toolkit for variant discovery and genotyping at scale.
Gaussian↗
Commercial quantum chemistry package for electronic structure and spectra.
GDAL↗
Translator library for raster and vector geospatial data formats.
Geant4↗
Monte Carlo toolkit for the passage of particles through matter.
Gene Ontology↗
Structured vocabulary for gene product functions across organisms.
GeoPandas↗
Pandas for geospatial vector data with Shapely and Fiona.
Giotto↗
Comprehensive toolbox for spatial transcriptomics visualization and analysis.
Giotto Suite↗
Modular successor to Giotto for multi-omic spatial data at tissue scale.
Gmsh↗
Three-dimensional finite-element mesh generator with a CAD engine.
GNINA↗
Deep-learning scoring on top of AutoDock Vina for molecular docking.
GNPS↗
Global Natural Products Social molecular networking for MS/MS.
Google AI Co-Scientist↗
Multi-agent system for hypothesis generation and research planning.
Google Earth Engine↗
Planetary-scale Earth observation analysis in the cloud.
GRASS GIS↗
Full GIS for raster, vector, and geospatial modeling, often under QGIS.
GROMACS↗
Workhorse molecular dynamics package for biomolecules and free-energy calculations.
h5py↗
Pythonic interface to HDF5 — the default on-disk container behind NWB.
Harmony↗
Fast, sensitive integration of single-cell data across batches and modalities.
HDMF↗
Hierarchical Data Modeling Framework — the extensible modeling engine underneath PyNWB.
HEASoft↗
FTOOLS / XANADU suite for high-energy astrophysics data.
HerdingSpikes↗
Spike detection and sorting built for very large high-density MEAs, prioritizing scalability.
HISAT2↗
Graph-based, splice-aware aligner for RNA-seq against a genome plus known splices.
HMDB↗
Human Metabolome Database — reference spectra, pathways, and concentrations.
Human Connectome Project↗
Open multimodal MRI resource for human brain connectivity.
Ilastik↗
Interactive machine-learning for image classification and segmentation — train a classifier by painting labels.
Imaris↗
Commercial 3D/4D microscopy visualization, tracing, and cell analysis.
IntAct↗
Open molecular-interaction database from the IMEx consortium.
InterPro↗
Classification of protein families and domains from many signature DBs.
IQ-TREE↗
Efficient maximum-likelihood phylogenetic inference with model selection.
IRAF↗
Classic Image Reduction and Analysis Facility, still used for optical pipelines.
Iris↗
Python library for analysing and visualising Earth-science cubes.
ITK↗
Insight Toolkit — the C++ foundation for medical image registration and segmentation.
Jmol↗
Interactive 3D viewer for chemical structures in the browser and desktop.
JSmol↗
JavaScript port of Jmol for embedding molecular viewers on the web.
Jupyter↗
Interactive notebooks that weave code, results and narrative — the lab notebook of computation.
Kallisto↗
Near-optimal RNA-seq quantification using pseudoalignment.
Kallisto bustools↗
Pseudoalignment + BUS files for scRNA-seq quantification and QC.
KEGG↗
Kyoto Encyclopedia of Genes and Genomes — pathways, genes, and compounds.
Keypoint-MoSeq↗
Discovers behavioral syllables from keypoints with a generative model that separates behavior from tracking noise.
Kilosort↗
Fast spike sorting with drift correction for high-density probes like Neuropixels. KS4 uses graph clustering.
Kratos↗
Framework for building multidisciplinary finite-element programs.
LabArchives↗
Commercial electronic lab notebook used across universities.
LabKey↗
Open platform for integrating, analyzing, and sharing lab data.
LAMMPS↗
Large-scale Atomic/Molecular Massively Parallel Simulator.
LIANA↗
Ligand–receptor consensus framework wrapping many CCC methods.
Lightkurve↗
Kepler / TESS light-curve analysis for exoplanets and stellar variability.
Lightning Pose↗
Semi-supervised pose estimation with Bayesian ensembling — accurate from far fewer labeled frames.
limma↗
Linear models for microarray, RNA-seq, and methylation differential analysis.
MadGraph5_aMC@NLO↗
Automated matrix-element generator for collider event simulation.
MAFFT↗
Accurate multiple sequence alignment for nucleotides and proteins.
Makie.jl↗
High-performance, interactive plotting for Julia.
MassBank↗
Community repository of tandem mass spectra for metabolite ID.
MAST↗
Mikulski Archive for Space Telescopes — HST, JWST, TESS, and more.
MatNWB↗
MATLAB API for NWB, generated from the schema so it stays in sync with the standard.
MaxQuant↗
Quantitative proteomics from shotgun MS, including Andromeda search and LFQ.
Mayavi↗
3D scientific data visualization and plotting in Python.
MERINGUE↗
Spatial gene-expression statistics and neighborhood analysis.
Mesmerize↗
Fast, memory-efficient batch management for CaImAn algorithms, designed to plug into napari.
MetaboAnalyst↗
Web and R toolbox for metabolomics statistical and functional analysis.
MetFrag↗
In-silico fragmenter that ranks candidate structures against MS/MS.
MetPy↗
Meteorological calculations and plotting built on Matplotlib.
Micro-Manager↗
Open microscope control software that drives hundreds of cameras and stages.
MIN1PIPE↗
A miniscope 1-photon signal-extraction pipeline that runs end-to-end with minimal manual work.
MiniAn↗
Open analysis pipeline for one-photon miniscope imaging, built on xarray and Dask for out-of-core work.
minimap2↗
Versatile pairwise aligner for long reads, assemblies, and full genomes.
MIST↗
Microscopy Image Stitching Tool for large tiled acquisitions.
MLflow↗
Tracks experiments, packages models and manages the ML lifecycle from prototype to deployment.
MMseqs2↗
Ultrafast protein sequence clustering and search, including structure-aware modes.
MNE-Python↗
State-of-the-art MEG/EEG processing: preprocessing, source localization, connectivity, time-frequency.
MolFormer↗
Transformer trained on SMILES for molecular representation learning.
MONAI↗
PyTorch-based AI framework for healthcare imaging.
MONAI Label↗
Active-learning server for AI-assisted annotation in 3D Slicer and others.
Monocle3↗
Trajectory inference, clustering, and differential expression for large scRNA-seq.
MOOSE↗
Multiphysics Object Oriented Simulation Environment for coupled PDEs.
MountainSort5↗
Density-based spike sorter, rewritten for the SpikeInterface era with isosplit clustering.
MRIQC↗
Automated quality control metrics and reports for MRI.
MRtrix3↗
Tools for diffusion MRI, constrained spherical deconvolution, and tractography.
MS-DIAL↗
Untargeted metabolomics and lipidomics with spectral deconvolution.
MSFragger↗
Ultrafast fragment-ion search engine for peptide identification.
MSstats↗
Statistical relative quantification for targeted, DDA, and DIA proteomics.
MUSCLE↗
Fast multiple sequence alignment widely used in phylogenetics pipelines.
MZmine↗
Interactive LC-MS data processing: peak picking, alignment, and ID.
NAMD↗
Highly scalable MD for large biomolecular systems, often paired with VMD.
napari↗
Fast n-dimensional image viewer with a deep plugin ecosystem — the Python-native canvas for imaging workflows.
NASA ADS↗
Astrophysics Data System — the literature index for astronomy and physics.
natverse↗
The NeuroAnatomy Toolbox suite in R for importing, transforming and analyzing connectomes and tracings.
NAVis↗
Analyze and visualize neuron morphologies and skeletons; interoperates with CloudVolume and natverse.
NCBI↗
National Center for Biotechnology Information — GenBank, PubMed, BLAST, SRA.
NCO↗
NetCDF Operators for slicing, averaging, and rewriting climate files.
NED↗
NASA/IPAC Extragalactic Database of galaxies and other extragalactic objects.
NeMoS↗
GPU-accelerated GLMs for spike-train analysis, powered by JAX, with a composable basis module. Pairs with pynapple.
Nengo↗
Builds large functional brain models with the Neural Engineering Framework; targets neuromorphic hardware.
Neo↗
Shared object model plus readers for dozens of proprietary ephys formats. The I/O layer under the stack.
NEST↗
Highly scalable simulator for large networks of point neurons — millions of cells across HPC clusters.
NetPyNE↗
Declarative interface for building, simulating (via NEURON) and analyzing multiscale network models.
neuroconv↗
Converts data from dozens of acquisition and analysis formats into NWB with one uniform interface.
neuroglancer↗
WebGL viewer for enormous volumetric EM/connectomics data. The standard for cloud-scale volume viewing.
NeuroMorpho.Org↗
Inventory of digitally reconstructed neurons from many labs.
NEURON↗
Simulation of detailed biophysical neurons with complex morphology and ion channels.
Nextflow↗
Dataflow workflow engine for scalable, portable pipelines — the backbone of the nf-core community.
Nextflow Tower↗
Seqera Platform for monitoring and launching Nextflow pipelines.
nf-core↗
Community collection of production Nextflow pipelines for genomics and beyond.
NicheNet↗
Predicts ligand–target links that explain receiver-cell expression changes.
Nilearn↗
Machine learning for neuroimaging on top of scikit-learn and NiBabel.
Nipype↗
Pipelines that glue FSL, FreeSurfer, AFNI, SPM and Python into one workflow.
nnU-Net↗
Self-configuring U-Net that is the default baseline for biomedical segmentation.
Noise2Void↗
Self-supervised denoising that trains on single noisy microscopy images.
NumPy↗
The foundational n-dimensional array library nearly every scientific Python tool builds on.
NWB Widgets↗
Interactive Jupyter widgets that let you browse and plot the full contents of any NWB file.
nwbinspector↗
Checks NWB files against best practices and schema compliance before you publish or archive.
NWChem↗
Scalable computational chemistry for molecules and periodic systems.
OMERO↗
Client–server platform for storing, managing, and analyzing microscopy data.
ONE↗
Open Neurophysiology Environment — a lightweight standard and API to search and load data across labs.
Open Babel↗
Chemical toolbox for converting and searching 100+ molecule file formats.
Open Ephys GUI↗
Free plugin-based system to acquire, process, record and visualize multichannel ephys. Includes an NWB engine.
OpenBIS↗
Open platform for managing biological and inventory data in the lab.
OpenEye Scientific↗
Commercial toolkit for shape, docking, and large-scale cheminformatics.
OpenFOAM↗
The leading open-source toolbox for computational fluid dynamics.
OpenFold↗
Trainable, open PyTorch implementation of AlphaFold2.
OpenMM↗
High-performance, extensible molecular simulation toolkit with GPU support.
OpenMS↗
Open framework for LC-MS data management, identification, and quantification.
OpenNeuro↗
Free archive for sharing BIDS-formatted neuroimaging datasets — hundreds of studies.
OpenSCAD↗
Programmatic 3D CAD for engineers who think in code.
ORCA↗
Efficient quantum chemistry package widely used for spectroscopy and catalysis.
Orfeo Toolbox↗
Remote-sensing image processing library (segmentation, classification, SAR).
pandas↗
Fast, expressive data structures for tabular and time-series data.
Pangeo↗
Community stack (xarray, Dask, Jupyter) for big geoscience data.
papermill↗
Parameterize and execute Jupyter notebooks programmatically for reproducible, scheduled reporting.
ParaView↗
Parallel scientific visualization for CFD, FEA, and volumetric data.
Parsl↗
Parallel scripting in Python for HPC and cloud scientific workflows.
PDB↗
Protein Data Bank — experimentally determined 3D structures.
Percolator↗
Semi-supervised SVM rescoring of peptide-spectrum matches.
Pfam↗
Protein family alignments and HMMs, now served through InterPro.
pFind↗
Open search engine for peptide identification including open-search PTMs.
Photutils↗
Source detection and photometry tools in the Astropy ecosystem.
Phy↗
GPU-accelerated GUI for manual curation — merge, split, label — of large-scale sorted ephys.
ProGen↗
Generative language model for protein sequences.
ProteinMPNN↗
Message-passing neural network for inverse protein design given a backbone.
Proteome Discoverer↗
Commercial proteomics identification and quantification platform.
Psi4↗
Open-source quantum chemistry with a Python-first API.
PubChem↗
Open chemistry database of molecules, bioassays, and patents.
PubChemPy↗
Python wrapper for the PubChem PUG REST API.
PyalData↗
Analysis of trial-based population data in a tidy trial_data structure ported from MATLAB TrialData.
pydicom↗
Read, modify, and write DICOM files in pure Python.
pyGLMnet↗
Elastic-net-regularized GLMs with a scikit-learn-style API, including Poisson GLMs for spike counts.
pymdp↗
Active inference and POMDP agents — simulate perception, learning and action under the free-energy principle.
PyMOL↗
The default molecular visualization program for structures, surfaces, and figures.
pynapple↗
Lightweight time-series and interval toolkit — tuning curves, correlograms, decoding, filtering. GPU via pynajax.
pynaviz↗
Visualization companion to pynapple — interactive views of time series, intervals, tuning curves and spectrograms.
PyNWB↗
Reference Python API for reading and writing Neurodata Without Borders files.
pyOpenMS↗
Python bindings to OpenMS for scripting proteomics and metabolomics workflows.
PySCF↗
Python-based ab initio quantum chemistry for molecules and extended systems.
pytest↗
The standard testing framework — what turns research code into software people can trust.
Pythia↗
Lund Monte Carlo for high-energy particle collisions and hadronization.
PyVista↗
Pythonic VTK for 3D plotting and mesh analysis.
Q-Chem↗
Commercial quantum chemistry with a broad method catalog.
QGIS↗
Free and open-source geographic information system for maps and analysis.
QSIPrep↗
BIDS-app for preprocessing diffusion MRI with reproducible defaults.
Quantum ESPRESSO↗
Plane-wave DFT suite for electronic-structure calculations and materials.
QuPath↗
Open-source digital pathology platform for whole-slide images and multiplex analysis.
RADMC-3D↗
Monte Carlo radiative transfer for dusty astrophysical environments.
RAMSES↗
Adaptive mesh refinement code for astrophysical hydrodynamics.
Rasterio↗
Pythonic GDAL for reading and writing geospatial rasters.
Rastermap↗
Nonlinear embedding that sorts neurons by activity similarity to reveal structure in huge population recordings.
RAxML-NG↗
Next-generation RAxML for phylogenetic trees on large alignments.
RDKit↗
Open-source cheminformatics: molecules, fingerprints, descriptors, and 2D/3D ops.
Reactome↗
Curated pathway database of human biological processes.
REDCap↗
Secure web application for building and managing research surveys and databases.
ResearchRabbit↗
Literature mapping that grows a collection from seed papers.
RFdiffusion↗
Diffusion model for generating novel protein backbones and binders.
RO-Crate↗
Packaging format that bundles data, metadata, and workflows for reuse.
ROOT↗
Data analysis framework for particle physics — histograms, trees, and fitting.
RoseTTAFold↗
Three-track network for protein structure prediction from Baker lab.
RSpace↗
ELN and inventory with inventory, samples, and integrations.
Sakana AI Scientist↗
Open experiment in fully automated scientific idea generation, coding, and paper writing.
Salmon↗
Fast transcript quantification from RNA-seq via quasi-mapping.
Salome↗
Open-source pre/post-processing platform for numerical simulation.
samtools↗
Standard utilities for manipulating SAM/BAM/CRAM alignments — sorting, indexing, pileups.
SAOImage DS9↗
Interactive astronomical imaging and data visualization for FITS.
SCAMP↗
Astrometric and photometric calibration against reference catalogues.
Scanpy↗
Scalable single-cell RNA-seq analysis — preprocessing, clustering, trajectory inference — on AnnData.
scCODA↗
Compositional differential abundance testing for cell types.
scikit-image↗
Image-processing algorithms on NumPy arrays — filtering, segmentation, morphology.
scikit-learn↗
General-purpose machine learning — classification, regression, clustering, model selection.
SciNote↗
Open-source ELN with protocols, inventory, and team workflows.
SciPy↗
Fundamental algorithms for scientific computing — optimization, signal processing, statistics.
SciSpace↗
AI reader that explains papers, equations, and related work in context.
Scrublet↗
Detects cell doublets in scRNA-seq via simulated doublets.
scvi-tools↗
Probabilistic deep-generative models for single-cell omics — integration, label transfer, DE.
Semantic Scholar↗
AI-powered academic search over a graph of papers, authors, and citations.
Sentinel Hub↗
API and processing for Sentinel, Landsat, and other EO archives.
Seurat↗
The standard R toolkit for single-cell genomics: QC, integration, clustering and differential expression.
SExtractor↗
Source Extractor — detects and measures objects on astronomical images.
Shapely↗
Manipulation and analysis of planar geometric objects.
Sherpa↗
Monte Carlo event generator for the Standard Model and BSM at colliders.
Signac↗
Single-cell chromatin analysis extending Seurat to scATAC-seq.
SimBA↗
GUI pipeline for building supervised behavioral classifiers from pose keypoints, focused on social behavior.
SIMBAD↗
Astronomical object database with identifications, measurements, and bibliography.
SimpleITK↗
Simplified ITK interface for registration, segmentation, and filtering.
SingleR↗
Reference-based automatic cell-type annotation for single-cell RNA-seq.
SIRIUS↗
CSI:FingerID molecular formula and structure annotation from MS/MS.
Skyline↗
Windows GUI for targeted proteomics method building and quantification.
SLEAP↗
Deep-learning system for fast multi-animal 2D pose tracking with a choice of network backbones.
Snakemake↗
Python-like workflow manager for reproducible pipelines that scale from laptop to cluster to cloud.
SNAP↗
Sentinel Application Platform for optical and SAR Earth observation.
SnapATAC↗
Single-nucleus ATAC-seq analysis with a disk-backed matrix format.
SnpEff↗
Genetic variant annotation and effect prediction for VCF files.
SoupX↗
Removes ambient RNA contamination from droplet scRNA-seq.
SpaGCN↗
Graph CNN that integrates gene expression, spatial location, and histology.
spatialdata↗
Unified data framework for spatial omics — images, points, shapes, and tables.
Spectronaut↗
Commercial DIA proteomics analysis from library to quantification.
Specutils↗
Data models and analysis for astronomical spectra.
SpikeGLX↗
High-channel-count acquisition GUI for Neuropixels with synchronized NI-DAQ. Read directly by SpikeInterface.
SpikeInterface↗
Unified API wrapping 15+ sorters plus preprocessing, metrics, curation and comparison — the hub of the ephys stack.
SPM↗
Statistical Parametric Mapping for PET, SPECT, EEG, and fMRI.
SpyKING CIRCUS↗
Fast, scalable template-matching spike sorter that handles dense arrays across CPUs and clusters.
Squidpy↗
Spatial single-cell analysis on top of Scanpy — graphs, images, and neighborhood stats.
ssm↗
Bayesian learning and inference for state-space models — HMMs, linear dynamical systems, recurrent SLDS.
STAR↗
Ultrafast splice-aware aligner for RNA-seq, the default in many transcriptome pipelines.
StarDist↗
Segments nuclei and other star-convex objects with high accuracy, even in crowded fields.
STARsolo↗
STAR's built-in droplet scRNA-seq quantification, Cell Ranger–compatible.
Stellarium↗
Free planetarium for the real and simulated night sky.
stLearn↗
Spatial transcriptomics analysis combining gene expression, location, and morphology.
STRING↗
Protein–protein interaction networks and functional enrichment.
StringTie↗
Transcript assembly and quantification from RNA-seq alignments.
STUtility↗
R package for visualization and analysis of Spatial Transcriptomics / Visium.
SU2↗
Open-source CFD and design optimization for compressible flow.
Suite2p↗
Registration, ROI detection and neuropil correction for two-photon imaging. Scales past 10,000 neurons.
SunPy↗
Solar-physics data analysis built on Astropy.
SWarp↗
Resamples and co-adds FITS images onto a common grid.
Tangram↗
Maps single-cell profiles onto spatial data by aligning gene expression.
TM-align↗
Sequence-independent protein structure alignment via TM-score.
Toil↗
Scalable workflow engine that runs CWL, WDL, and Python workflows.
TOPCAT↗
Interactive table viewer for catalogues, with VO and plotting.
TorchDrug↗
PyTorch library for drug discovery, graph ML, and biomolecules.
TorchIO↗
PyTorch data loading and augmentation for 3D medical images.
TotalSegmentator↗
nnU-Net model that segments 100+ anatomical structures from CT.
Tridesclous↗
Transparent, GUI-driven spike sorting emphasizing visualization of every step.
UCSF ChimeraX↗
Next-gen Chimera for interactive visualization of atomic models and density maps.
Uni-Mol↗
3D molecular representation learning for docking, properties, and design.
UniProt↗
Universal protein knowledgebase — sequences, function, and annotations.
VAME↗
Clusters behavior into motifs using a variational autoencoder over aligned pose sequences.
VEP↗
Ensembl Variant Effect Predictor — annotate variants against transcripts and regulatory features.
VisIt↗
Interactive parallel visualization and graphical analysis of scientific data.
VizieR↗
Query service for astronomical catalogues published in journals.
VMD↗
Visual Molecular Dynamics — trajectories, membranes, and huge biomolecular systems.
VTK↗
Visualization Toolkit — 3D computer graphics and image processing.
WaveClus↗
Unsupervised spike detection and sorting via wavelets and superparamagnetic clustering.
WDL↗
Workflow Description Language used by Cromwell, Terra, and many genomics pipelines.
WorkflowHub↗
Registry for describing and sharing computational workflows across domains.
WRF↗
Weather Research and Forecasting model for mesoscale NWP.
xarray↗
Labeled n-dimensional arrays for multi-dimensional scientific data; integrates with Dask and Zarr.
XCMS↗
LC-MS feature detection, alignment, and correspondence for metabolomics.
yt↗
Volume analysis and visualization for astrophysical simulation datasets.
Zarr↗
Chunked, compressed n-dimensional arrays for parallel and cloud computing. An optional NWB backend.
ZeroCostDL4Mic↗
Google Colab notebooks that put DL microscopy models in reach without local GPUs.
ZINC↗
Free database of commercially available compounds for virtual screening.
About the Open Science Index
- What is the Open Science Index?
- A curated directory of scientific software — genomics, structural biology, chemistry, microscopy, neuroscience, medical imaging, astronomy, climate, physics, and more — filterable by domain, language, and format.
- Which domains are covered?
- Life sciences first (genomics, chemistry, structural biology, microscopy, neuroscience), plus medical imaging, astronomy, Earth/climate, physics, engineering, lab notebooks, and scientific databases.
- Do you host the software?
- No. Each card links to the project’s official site or GitHub. Install from the maintainers.
- How is this different from an Awesome list?
- Awesome lists are markdown dumps. This index is filterable by language, I/O, and maintenance status, and it sits next to Bibby’s writing tools.