Cytoscape
Network analysis and visualisation for biology and beyond: import interaction networks and tables, map attributes to node and edge styles, lay out and filter graphs, run analyses and extend it with apps from the Cytoscape App Store.
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Network analysis and visualisation for biology and beyond: import interaction networks and tables, map attributes to node and edge styles, lay out and filter graphs, run analyses and extend it with apps from the Cytoscape App Store.
More in Science & Research
Avogadro 2
Build molecules in 3D and set up computational chemistry: draw and optimise structures with force fields, generate input for NWChem, Gaussian, ORCA and Psi4, and visualise orbitals, vibrations and electron density from the results.
Gephi
Interactive graph and network visualisation: import nodes and edges from CSV, GEXF or GML, lay them out with force-directed algorithms, filter and rank by statistics such as modularity and centrality, and export publication-ready images.
JabRef
Reference manager built on BibTeX: collect papers by DOI, ISBN or arXiv id, keep PDFs and metadata together, organise with groups and keywords, and cite straight into LaTeX, Word or LibreOffice — with the library stored as a plain text .bib file you own.
Ketcher
Chemical structure editor: draw molecules and reactions, check valences, generate SMILES/InChI, and edit macromolecules (peptides, RNA/DNA, CHEM) — with the Indigo cheminformatics engine compiled to WebAssembly so every calculation runs locally.
Mol*
Molecular visualisation for structural biology and chemistry: renders proteins, nucleic acids, ligands, density maps and trajectories in the browser, reading mmCIF, PDB, SDF, MOL2, XYZ and MDTraj formats. The viewer behind RCSB PDB and PDBe.
napari
Multi-dimensional image viewer for microscopy and bioimaging: browse 2D–5D arrays and terabyte-scale datasets, overlay labels, points, shapes and tracks, annotate segmentations by hand, and drive it all from Python or its plugin ecosystem.
Open Science
Local-first AI research workbench: agents work with your files, run Python and R, query scientific databases, and produce reproducible reports, figures and tables.
SciQLop
Browse, plot and label in-situ space plasma data from MMS, Cluster, Solar Orbiter, Parker Solar Probe and many more missions (AMDA, NASA CDAWeb, ESA CSA): fast zoomable time series, event catalogs, Python products and Jupyter notebooks side by side.
