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.
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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.
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Avogadro 2
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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.
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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.
