Early stage: sysbioverse is under active development and not stable yet. Only some of its components are ready for reproducible and reliable research use. We make the others public as previews, so their interfaces and results can still change.

Sysbioverse is an ecosystem of free open source packages for molecular systems biology, which are linked by common data structures, design principles and higher level workflows. It builds on and extends the scverse single-cell omics analysis ecosystem where it provides rich prior knowledge integration, methods for functional and mechanistic analysis and bridges to related fields such as metabolomics, microbiomics, nutrition, and exposomics.

Packages

annnet

Interoperable network data structure with hypergraph and multi-layer support.

docs | GitHub | PyPI

omnipath

Integrated access to 200+ databases of diverse prior knowledge.

docs | GitHub | PyPI | omnipathdb.org
stable legacy client: docs | GitHub | PyPI

corneto

Flexible and high-performance network optimization framework.

corneto.org | GitHub | PyPI

networkcommons

Benchmarking network optimization methods.

docs | GitHub | PyPI

Papers

AnnNet: multi-layer hypergraph data structure for science.
Daniele Bottazzi, Youssef Zerta, Pablo Rodríguez Mier, Dénes Türei, Julio Saez-Rodriguez (2026) in prep.

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome.
J Schaul, Y Bai, D Bottazzi, J Franken, T Lawrence, N Palacio-Escat, E Carreño, M Daley, L Gul, A Sahin, D Mañanes, B Bohar, A Dugourd, T Korcsmaros, D Turei, C Schmidt and J Saez-Rodriguez (2026) bioRxiv
DOI: 10.64898/2026.06.18.733117

OmniPath: integrated knowledgebase for multi-omics analysis.
D Türei, J Schaul, N Palacio-Escat, B Bohár, Y Bai, F Ceccarelli, E Çevrim, M Daley, M Darcan, D Dimitrov, T Doğan, D Domingo-Fernández, A Dugourd, A Gábor, L Gul, BA Hall, CT Hoyt, O Ivanova, M Klein, T Lawrence, D Mañanes, D Módos, S Müller-Dott, M Ölbei, C Schmidt, B Şen, FJ Theis, A Ünlü, E Ulusoy, A Valdeolivas, T Korcsmáros and J Saez-Rodriguez (2026) Nucleic Acids Research 54(D1):D652–D660
DOI: 10.1093/nar/gkaf1126

Unifying multi-sample network inference from prior knowledge and omics data with CORNETO.
P Rodriguez-Mier, M Garrido-Rodriguez, A Gabor and J Saez-Rodriguez (2025) Nature Machine Intelligence 7(7):1168–1186
DOI: 10.1038/s42256-025-01069-9

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks.
V Paton, D Türei, O Ivanova, S Müller-Dott, P Rodriguez-Mier, V Venafra, L Perfetto, M Garrido-Rodriguez and J Saez-Rodriguez (2025) Bioinformatics 41(2):btaf048
DOI: 10.1093/bioinformatics/btaf048

About

Sysbioverse is an open-source, community-driven ecosystem of Python packages for molecular systems biology. The packages share data structures and conventions, so prior knowledge, networks and models can move between them without conversion work. Sysbioverse builds on the data structures of scverse, and its packages are designed to be used together with scverse packages.

License: sysbioverse packages are released under the permissive BSD-3-Clause license. You can use, modify and redistribute them freely, in academic and commercial settings alike.

Sysbioverse was initiated by the Saez Lab (Heidelberg University & EMBL-EBI), the Korcsmaros Lab (Imperial College London), the Petsalaki Group (EMBL-EBI) and scverse. It is open to contributions from the whole community: new packages, methods, data resources and improvements to the existing tools are all welcome. Please reach out if you would like to be involved!

Questions and feedback: open an issue in the repository of the package, or write to omnipathdb@gmail.com.