miso(soup)
misosoup is a Python package for identifying minimal communities (minimal supplying community search). Through genome-scale constraint-based metabolic modeling, misosoup enables the systematic identification of communities that support microbial growth in environments where individual strains fail to survive alone.
misosoup provides a powerful tool for microbial ecology and community design, with potential applications in both research and biotechnological innovation.
Basic Information
| Repository | https://github.com/sirno/misosoup |
| Documentation | https://sirno.github.io/misosoup/ |
| Main publication (DOI) | 10.1128/msystems.00688-26 view |
| Contact email | alberto.pascual.garcia@gmail.com |
| Authors/Maintainers | Alberto Pascual García |
| Type of application | R/python package |
| Programming languages | Python |
| Keywords | Computational Methods, Computational models and simulations, Metabolic modelling, Ecological modelling |
Technical details
| Input file formats | |
| Output file formats | |
| Software compatibility | Linux, Mac, Windows |
| Hardware requirements | |
| Type of containerization | Conda |
| Wrapper type | Snakemake |
| Compatible tools | |
| Funding resource | Research charity funding |
| Funding support | No funding |
Statistics
| Unique users (last 12 months) | |
| Unique users (since first release) | |
| Software downloads (last 12 months) | |
| Software downloads (since first release) | |
| Jobs submitted (last 12 months) | |
| Jobs submitted (since first release) | |
| Repository clones (last 12 months) | |
| Repository clones (since first release) | |
| Citations (last 12 months) | <100 (~0 as of 15/10/2026) |
| Citations (since first release) | <100 (0 as of 15/10/2026) |
| Early-stage researcher effort (development) | |
| Early-stage researcher effort (maintenance) | |
| Technician-supported effort (development) | |
| Technician-supported effort (maintenance) | |
| Other effort (development) | |
| Other effort (maintenance) | |
| Total effort (development) | |
| Total effort (maintenance) |