Welcome to the Medema Group GitHub page!
The Medema research group at Wageningen University, develops and applies algorithms for the (meta)genomic identification and functional prediction of microbial and plant biosynthetic pathways, with the aim to unravel the chemical language of microbiomes, and host-microbe interactions and accelerate natural product discovery.
To this end, we develop tools and algorithms for the analysis and integration of omics data, curate and maintain databases, and collaborate with wet-lab scientists.
Together with our collaborators, we have created numerous state-of-the-art tools, such as antiSMASH and BiG-SCAPE, and gold-standard databases such as MIBiG and antiSMASH-DB.
Here, we provide documents describing the collaborations within the Medema research group. These guidelines apply to all repositories governed by this GitHub Organization.
- 📜Code of Conduct: guidelines for interacting with the projects.
- 👥Onboarding Docs: A number of documents to facilitate onboarding.
Overview of the projects/repositories governed by the Medema group.
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| BiG-FAM | BGC Family Database | AGLP-3.0 | N/A | Invited (internal) |
| BiG-SCAPE | BGC clustering tool | AGLP-3.0 | N/A | Invited (public) |
| BiG-SLICE | BGC clustering tool | AGLP-3.0 | N/A | Invited (public) |
| CAGECAT | BGC comparison and visualization toolobx | MIT | N/A | Invited (public) |
| Decrippter | RiPP BGC mining tool | N/A | N/A | N/A |
| GutSMASH | N/A | N/A | N/A | N/A |
| iPRESTO | N/A | N/A | N/A | N/A |
| Multismash | N/A | N/A | N/A | N/A |
| PKSPop | N/A | N/A | N/A | N/A |
| rhizoSMASH | Genome mining tool for plant-rhizobacteria interaction | GNU Affro GPL 3.0 |  | N/A |
| RRE-finder | N/A | N/A | N/A | N/A |
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| BiG-MAP | BGC Meta'omics abundance profiler | MIT | N/A | Invited (public) |
| COCOLOCUS | Co-expression analysis for BGC functional inference | TBA | N/A | N/A |
| LogoMotif | TBA | TBA | N/A | N/A |
| MiniMotif | TBA | TBA | N/A | N/A |
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| biosynfoni | Substructure-based fingerprint for estimating biosynthetic similarity between natural products. | MIT | TBA | TBA |
| CineMol | Direct-to-SVG 3D molecule drawer. | MIT | TBA | TBA |
| CytoMol/COMET | Substrucutre-based inference of natural product bioactivity. | MIT | TBA | TBA |
| Donphan | TBA | TBA | TBA | TBA |
| PARASECT | NRP A-domain substrate specificity prediction models. | MIT | TBA | TBA |
| PIKAChU | Cheminformatics toolkit. | MIT | TBA | TBA |
| RAIChU | Python-based informatics tool for the visualisation of natural product chemistry. | MIT | TBA | TBA |
| RetroMol | Rule-based retrobiosynthesis for natural products. | MIT | TBA | TBA |
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| Whokaryote | Classify metagenomic contigs as eukaryotic or prokaryotic | GNU Affro GPL 3.0 | N/A | N/A |
| PlantMAGIC | Plant-associated microbiome MAG database | TBA | N/A | private |
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| MIBiG submission portal | Submission portal for the MIBiG database | TBA | TBA | TBA |
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| MEANTools | TBA | TBA | TBA | TBA |
| MetaBrassPW | TBA | TBA | TBA | TBA |
| Name | Description | License | Zenodo | Contribution |
|---|---|---|---|---|
| modern_python | A template to set up Python projects | Unlicense |  | Invited(public) |
Organizations and projects the Medema group is involved with.
| Name | Description |
|---|---|
| antiSMASH | Genome mining tool |
| MIBiG | Database on biosynthetic gene clusters |
| MITE | Database on tailoring enzymes |
| MolTools | Tooling for cheminformatics |
| FERMO | Metabolome mining tool |
| Pathway Linked Open Data | Linked Open Data for Pathway Information |
| plantiSMASH | Genome mining tool |
A number of documents to facilitate onboarding, including standard operating procedures.
| Name | Description |
|---|---|
| TRANSFER REPO | Instructions on transferring repositories to the Medema group GitHub organization |