Lista de herramientas interesantes para el modelado metabólico
- Cobra toolbox: https://opencobra.github.io/cobratoolbox/stable/
- Cobrapy: https://cobrapy.readthedocs.io/en/latest/
- Raven 2 : https://github.com/SysBioChalmers/RAVEN --> Framework , requiere MATLAB 2016 o más nuevo
- Aureme: http://aureme.genouest.org/ --> linea comando, hasta que no actualicen los errores, no usar
- Merlin: https://merlin-sysbio.org/index.php/Home
- Carveme: https://carveme.readthedocs.io/en/latest/
- ModelSEED: http://modelseed.org/ --> Online
- MetaDraft: https://systemsbioinformatics.github.io/metadraft/
- Blast todo contra todo:
- Escher: https://escher.github.io --> It includes framework (Ecoli,yeast,human)
- Model Explorer: https://almaaslab.nt.ntnu.no/index.php/resources/metabolic-modeling/
- GEMSiRV: http://sb.nhri.org.tw/GEMSiRV/en/GEMSiRV
- iMet: https://github.com/rmohamadi/iMet-Samples --> merge metabolic networks
- MOST: http://most.ccib.rutgers.edu/index.html
- Pathway tools: http://bioinformatics.ai.sri.com/ptools/ptools-overview.html
- CellDesigner: http://www.celldesigner.org/
- Cytoscape + Pluggin: https://apps.cytoscape.org/apps/with_tag/pathwaydatabase
- KBase: https://kbase.us -- online
- Memote: https://memote.io/
- Pan genome analysis: http://sanger-pathogens.github.io/Roary/
- Annotation: https://github.com/tseemann/prokka
- Descargar genomas: https://github.com/kblin/ncbi-genome-download
- MetaCyc: https://metacyc.org/
- EcoCyc: https://ecocyc.org/
- BIGG: http://bigg.ucsd.edu/
- KEGG: https://www.genome.jp/kegg/
- Reactome: https://reactome.org/
- BioModels: https://www.ebi.ac.uk/biomodels/
- Wikipathway:https://www.wikipathways.org/index.php/WikiPathways
- PANTHER: http://www.pantherdb.org/pathway/