Introduction Biomass reaction table importer Context builder Context exporter Context importer Convert Model Annotation Draft recon Draft recon EC number table importer Entity ID table importer FBA Flux Table Analysis Flux table importer FVA Gap filler Isolate finder KOA KOA result extractor Medium table importer Network exporter Network importer Network merger Orphan remover Phenotype table importer Reaction adder Reaction remover Smart json modificator (cobra) Transporter adder Twin annotator Twin builder Twin exporter Twin flattener Twin importer Twin reducer XML/Matlab to JSON
Technical Documentation
Resources
Tasks
Protocols
Smart json modificator (cobra)
Generate an json model with modifications asked.
This task is still in beta version.
This task uses openAI API to generate python code that modify a genome scale metabolic model stored in a json format; using cobra library. This code is then automatically executed.
Here are few examples of what you can ask for: Please change the id of the metabolite "xxx" by "yyy" Please change the id of the reaction "xxx" by "yyy" Please change the id of the gene "xxx" by "yyy" with the function cobra.manipulation.modify.rename_genes
The data of the model is not transferered to OpenAI, only the provided text.
Input
File
Output
Model Modified
Model modified.
Configuration
prompt
open_ai_chat_param