tutorial_bioservices

Codes to use bioservices for querying genes, metabolites and reactions using UniProt, CheBI, Rhea and KEGG in three workbooks (Uniprot.ipynb, Rhea.ipynb and kegg.ipynb).

Weblinks for accessing their source codes are provided below:

1. UniProt
   https://bioservices.readthedocs.io/en/latest/_modules/bioservices/uniprot.html
2. Rhea https://bioservices.readthedocs.io/en/latest/_modules/bioservices/rhea.html
3. CheBI https://bioservices.readthedocs.io/en/latest/_modules/bioservices/chebi.html
4. KEGG https://bioservices.readthedocs.io/en/latest/_modules/bioservices/kegg.html

Access to the core model reactions and metabolites: https://docs.google.com/spreadsheets/d/1N6Mi1J9wbXRSIOvNGcvR8fBHkMbqZ6ycknRxeYALy8o/edit?usp=sharing

Instructions to install pathway tools for using pythoncyc

Pythoncyc is a python module to access metacyc. Pathway tools software needs to be installed for using pythoncyc. The instructions to download pathway tools are provided below.

Step 1: Go to https://bioinformatics.ai.sri.com/ptools/licensing/ptools-license-intermediate.shtml and choose REQUEST USE UNDER EXISTING LICENSE

Step 2: Fill up the details and wait for license. You will receive the link to download the softwares within 24 hours.

Step 3: With the username and password provided, download and finish up the installation as mentioned in the instructions. https://bioinformatics.ai.sri.com/ptools/installation-guide/released/index.html

Pthoncyc applications are given in the links below:

https://github.com/ecocyc/PythonCyc/blob/master/doc/tutorial.md

https://bioinformatics.stackexchange.com/questions/623/what-methods-should-i-use-from-pythoncyc-api-to-query-metabolites-in-biocyc-data?rq=1