Kinetic_Interactions

this repository creates a data warehouse to caculate allosteric regulation for each enzyme of each organism. This repository collects kinetic regulation from the in-house database and apply ML algorithms to estimate missing values.

Required modules:

Please follow these steps to install all required packages on your device.

• create a conda environment

conda create -n my_new_env python

• check if the env is created

conda env list

• activate env

conda activate my_new_env

• add conda forge to channels:

conda config --append channels conda-forge

• set channel priority

conda config --set channel_priority strict

• pandas

conda install pandas

• mysql connector

pip install mysql-connector-python

• Install pycurl on your device

pip install pycurl

• if the version of pycurl is not compatible with openssl, you will face this error:

pycurl: libcurl link-time ssl backend (nss) is different from compile-time ssl backend (openssl)

• To debug, follow these steps:

pip uninstall pycurl
export PYCURL_SSL_LIBRARY=nss
pip install --compile --install-option="--with-nss" --no-cache-dir pycurl

References:

• How to compute standard deviations from confidence intervals
• Propagation of error for multiple variables
• assume 5% standard error for measurements without error
• metabolomics dataser for E coli
• Slides for data pipeline