Add mets concentration from ymdb

[cheng-yu-zhang]

Main improvements in this PR:

Defined concentration ranges for 125 metabolites. All files and codes are stored in ./add_conc.

• ./add_conc/code/get_YMDB_data.py was written by @qqlaoxia to get metabolites information in YMDB.
• ./add_conc/code/organise_data.py was used to make metabolites information easy to intergate into model.
• ./add_conc/code/add_conc.m was used to add concentration ranges into model. And model file with concentration information is store in ./add_conc/modelWithConc.mat
• ./add_conc/data/allConcData.csv contains 869 metabolites concentration data. However, only 125 metabolites (315 if concern metabolites in different compartments) are present in the model.

The concentration range is calculated according to the following logic:
For example: In YMDB, three conc is recorded for glutamine ('17140.0 ± 1971.0 umol/L', '2500.0 ± 500.0 umol/L', '15000.0 ± 0.0 umol/L')

• Maximal conc: The maximum concentration plus the corresponding error. In this case, is "17140.0 + 1971.0 umol/L"
• Minimal conc: The minimum concentration minus the corresponding error. In this case, is "2500.0 - 500.0 umol/L"

I hereby confirm that I have:

• Selected develop as a target branch (top left drop-down menu)

[edkerk]

• Squashed earlier commits together, to remove 16000+ Excel files from the git history.
• Refactored the code and data in code/missingFields/addYMDBconcentrations.m and data/databases/YMDBconcentrations.csv to:
  • Move files into appropriate code and data subfolders, to keep a tidy repository.
  • Transposed the CSV file with concentration data for easier inspection.
  • Refactored the code to only download data for metabolites with concentration data. Download + parsing takes 2 mins, instead of many hours.
  • Avoid unnecessary dependency on python.
  • Do not store a modelWithConc.mat file, as this file will soon enough be out of sync with the latest model release.
  • Also try to match YMDB to the model by metabolite names.