Code, proteomics data, and other resources for generating proteomaps graphics and proteomovies
For general information about proteomaps, see www.proteomaps.net
DOCUMENTATION documentation - General documentation proteomovies - Instructions and example files for generating proteomovies
CODE python - python code matlab - matlab code
DATA RESOURCES (information about proteins, hierarchy of protein functions) genomic_data
PROTEOME DATA (storage space for data at different stages of processing) data_original - directories with original proteomics data data_sets - data preprocessing (one directory for each data bundle) data_paver_input - input data for paver data_paver_output - output data generated by paver (images and html files) data_html - processed html (to be copied into website directory)
For running the python and matlab code on your computer, you need to update the path names. They are set in the following files:
../python/proteomaps_PATHNAMES.py ../matlab/proteomaps_path_names.m
Of course, also the path names in your scripts CreateProteomaps.sh have to be adjusted.
Data sets to be analysed together are called a "bundle". To create a new data bundle (called [DATA_BUNDLE]), create a new directory for the data bundle, with directory name: ../data_sets/[DATA BUNDLE]
Within this directory, prepare the necessary control files (for file formats, have a look at the corresponding files in existing file bundle directories)
o create the file filenames.csv with all necessary information
o create a new directory for the paver input files directory name: ../data_paver_input/data_for_paver_[DATA BUNDLE]
o create a new directory for the paver output files directory name: ../data_paver_output/proteomaps_[DATA BUNDLE]
o create a new shell script CreateProteomaps.sh calling CreateProteomaps.py
o run the shell script
This will create intermediate files in ../data_sets/[DATA BUNDLE] as well as files for paver in ../data_paver_input/data_for_paver_[DATA BUNDLE]
Then, proceed as follows:
o run paver with the input files from ../data_paver_input/data_for_paver_[DATA BUNDLE]
o save the output files in ../data_paver_output/proteomaps_[DATA BUNDLE]
o use the script Make_proteomaps_html.py to create the html files in ../data_html/ (you will have to edit the script and create a new entry for your file bundle; use the syntax you see in the existing entries)
o If you want to put the new proteomaps on the Proteomaps online website, use copy_files_to_website.py. You have to modify the script: insert the [DATA_ BUNDLE] in the list "data_set_collections" and run the script.
To generate proteomovies from your data files, please see the instructions in proteomaps-workflow/proteomovies/README
This package is released under the GNU General Public License.
Please contact Wolfram Liebermeister with any questions or comments.
Liebermeister W., Noor E., Flamholz A., Davidi D., Bernhardt J., Milo R. (2014), Visual account of protein investment in cellular functions, PNAS 111 (23), 8488-8493