Project layout

• data: Original source data, consider this read-only.
• output: Generated data files, do not check in anything in here.
• src: Source code for data processing.
• static: Static resources for the web UI.
• templates: Django templates for the web UI.

Build instructions

• To obtain content of data/networks/:

  1. Unpack data.tgz from the Dropbox folder into this directory, producing data/networks/data containing several .csv files (see data/networks/README.rst for details)

• To prepare data files for loading into Cytoscape (version 3):

  1. Run python build_cytoscape_network_csv.py
  2. Run bash src/build_cytoscape_node_data.sh
  3. Import output/wtmat_cytoscape_0.53.csv into Cytoscape via File > Import > Network > File
  4. Import output/node_all.tsv into the resulting network via File > Import > Table > File

• To build the web content:

  1. Merge graph (.cyjs) file with tissue data:

     python src/add_tissue_data_to_graph.py data/wt_53.cyjs data/tmat_40.tsv > output/web/data.json

  2. Run src/build_web.sh

  3. View output/web/index.html

Local viewing

Use chrome/chromium, with the following command line arguments:

--temp-profile --no-first-run --no-default-browser-check --allow-file-access-from-files output/web/index.html