Example usage for CM4AI data

The cell maps pipeline requires two RO-Crate directories from CM4AI data site

Step 1) Get data from CM4AI site

Visit https://cm4ai.org/data, login and accept agreement

For ImmunoFluorescent images RO-Crate

  1. If not already set, navigate to Data tab:

    Screenshot of data, cell maps, and intermediate other tabs with data selected
  2. On left side bar under Name check IF images checkbox, check MDA-MB-468 for Cell Line, untreated for Treatment, chromatin for Gene Set, and 0.1 alpha for Version:

    Screenshot of left side bar showing IF images, MDA-MB-468, untreated, chromatin, and 0.1 alpha boxes checked
  3. Click Download link on row:

    Screenshot of browser showing row of ImmunoFluorescent image dataset to download

For AP-MS RO-Crate

  1. If not already set, navigate to Data tab

    Screenshot of data, cell maps, and intermediate other tabs with data selected
  2. On left side bar under Name check AP-MS checkbox, check MDA-MB-468 for Cell Line, untreated for Treatment, chromatin for Gene Set, and 0.1 alpha for Version

    Screenshot of left side bar showing AP-MS, MDA-MB-468, untreated, chromatin, and 0.1 alpha boxes checked
  3. Click Download link on row

    Screenshot of browser showing row of AP-MS dataset to download

Step 2) Uncompress downloaded data from CM4AI site

The above steps will download two files:

  • cm4ai_chromatin_mda-mb-468_untreated_apms_0.1_alpha.tar.gz containing the AP-MS dataset

  • cm4ai_chromatin_mda-mb-468_untreated_ifimage_0.1_alpha.tar.gz containing ImmunoFluorescent image dataset

These files need to be untarred and gunzipped to be used by the cellmaps_pipeline

Easiest way to do this on Linux/Mac is to open and terminal and run the following:

tar -zxf cm4ai_chromatin_mda-mb-468_untreated_apms_0.1_alpha.tar.gz
tar -zxf cm4ai_chromatin_mda-mb-468_untreated_ifimage_0.1_alpha.tar.gz

Note

Before running above command be sure to change to directory where those files reside

Step 3) Run the cellmaps_pipeline on CM4AI data

cellmaps_pipelinecmd.py . --example_provenance > pipe_prov.json
# be sure to update pipe_prov.json file

cellmaps_pipelinecmd.py  --provenance pipe_prov.json \
                        --cm4ai_apms cm4ai_chromatin_mda-mb-468_untreated_apms_0.1_alpha/apms.tsv \
                        --cm4ai_image cm4ai_chromatin_mda-mb-468_untreated_ifimage_0.1_alpha/MDA-MB-468_untreated_antibody_gene_table.tsv

Note

Above command may fail to run on machines with 16gb of ram or less