Merge pull request #28 from loucerac/develop

Develop

.vscode/ltex.dictionary.en-US.txt

@@ -0,0 +1 @@
+Hipathia

README.md

@@ -1,12 +1,71 @@
-# Drug REpurposing using Mechanistic Models of signal transduction and eXplainable Machine Learning
+# Drug REpurposing using Mechanistic Models of signal transduction and -eXplainable Machine Learning
 
-Repository for the drexml python package: (DREM³L) Drug REpurposing using Mechanistic Models of signal transduction and eXplainable Machine Learning 
+Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using Mechanistic Models of signal transduction and eXplainable Machine Learning 
 
 ## Setup
 
 To install the `drexml` package use the following:
 
 ```
-conda create -p ./.venv python=3.8
-conda run -p ./.venv git+ssh://[email protected]:loucerac/drexml.git
+conda create -n drexml python=3.8
+conda run -n drexml pip install git+ssh://[email protected]:loucerac/drexml.git
 ```
+
+## Run
+
+To run the program for a disease map that uses circuits from the preprocessed `KEGG` pathways and the `KDT` standard list, construct an environment file (e.g. `disease.env`) using the following template:
+
+```
+gene_exp=$default$
+pathvals=$default$
+circuits=circuits.tsv.gz
+circuits_column=in_disease
+genes=$default$
+genes_column=approved_targets
+```
+
+Where `circuits.tsv` has the following format (tab delimited):
+```
+index	in_disease
+P-hsa03320-37	False
+P-hsa03320-61	False
+P-hsa03320-46	False
+P-hsa03320-57	False
+P-hsa03320-64	False
+P-hsa03320-47	False
+P-hsa03320-65	False
+P-hsa03320-55	False
+P-hsa03320-56	False
+P-hsa03320-33	False
+P-hsa03320-58	False
+P-hsa03320-59	False
+P-hsa03320-63	False
+P-hsa03320-44	False
+P-hsa03320-36	False
+P-hsa03320-30	False
+P-hsa03320-28	True
+```
+
+where:
+* `index`: Hipathia circuit id
+* `in_disease`: boolean if a given circuit is part of the disease
+
+```
+conda run -n drexml drexml run --n-gpus 0 --n-cpus 10 $DISEASE_PATH
+```
+
+where:
+* `--n-gpus` indicates the number of gpu devices to use in parallel (-1 -> all) (0 -> None)
+* `--n-cpus` indicates the number of cpu devices to use in parallel (-1 -> all) 8
+* `DISEASE_PATH` indicates the path to the disease env file (e.g. `/path/to/disease/folder/disease.env`)
+
+Use the `--debug` option for testing that everything works using a few iterations.
+
+Note that the first time that the full program is run, it will take longer as it downloads the latest versions of each background dataset from Zenodo:
+
+https://doi.org/10.5281/zenodo.6020480
+
+## Documentation
+The documentation can be found here:
+
+https://loucerac.github.io/drexml/

docs/source/index.rst

@@ -1,7 +1,7 @@
-DREXM³L Drug REpurposing using Mechanistic Models of signal transduction and eXplainable Machine Learning 
+DRExM³L Drug REpurposing using Mechanistic Models of signal transduction and eXplainable Machine Learning 
 =========================================================================================================
 
-DREXM³L or drexml is a Python package for finding links between Known Drug Targets (KDTs) 
+DRExM³L or drexml is a Python package for finding links between Known Drug Targets (KDTs) 
 and signaling circuits.
 
 .. figure:: ../fig/holird.png
@@ -16,7 +16,7 @@ You can install drexml from PyPI using pip:
 
 .. code::
 
-   pip install drexml
+   pip install git+ssh://[email protected]:loucerac/drexml.git