HOPER Instalation Steps For Models

PPI Model Instalation Instructions

To install packages to use for Node2vec and HOPE in your home directory, use:
- GEM version 213189b; use for old version:
  
  git clone [https://github.com/palash1992/GEM.git]
  
  git checkout [213189b]
To make Node2vec executable; Clone repository git clone https://github.com/snap-stanford/snap and Compiles SNAP. The code for compiles is as below:
- cd snap/
- rm -rf examples/Release
- make all
- cd examples/node2vec
- chmod +x node2vec
- ls -alh node2vec
Make node2vec executable and add to system PATH or move it to the location you run.

To use text representation generator, copy uniprot and pubmed text files to HOPER/text_representations/representation_generation/data/ in separate folders named as uniprot and pubmed.
biosentvec and biowordvec models must be downloaded to HOPER/text_representations/representation_generation/models from the urls given below. Alternatively model_download parameter must be set as "y" to download models automatically if biosentvec or biowordvec representations selected to be generated.