reproduce the work

[dyusuf]

be able to reproduce the steps in the documentation with the following focus:

• build neo4j

  • String download: https://string-db.org/cgi/download.pl?sessionId=2678TKV1xrxX
    • FULL DATABASE DUMPS
      • ignore homology_schema.v11.0.sql.gz (2700 Gb)
        • build local DB
        • example: https://github.com/BackofenLab/protein-graph-database/blob/master/sql/dump_mouse.sh
        • relevant credential in email
        • how to update?
        • first update String sql
        • https://github.com/BackofenLab/protein-graph-database/blob/master/build_graph_db.py
          • replace create with merge statement in https://github.com/BackofenLab/protein-graph-database/blob/master/cypher_queries.py
          • specify all the properties of a node
        • how long to take from scratch: few minutes
        • neo4j
  • dumps -> need to get them
  • in docker container
    • example: docker run -p 5000:5000 bornabesic/pgdb-web
      • build the docker images
  • Borna will add to the documentation
    • run a server
  • conda
  • neo4j
  • python server.py
    • needs to fix the issue related to credentials.yml in the relevant scripts
      • how to create an event on frontend?
      • frontend folder -> index.html
      • dependencies
      • local components
      • make a query with ptotein ids
      • example of zoom
      • how vue.js frontend, gephi backend and neo4j communicate with each other?
      • how sigma.js being integrated to vue.js?
      • visulizaition.js
      • command line query over neo4j database
      • production webserver
      • frontend <-> ngins/apache <-> guincorn <-> backend
        @bornabesic hope u can help me out in regards tomorrow.