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.