gene-network-visualizer

Application for lawrence-dill plant informatics & computation lab

Visualizes & tabulates user provided gene data + relatedness data.

Dependencies

.js: npm / yarn, react, react-scripts, semantic ui, see package.json in client .go: bitcask, mux, golang-set

Getting started

Install npm / yarn and go

Use BuildDb.go to build a database from two csv files

Builds a local read/write store of Gene UIDs mapped to their details and relationships with other genes.

usage:

go run BuildDb.go [gene_info_file.csv] [gene_edges_file.csv]

info_file columns

• uid: unique gene identifer (per dataset)
• species: species symbol
• gene_names: various names delimited by |
• term_ids: go_terms
• gene_display_name: label gene will have as a node on visualizer
• color: color of node

edges_file columns

• from: uid of edge source
• to: uid of edge target
• distance: weight of edge
• ...: more edge weights may be comma seperated per row, but only 'distance' is recorded

Install client dependencies

cd client; npm install

Run dev servers

• cd /client; npm run start start the frontend at localhost:3000/landing
• cd /server; go run main.go start the backend to listen for requests
• cd /server/router; python3 router.py auxillary handler for requests to be handled in pure python

Visit application

localhost:3000/landing

Synopsis / Dataflow

• client - react frontend
  • public - contains documentation static files, served by react
  • src - contains react source
• server - contains main.go entry for backend
  • database - contains BuildDb.go and directory for data storage
  • middleware - logic handling endpoint requests
  • models - typing & backend auxillary functions
  • router - defines how urls are listened for, contains router.py

Clients issue input to the application primarily in /client/src/Home.jsx

Functions from /client/src/utils invoke endpoints being listened for in /server/router/router.go which handles requests based on url prefixes. Once an endpoint is caught it's handled in /server/middleware/middleware.go which returns an appropriate response.

Many helper functions and constructors compose our data to how our frontend wants them. These can be found in /server/models/models.go.

Currently Flask returns an assortment of random genes. /server/router/router.go listens for a search type 'flask' (via url param) before sending a request to the running /server/router/router*.py*. The flask server sends back a list of random UIDs from the database before the golang backend aggregates the gene / edge information from it.

Aside: Client request Errors crash the server immediately. This can be changed in main.go (set to Fatal.log)