README.md

cfosdb

Prototyping

Full featured prototype: https://www.figma.com/proto/omgiSy8oK0iAFBXoCVWQbJ/cfosdb?node-id=3%3A25&scaling=min-zoom

API script

Start api service

Run the nodejs file: api.js

API

localhost:8081?behavior=<behavior_list>&brain_code=<brain_area_list>&gender=<gender>&species=<species>
behavor_list: the list of behavior, seperated by comma.
brain_area_list: the brain area list, seperated by comma.
gender: "male", "female", or "%" for both.
species: "Rat" or "Mouse"

Exp.

localhost:8081?behavior=pain,aggression&brain_code=R5,R7,R37&gender=%&species=Rat

Dataset

Database

The SQLite database: cFosDB.db There are two table in the database.

brain_area_annotation:

CREATE TABLE brain_area_annotation ( 
  brain_code text primary key, 
  main text,
  long_1 text,
  short_1 text,
  long_2 text,
  short_2 text,
  long_3 text,
  short_3 text,
  species text
)

brain_area_behavior:

CREATE TABLE brain_area_behavior ( 
  brain_code text, 
  behavior text, 
  species text, 
  gender text, 
  doi text, 
  condition text, 
  figure text, 
  cell_type text 
)

Other json files

The files useful for frontend is in frontend/src/assets/.

Update data

Update the data (data subfolder)

Changes the data in numbers.

Save the sheets in numbers as tsv format to data_table fold.

Run clean.R to format the data. It generates two files:

• ./clean_behavior_brain_area.tsv
• ./clean_brain_area_annotation.tsv

Generate database

1. Update the data for download

• Copy the neo_cfosdb/frontend/public/download/ data to neo_cfosdb/frontend/public/download_bk.
• Update the file name under "## Create file for download" section in neo_cfosdb/data/to_json.R file.

2. Generate data

Enter the neo_cfosdb/data fold. Generate the database by runging the Makefile.

Check the output information, make sure the behavior is good.

Update online database

1. Compile website:

Run Makefile in the root fold.

2. Upload website to server:

Run Makefile in the frontend fold