nickp60 / genvis_lite

GeneExpressionAging

Overview

The goal of our project is to leverage web technologies to build a modular gene expression viewer for large-scale, complex experiments. The data included in this repo is just a sample of what can be achieved with this scheme. By using Django and Polymer for optimal performace, ease of use, and consistency.

Audience

We want people with little to no bioinformatics experience to be able to set up a custom gene expression viewer for their lab's data. We want to provide an interface that allows biologists to get what they need from the data. Fast.

Structure

Django serves the data through API calls, and Polymer builds the front end from nice reusable web components.

Requirements

• python3
• npm

Django

##Installation In order to install, you should create a virtual env using Python 3 and install the requirements listed on 'requirements.txt':

$ mkvirtualenv -p `which python3` GeneExpressionAging
$ pip install -r requirements.txt

To run the server:

$ cd webapp
$ workon GeneExpressionAging
$ python manage.py runserver

You can browse:

http://127.0.0.1:8000/genvis/ideogram

or:

http://127.0.0.1:8000/index.html

webserver

The server is running on the server (ask for the IP). In order to connect, use tunneling.

screens

The django server is running directly (django runserver) and using 'screen' to detach the window between SSH sessions:

• Create the window: Run 'screen' and run the server

• Detach the window: On the screen, type "Ctrl" + a + d

• Reatach window: On the ssh session, type screen -r

Datasets

Dataset structure:

• TODO

REST API

http://127.0.0.1:8000/api/series/detail

Input: {"dataset": "mouse_aging",
        "serie": <serie-name>}
Output: {"ok": True/False,
         "values": <list-of-values>,
         "wizard": <wizard-name>}

If the serie has a lot of values, the output will not have "values" field.

http://127.0.0.1:8000/api/series/find

Input:  {"dataset": "mouse_aging",
         "serie": <serie-name>,
         "text": <search-text>}
Output: {"ok": True/False,
         "dataset": "mouse_aging",
         "result": [ <result-1>, <result-2>, ...]}

result: [<ensembl_gene_id>, <external_gene_name>, <entrezgene>]  (yes, an array of three element for each gene)

http://127.0.0.1:8000/api/timeseries

Input: {"dataset": "mouse_aging",   // We only have this
        "xaxis": <dimension-name>,
        "series": <dimension-name>,
        "restrictions": <list-of-restrictions>}

Restriction: [<dimension-name>, <operation>, <parameter>]
Operation: "eq" or "in"
Parameter: if operation is "eq", parameter should be a string
           if operation is "in", parameter should be a list of strings

Example:
    {"dataset": "mouse_aging",
     "xaxis": "age",
     "series": "gene",
     "restrictions": [
         ["tissue", "in", ["AM", "LUNG"]],
         ["flu", "eq", 150],
         ["gene", "in", ["ENSMUSG00000000088", "ENSMUSG00000000001"]]
         ]}

Output:
    {"ok": True/False,
     "dataset": "mouse_aging",
     "field_values": { "name": <field-value> },
     "xvalues": <list-of-floats>,
     "series": [
         {"values": [ value ],
          "name": <string>}
     ]}

Field-value: {"truncated": True/False,
              "values": <list-of-values>}
value: [ <mean>, <stderr> ]

Polymer

Installation

npm install bower
npm install polymer-cli
bower install

Building and serving the site

./node_modules/.bin/polymer build
./node_modules/.bin/polymer serve