data base of microarray experiments on preeclamptic placenta tissue
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
.idea
articles
db_backups
outputs
preeclampsia_db
static
temp
templates/admin/articles/experiment
xls
.Rhistory
.dockerignore
.gitignore
LICENSE
Procfile
Readme.md
annual_output
backupnov132017
log
manage.py
mapping.txt
mesh_term_suggestions
placenta_experiment.txt
placenta_experiments.txt
requirements.txt
runtime.txt
samples.tsv
samples_E-GEOD-74341.txt
venv

Readme.md

IGEA

IGEA is a web-based tool for integrative analysis of gene expression data.

Development progress

  • [DONE] Database

    • schema to store Eperiment, Sample and Microarray metadata
    • schema to store additional info on sample attribute names and values
    • Store additional info on sample attribute standard names and values: link to ontologies (MeSh, EFO), explanation, synonyms
    • [MOSTLY DONE] store and update in background Experiment status: standardized; mail sent, mail received, has minimal data for integration, is excluded etc.
  • [DONE] Automate downloading metadata form ArrayExpress

  • [DOING] Admin interface

    • autocomplete lookup fields and "for each" checkboxes for easier input
    • reduce loading form loading time
    • samples metadata standardization form
    • samples attribute add or replace form
    • test data for duplicate entities
  • [DOING] Deployment

    • Deploy to Heroku hosting service; suspended due to exeeded space limit for a free account
    • Deploy to the server at Institute of Molecular Biology and Genetics; accessible at http://194.44.31.241:24173/
    • deploy to a server at European Grid Infrastructure
  • [DONE] Data plots

  • [DOING] Data access user interface

    • Basic interface with header nav bar
    • Experiments page with basic table of experiments
    • Samples page with basic table of samples
    • Upd tables with filter rows by column value
    • [DOING] Side bar for Samples table to show/hide certain columns and rows with certain values
    • Intro page
    • Logo
    • Downlowdable BibTex citations on nav bar
    • [Х] Order columns properly
    • [Х] Download Experiments, Samples tables as TSV files
    • Upload Experiment, Sample metadata from TSV files provided by user
    • Slider widgets to Samples side bar as search filters for numeric columns
    • Exclude rows with empty values option
  • Construct study groups based on metadata

    • send study groups' meta- and expression data to Inmex
  • Automate downloading and processing sample expression data from ArrayExpress

  • Integrate sample expression data for study groups

  • Search for differentially expressed genes.

  • Embed earlier developed BNFinder tool for gene regulatory networks construction https://github.com/sysbio-vo/bnfinder/

  • Data analysis user interface

  • Embed Telegram bot featured for automated solving bioinformatican's minor problems, which is under development https://github.com/Dantistnfs/telegram-genetic-bot

  • Specialized blog to quickly post new analysis results to IGEA site and to social media

Built With

License

This project is licensed under the GNU General Public License - see the LICENSE file for details