BC-BET update_platforms process_data .github/workflows/create_db.yml

Version 2 of the Bladder Cancer Biomarker Evaluation Tool (BC-BET).

Description

Rapid evaluation of candidate diagnostic and prognostic gene expression biomarkers in 15 bladder cancer patient cohorts (N = 1559). BC-BET calculates how strongly a gene’s expression is associated with tumor presence (distinguishing tumor from normal samples), tumor grade (distinguishing low- from high-grade tumors), tumor stage (distinguishing non-muscle invasive from muscle invasive samples), and patient outcome (e.g., disease-specific survival) in each cohort. Versions of BC-BET for the evaluation of methylation biomarkers in 4 cohorts (N = 271 samples), for distinguishing tumor from normal samples, and for expression analysis across 40 commonly used bladder cancer cell lines are also available upon request.

BC-BET: https://bioinformatics.easternct.edu/app/bcbet

Citation

Dancik, G.M. An online tool for evaluating diagnostic and prognostic gene expression biomarkers in bladder cancer. BMC Urol 2015, 15:59. (link)

Running BC-BET

BC-BET v2.0 is available from the following URL: https://bioinformatics.easternct.edu/app/bcbet

Instructions for running BC-BET locally using Docker

In most cases, the web version (https://bioinformatics.easternct.edu/app/bcbet) will be preferred. However, BC-BET can also be run locally using Docker:

  1. First, download and install docker from https://docs.docker.com/get-docker/.

  2. Save the docker compose script, available at https://raw.githubusercontent.com/gdancik/BC-BET/main/local/docker-compose.yml, to a file named ‘docker-compose.yml’

  3. From your docker terminal, run the following from the directory containing the docker-compose.yml file:

     docker compose up -d

    Note that the first time you do this may take several minutes.

  4. You can now access BC-BET by opening your browser and entering the following:

     http://localhost:3838

    Note that it may take a minute or so for the mongo db to fully load.

    If interested, you can also access the mongo db directly from the following URL:

     http://localhost:8081/

  5. If you wish to shutdown BC-BET, you can run the following docker command from the directory containing the docker-compose.yml file:

     docker compose down

Instructions for developers

See docs/developers.md

Page theme

This page uses a slightly modified version of the Cayman theme (https://github.com/pages-themes/cayman)