RMDB RNA Mapping DataBase

⚠️ This server has been decommissioned (May 2026). The AWS EC2 instance has been terminated. See Migration below for the current site and archive details.

This is the Source Code repository for RMDB RNA Mapping DataBase Server. The production server was freely accessible at https://rmdb.stanford.edu/.

Migration

In May 2026, rmdb.stanford.edu was migrated from this Django/MySQL AWS server to a static GitHub Pages site.

	Details
New site	https://rmdb.stanford.edu/ (GitHub Pages)
New site repo	https://github.com/DasLab/rmdb.github.io
RDAT data hosting	GitHub Releases on the new-site repo, split across 5 subcategory tags: data-eterna, data-puzzle, data-riboswitches, data-rna-structures, data-general
rdat_kit package	https://github.com/ribokit/rdatkit (v1.8.1, Python 3) — provides rdat_kit validate, rdat_kit to_md, rdat_kit thumbnail for contributors
Archive	DasLab Shared Drive → Projects → AWS Server Archives → RMDB_2026/
Archive contents	rmdb_aws_archive.tar.gz (Django app, 14 GB), rmdb_db.sql.gz (MySQL dump, 1.4 GB), README.docx + README.md
AMI snapshot	rmdb-final-2026-05-15 (us-west-2)

To run the old site locally from the archive, see README.docx in the Google Drive folder above. The bundled Dockerfile + docker-compose.yml + entrypoint.sh bring up a faithful copy at http://localhost:8001/.

To contribute a new entry to the new site, see https://rmdb.stanford.edu/contribute/.

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Installation

RMDB Server requires the following Python packages as dependencies, most of which can be installed through pip.

boto >= 2.38.0
Django >= 1.9.1
django-adminplus >= 0.5
django-crontab >= 0.7.0
django-environ >= 0.4.0
django-filemanager == 0.0.2
django-suit >= 0.2.15
django-widget-tweaks >= 1.4.1
gviz-api.py == 1.8.2
MySQL-python >= 1.2.5
PyGithub >= 1.26.0
pytz >= 2015.7
requests >= 2.9.1
simplejson >= 3.8.1
Biopython >= 1.70

rdatkit >= 1.0.2

The rdatkit package is available internally at RDATKit.

The gviz-api.py is available at google-visualization-python.

The django-filemanager is a modified version of django-filemanager. The source code is available internally at this fork.

Install with:

cd ~
git clone https://github.com/ribokit/rdatkit.git
cd rdatkit
sudo python setup.py install

cd ..
git clone https://github.com/google/google-visualization-python.git
cd google-visualization-python
sudo python setup.py install

cd ..
git clone https://github.com/t47io/django-filemanager.git
cd django-filemanager
sudo python setup.py install

RMDB Server also requires proper setup of imagemagick, optipng, VARNA.jar, mysql.server, apache2, mod_wsgi, openssl, gdrive, awscli, and cron jobs.

Lastly, assets preparation is required for the 1st time through running sudo python manage.py versions, sudo python manage.py dist, util_prep_dir.sh, util_src_dist.sh, util_minify.sh, util_chmod.sh and manually replacing config/*.conf. For full configuration, please refer to Documentation.

Usage

To run the test/dev server, use:

cd path/to/server_RMDB/repo
python manage.py runserver

The server should be running at localhost:8000 with a python session interactive in terminal.

To generate the JSON file for one entry, use:

cd path/to/server_RMDB/repo
python manage.py make_json RMDB_ID

for all entries:

cd path/to/server_RMDB/repo
python manage.py make_json -A

TODO

• The major incomplete task is a total transfer of licensing of RiboKit packages out of RMDB and into ribokit-license.stanford.edu. That repo is hosted at https://github.com/DasLab/Server_Ribokit_License . Its almost ready except for automatic pulls of RiboKit packages, which is coded up in Server_RMDB dist.py but has not yet been transferred over due to problems setting up oauth/Github authorization.
• Other RMDB server issues and feature wish list are described in issues.

License

Copyright © 2014-2017: Siqi Tian [t47]; 2017 Chunwen Xiong; 2017 Das Lab, Stanford University. All Rights Reserved.

RMDB Server Source Code is proprietary and confidential. Unauthorized copying of this repository, via any medium, is strictly prohibited.

Maintenance for RMDB ops

0. Server login and update:

• contact admin for the amazon.pem
• use ssh -i amazon.pem ubuntu@ec2-35-91-89-102.us-west-2.compute.amazonaws.com to login
• use sync to merge and update produciton version

1. 500 Errors:

• Investigate immediately (you get admin email notice)
• Hot fix or escalate issue, or disable

2. AWS instance monitoring:

• Subscribe to alerts
• Respond when server is down (e.g. check logs, restart)

3. New entry actions:

• Examine and approve for newly submitted entries by non-Admin users (rare)
• Check if heatmap and meta data for new entry is correct (should success)

4. HTTPS certificate renewal:

• Due on Sep 22 2018

Things that should NOT need care (done automatically):

• Indexing of all entries [triggered by CRUD]
• Image (thumbnail) and JSON meta for entries [triggered by CRUD]
• Tools repository update download [GitHub Webhook]
• Data/config backup [weekly on Sun morning by cron]

Keep an eye on them when fail (you get admin email notice)

Reference

Cordero, P., et al. (2012)
An RNA Mapping DataBase for Curating RNA Structure Mapping Experiments.
Bioinformatics 28 (22): 3006-3008.

by t47, March 2016.