MINERVA Platform website
MINERVA (Molecular Interaction NEtwoRk VisuAlization) Platform is a standalone
webserver for visual exploration, analysis and management of molecular networks encoded in systems biology formats, including CellDesigner, SBML and SBGN.
For platform configuration and management, consult the Administrator manual.
For instructions on content upload, see Administrator manual - Add project and Examples for more details.
MINERVA is a quickly developing platform, to find out more about its latest changes see Release notes.
Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource. See User manual for a description of functionalities available in the map.
[!New] a website with MINERVA tutorials can be found here.
Table of contents
- Source code
- Supported projects
When using or referring to MINERVA Platform, please cite our publications
“MINERVA—a platform for visualization and curation of molecular interaction networks” by
P. Gawron, M. Ostaszewski, V. Satagopam, S. Gebel, A. Mazein, M. Kuzma, S. Zorzan, F. McGee, B. Otjacques, R. Balling, and R. Schneider
in npj Systems Biology and Applications, vol. 2, p. 16020, Sep. 2016, doi:10.1038/npjsba.2016.20.
available online: http://www.nature.com/articles/npjsba201620
“MINERVA API and plugins: opening molecular network analysis and visualization to the community” by
D. Hoksza, P. Gawron, M. Ostaszewski, E. Smula, R. Schneider
in Bioinformatics, 25 April 2019,
available online: https://www.ncbi.nlm.nih.gov/pubmed/31074494
“Closing the gap between formats for storing layout information in systems biology” by
D. Hoksza, P. Gawron, M. Ostaszewski, J. Hausenauer, R. Schneider
in Briefings in Bioinformatics, 05 July 2019,
available online: https://www.ncbi.nlm.nih.gov/pubmed/31273380
MINERVA Platform is released under the Affero General Public License (AGPL).
MINERVA relies on these following external data sources:
|ChEMBL||The ChEMBL database in 2017.
Gaulton A et al. PubMed ID: 27899562
Nucleic Acids Res. 2017 Jan 4; 45(Database issue): D945–D954.
|CTDbase||The Comparative Toxicogenomics Database: update 2019.
Davis AP et al. PubMed ID: 30247620
Nucleic Acids Res. 2019 Jan 8;47(D1):D948-D954. doi: 10.1093/nar/gky868.
|DrugBank||DrugBank 4.0: shedding new light on drug metabolism.
Law V et al. PubMed ID: 24203711
Nucleic Acids Res. 2014 Jan;42(Database issue):D1091-7. doi: 10.1093/nar/gkt1068.
|mirTarBase||Tools and data services registry: a community effort to document bioinformatics resources.
Ison J et al. PubMed ID: 26538599
Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116.
|OpenTargets||Open Targets Platform: new developments and updates two years on.
Carvalho-Silva D et al. PubMed ID: 30462303
Nucleic Acids Res. 2019 Jan 8;47(D1):D1056-D1065. doi: 10.1093/nar/gky1133.
The source code for the MINERVA platform is currently available on git.
MINERVA Platform supports the following projects:
- Ageing map
- Asthma map
- Atlas of Inflammation Resolution
- Chronic Inflammatory Diseases
- COVID-19 Disease Map
- Parkinson’s disease map
- Recon map
- Rheumatoid arthritis map
curl: command not found
Usually curl should be installed on you machine. In case it is not, you can install it by yourself:
sudo apt install curl
update of minerva
Minerva installed as debian package could be updated as other packages in your OS. You can manually trigger update of the minerva package:
sudo apt-get update sudo apt-get --only-upgrade install minerva
If these commands do not update minerva on your machine then probably some tool overridden list of repositories on your machine (for example: puppet-agent). In such situation you can fix the list of repositories and update minerva by:
echo "deb http://repo-r3lab.uni.lu/debian/ stable main" | sudo tee /etc/apt/sources.list.d/repo-r3lab.list sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xcb185f4e31872412 sudo apt-get update sudo apt-get --only-upgrade install minerva
Prior to minerva 13.0.0 Debian package installing minerva would install oracle java 8 and will make it a default version of a java running on Debian. So if you were using older version of java you might notice that something has changed. Currently minerva uses openjdk-8/openjdk-11.
Upload of a big map
By default tomcat is running on limited amount of memory. If you upload big map you might encounter failure problem that was raised by out of memory error. To increase amount of available memory, please read here.
Exported CellDesigner file
Very rarely, generated CellDesigner files might be corrupted and cannot be opened using CellDesigner. We are aware of this and we are constantly working on updating the export function. If this error happens to you, please send us small examples so we can track problem faster.
Installation of debian package
In case you have some problems with installing debian package (apt-get fails) you will be able to find more information in the log file:
When minerva is working on tomcat8 the log file is located in:
You can also check tomcat8 logs:
For more information, please, contact:
Université du Luxembourg
Campus Belval | House of Biomedicine
6, avenue du Swing
T: +352 46 66 44 5526 or 5604
F: +352 46 66 44 6949