MINERVA Platform website

Introduction

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 - Source file 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.

MINERVA is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java 8. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated in JavaScript and content is visualized by OpenLayers/Google Maps API.

[!New] a website with MINERVA tutorials can be found here.

Table of contents

Citation
Licensing
Sources
Source code
Supported projects
Troubleshooting
Contact

Citation

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

Licensing

MINERVA Platform is released under the Affero General Public License (AGPL).

Sources

MINERVA relies on these following external data sources:

Name	Citation
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.

Source code

The source code for the MINERVA platform is currently available on git.

Supported projects

MINERVA Platform supports the following projects:

Ageing map
Asthma map
Atlas of Inflammation Resolution
Chronic Inflammatory Diseases
Parkinson’s disease map
Recon map
Rheumatoid arthritis map (to be released)
Atlas of Cancer Signaling Networks (source accessible here, to be released on MINERVA)

Troubleshooting

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

java installation

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: click

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.