MINERVA project website

Introduction

MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using (CellDesigner) or (SBGN editors). For platform configuration and management, please, consult the Admin manual. For detailed instructions on content upload, please, see Admin manual - Source file and Examples for more details.
MINERVA is 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 using JSF and PrimeFaces. The displayed content is visualized by Google Maps API, dedicated JavaScript and CSS.


Table of contents


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

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.

How to install

Debian/Ubuntu operating system

Installation instructions are for Debian (tested on stretch) and Ubuntu (tested on 16.04, 18.04). Please install minerva using the following command:

curl -s https://minerva.pages.uni.lu/doc/scripts/install.sh -o minerva-install.sh; \
sudo bash minerva-install.sh; \
rm minerva-install.sh
Run MINERVA platform by entering:
http://localhost:8080/minerva/ in the web browser
Use the following admin credentials to log in to the admin panel
login: admin
password: admin
Follow instructions in the Admin manual to change the password and, if needed, to add new users.


Virtual Machine image

You can download an image of a virtual machine running Debian Linux and a working instance of MINERVA platform using the following link. Choose the version you would like to try and download minerva-*_release.ova file. Suggested tool to open and use is Oracle VM VirtualBox.

Once the VM is running, run MINERVA platform by entering: http://localhost:8080/minerva/ in the web browser of the VM.

Use the following admin credentials to log in to the admin panel:

login: admin
password: admin

In case you’d like to configure the VM, root credentials are

login: root
password: 123qweasdzxc


Docker

We prepared a docker compose configuration. To make it running just clone the repository and start it:

git clone https://git-r3lab.uni.lu/minerva/docker.git
cd docker
docker-compose up

Once the container is installed, run MINERVA platform by entering: http://localhost:8080/minerva/ in the web browser.

Use the following admin credentials to log in to the admin panel:

login: admin
password: admin

Source code

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

Supported projects

MINERVA platform supports the following projects:

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.

Upload of a big map

By default tomcat7 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.

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:

/var/log/minerva-install.log

When minerva is working on tomcat7 the log file is located in:

/var/log/tomcat7/minerva.log

You can also check tomcat7 logs:

/var/log/tomcat7/catalina.out

Contact

For more information, please, contact:

Piotr Gawron

or

Marek Ostaszewski

or

Ewa Smula

Université du Luxembourg

Luxembourg Centre for Systems Biomedicine (LCSB)

Campus Belval | House of Biomedicine

6, avenue du Swing

L-4367 Belvaux

Luxembourg

T: +352 46 66 44 5526 or 5604

F: +352 46 66 44 6949