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 (www.celldesigner.org/) or SBGN editors (www.sbgn.org/Main_Page). 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.

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 publication

“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

Licensing

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

Disclaimer

Content visualization of MINERVA platform is supported by Google Maps API. Users of MINERVA platform are obliged to comply with the Google Maps/Google Earth APIs Terms of Service.

How to install

Installation instructions are for Debian Linux, but they are also applicable for Ubuntu Linux (tested on 14.04 LTS).

Step 1
Add the Oracle Java v8 repository. In particular, we use oracle-java8-set-default package. Either folow the instructions here, or execute the following commands:
1.sudo apt-add-repository "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main"
if you see sudo: apt-add-repository: command not found
you have to install software-properties-common: sudo apt-get install software-properties-common
2.sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
3.sudo apt-get update
Step 2
Add our repository to the list:
1.sudo apt-add-repository "deb http://repo-r3lab.uni.lu/debian/ stable main"
2.sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xcb185f4e31872412
3.sudo apt-get update
Step 3
Install MINERVA platform
sudo apt-get install minerva
Step 4
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 (http://r3lab.uni.lu/web/minerva-website/admin.html) to change the password and, if needed, to add new users.

Alternatively, you can download an image of a virtual machine running Debian Linux and a working instance of MINERVA platform using the following link. 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

Alternatively, you can download a Dockr container with a working version of MINERVA platform using the following command:

docker run -p 8080:8080 -t -i docker-r3lab.uni.lu/minerva/minerva:10.0.1

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 avaialable on git and as a zipped package. Git repository hosting the project is under development.

Supported projects

MINERVA platform supports the following projects:

Troubleshooting

### java installation Debian package installing minerva will 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.

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: http://stackoverflow.com/questions/6897476/tomcat-7-how-to-set-initial-heap-size-correctly

Exported CellDesigner file

Very rarelly generated celldesigner files might be corrupted and cannot be opened using CellDesigner. We are aware of this issue and plan to fix it as soon as possible, but 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 (piotr.gawron@uni.lu)

or

Marek Ostaszewski (marek.ostaszewski@uni.lu)

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



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