MINERVA
Platform Documentation

Quick Start#

Quick start v17 available here

Quick reference guide#

View the MINERVA Quick Reference Guide to get the brief introduction to the MINERVA Platform. Open Parkinson’s Disease map and follow the steps of the Quick Reference Guide.

What is difference between the MINERVA Platform and Disease map?#

The MINERVA Platform is a open source software for the system biology networks visualization in a web browser.
Networks displayed by MINERVA are interactive - you can search for elements and see their details and check their annotations. The formats supported by the MINERVA Platform are: CellDesigner, SBML, SBGN and GPML.
Because they are computer-readable, you can explore and analyse them either via the user interface, or a dedicated API.

Who needs a MINERVA account?#

The MINERVA Platform supports various projects. In majority of cases, no account is required to access or explore any map.
If you wish to upload your own dataset (e.g. gene expression), or display your own diagrams, an account with proper access rights is necessary. Ask your MINERVA admin for an account, or use ORCID login if it is configured for the project you’re interested in.

To recap, if you want to:

How to start?#

To work with your own instance of The MINERVA Platform, read the section Install. There are few possibilities to set up the instance, e.g. Docker or Virtual Machine image. If you are interested in advanced features of the MINERVA Platform, try them out on our instance devoted for the new users. Just request an account on the Pathway lab and discover the MINERVA Platform.

Main features#

Here you find the key features of the MINERVA Platform and references to the manuals for more details.

Explore the map#

The disease maps displayed by the MINERVA Platform are interactive. You can zoom the map in/out and click on any element or reaction to view their annotations in the panel on the left side of screen.

Read about exploring the display area in the user manual.

You can search for any element (content - Drug/Small molecule targets) or reaction in the map. To search for the elements, you may use their names or identifiers. Results are marked with color pins on the Core map and the submaps.

Read more about search in the user manual.

Additionally, Providing multiple queries is possible, queries must be separated by ;.

Submaps#

Discover submaps by clicking on the Submaps button. Additionally, you can open them through anchor points on the map. Read more in submaps in the user manual.

Backgrounds and general overlays#

Customize display of the map by selecting a view of the map. Display the general overlays provided with a map. Read more in overlays tab in the user manual.

Add your own overlay#

You can upload to a map a dataset (e.g. genes expressions), what we call a general overlay. Or if you have genetic dataset, you can also upload it to the project. It is called a genetic overlay, and additionally displays the reference genome. Your dataset has to be a text file with a strictly specified syntax. Learn more about overlays upload in the user manual.

Export#

Export the list of your desired annotations via the ELEMENTS or NETWORKS tab. Also, exporting a submap as an image is available in GRAPHICS tab. Read more about export in the user manual.

Add comment#

Right click of mouse displays the context menu. Add comment allows you to leave a comment on a map, which will be visible to everyone on the map. Read more in comments in the user manual.

View protein structure#

The proteins structure display is available for the proteins annotated with UniProt ID. Click right on the protein and choose Open MolArt. Read about MolArt in the user manual.

Plugins#

Plugins allow to use or create client-side custom visualizations. Learn more about plugins in the user manual

Page outline