Table of contents
- Quick reference guide
- What is difference between the MINERVA Platform and Disease map?
- Who need a MINERVA account?
- How to request an account
- How to start
- Main features
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. What more, these networks displayed by MINERVA, become 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. The Disease maps are the networks (disease pathways) themselves, displayed by the MINERVA Platform in a web browser, where user can explore and analyse them.
Who need a MINERVA account?
Access to any MINERVA instance is for free. No account is required to access or explore any map. But, if you wish to upload your own dataset (e.g. genes expression) to the map or display your own network and analyze it with MINERVA - an account with proper access rights is necessary. Ask your MINERVA admin for an account.
To recap, if you want to:
access and explore a map - no account is required, just open a map with its weblink.
display your own dataset - ask your MINERVA admin for user account.
upload your own network - ask your MINERVA admin for curator account.
there is also admin account - it is used when you have your own MINERVA instance, read more in Install.
How to request an account
Request an account option is available while login. Click on lock icon or directly Request an account at the bottom of INFO tab to request an account.
How to start
If you would like to work with your own instance of The MINERVA Platform, read the section Install. There are few possibilities to obtain 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.
Here you find the key features of the MINERVA Platform and references to the manuals for more details.
- Explore the map
- Search in content
- Search for targets of drugs/chemicals/miRNA
- Export as map/image
- Add comment
- View proteins structure
- Backgrounds and general overlays
- Add your own overlay
- Add project
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.
Search in content
You can search for any element 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.
Search for targets of drugs/chemicals/miRNA
In the MINERVA Platform you can search for targets of drugs/chemicals/miRNA in the map. The results are marked with color pins on the Core map and the submaps. Providing multiple queries is possible, queries must be separated by ;.
Read more about targets search in the user manual.
Export as map/image
Export current model to any format supported by the MINERVA Platform. The currently view of the map will be exported. Also, export as image is available. To export a map right click on the map to display the context menu.
Read more about export of map in the user manual.
Right click of mouse displays the context menu. Add comment allows you to leave a comment on a map. It may, but does not have to be visible on the map.
Read more in the user manual - comments.
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.
Backgrounds and general overlays
Customize display of the map by turning on/off Pathways and Compartments view. Display the general overlays provided with a map.
Read more in the user manual - overlays tab.
Login is available in INFO tab, OVERLAYS tab or by click on lock icon (in left top corner of the screen).
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.