Examples
In this section we are providing step-by-step explanation of the MINERVA Platform functionalities. You can follow the steps of each example using any MINERVA instance, but preferably version 17.x.x.
Note: a MINERVA account with proper access rights is necessary to work with these examples. Read more about users access rights in Quick Start.
Project upload
Uploading own projects (maps) to the MINERVA Platform is available for curator or admin accounts.
- CellDesigner file upload and annotation
Here we present how to upload a simple CellDesigner file to the MINERVA Platform and set its annotations. Discover the annotations types the MINERVA Platform supports.
- Advanced upload of the map
Explanation what the advanced map and its components are. Here, you will download an advanced map and follow the process of uploading it to the MINERVA Platform.
Systems biology formats
The MINERVA Platform handles four types of system biology formats. Learn how SBML and GPML files are displayed in the MINERVA Platform. Curator or admin account is required to work with this examples.
- SBML-format file modifications
SBML format is used for the mathematical models. The visualization of SBML models and recognition of the elements or reactions types are possible thanks to SBOTerms. In this example, you find out how the MINERVA Platform uses SBOTerms to customize SBML display. You will download simple SBML file and modify it with SBOTerms to understand the enhanced display.
- GPML file display and export
The elements and reactions are represented in various ways in different system biology formats. The MINERVA Platform handles four formats. Here you can learn how the MINERVA Platform visualize GPML models. Also, learn how GPML models elements are represented after being exported from the MINERVA Platform.
Data upload
Uploading dataset to the MINERVA Platform is available at least user access rights.
- Custom data upload
Having own dataset of e.g. genes expression level? If you are interested how the dataset occurs in your disease model upload it to the map. In this example you will work with simple model, plus basic and advanced datasets. You will learn how to create basic and advanced overlays files from your dataset.
Custom map configuration
Set of advanced examples for curators and admins of the MINERVA Platform.
- Procedural semantic zoom
Semantic zoom is the solution for the big models, to facilitate browsing through them. The MINERVA Platform by default displays models in a semantic zoom mode, where bigger elements cover smaller one, and as zooming a map in, the smaller elements begin to be visible. In this example, learn how you can customize semantic zoom.
- Custom Z-Index
Z-Index is feature the procedural semantic zoom. By using Z-Index you can specify the order of overlapping elements, defining which element is displayed more in the front of the map.
- Map with glyphs
The MINERVA Platform allows to add images (glyphs) to your model. Learn what types of images and how to add them to your model so they are displayed in the MINERVA Platform correctly.