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The rxncon workbench - getting started

If you are reading this, you have successfully installed the rxncon workbench. This page shall give you a quick overview on how to use it.

First step: the rxncon format

The rxncon workbench's purpose is to make the rxncon toolbox available to everyone despite the prior knowledge in computer science. One must only be able to create a rxncon system definition in MS Excel. If this is not the case yet, I strongy suggest you check out the Publications page and read the provided papers, in order to understand the rxncon format.

Creating a project

On the left hand side you see your project sidebar. Here, all rxncon systems you create will be displayed.

After clicking the "New" button, you can create a project by either providing a spreadsheet file in the SBtab rxncon format (see Romers, Krantz paper), or by direkt text input. Furthermore you must provide a project name and can add a comment.

Once created, the project will pop up in the project sidebar amongst buttons to view its details, load it to the workspace(explained later), delete it or edit it. If the source was a spreadsheet file, you can also add updated system definitions to the project. Older versions are kept to prevent accidental data loss and must be deleted manually in the respective detail view of the project. Hitting the delete button in the project sidebar will delete all versions at once.

When a project is created, it automatically is loaded to the workspace.

Exporting visualization and simulation files

The rxncon workbench enables you to compare project definitions amongst each other and export them to visualization and simulation files. We use the XGMML format for visualization, that can be opened with Cytoscape software. Mathematical simulation is enabled with the automatic export to a rule-based model and a boolean model for the R package "BoolNet" (CRAN). In order to do so, one must specify the project of interest, by loading it to the workspace.

The exported files will are made available in the respective detail view. You can also compare every project, by clicking the "Compare" button in every detail view, that is not the one of the loaded project.

Loading a project to the workspace

You can load a project, by clicking the respective lightning button in either the project sidebar or the respective detail view. This changes the navigation bar on the top and shows all export possibilities.

Before a project is loaded to the workspace, rxncon checks the system for errors or missing information. Therefore only a consistent project can be loaded. An error message is shown otherwise.

When a project is created, it automatically is loaded to the workspace.

Error handling: The underlying database

The underlying meta data of any project or export is saved in an underlying database. Due to unexpected/ unknown errors, it may happen that the project directory and the data base are out of synchronization, e.g. when a project exists in the database, but not in the sidebar. This can cause the workbench to only display error messages, no matter what you click. In this case, call the URL of your home directory and add "/admin" to its end (e.g. localhost:8000/admin) in your URL bar or clicking here.

You can log into the database administration with the following account:

User: admin
Password: adminrxncon

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