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The first step is to provide a rxncon model. The workbench takes two types of input, quick and spreadsheet. The quick format is text based and typed directly into the workbench, which makes it good for trying out small models. For larger networks, we strongly encourage the use of the spreadsheet template. The template and example models can be downloaded from GitHub (download here).
The workbench is installed with an example model of the High Osmolarity Glycerol (HOG) pathway from baker's yeast.
Read more: The rxncon language; model building workflow (coming soon); network reconstruction
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 or by direkt text input. Furthermore you must specify a project name and can add a comment.
Once created, the project will appear in the project sidebar together with buttons to view details, load it to the workspace (see below), delete it or edit it. If the source was a spreadsheet file, you can update the model by loading a new file in project. The older versions are kept to and versioned, preventing accidental data loss and allowing you to go back to an older version. 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.
The rxncon workbench enables you to compare project definitions amongst each other and export them to visualization and simulation files.
There are three graphical compialtion targets:
To create a graph, select the desired type from "visualisation" in the top menu and click "create graph". Note: you can keep the layout of previous versions by loading an .xgmml file with layout as template. Nodes with identical names will retain their positions.
There are two executable compilation targets:
To create a model, select the desired type from "Model export" in the top menu.
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.
Visualisation and simulation rely on external software (cytoscape, Boolnet, NFsim), and cannot be done within the workbench.
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.
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