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The rxncon workbench - getting started

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

First step: the rxncon model

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.

Read more: The rxncon language; model building workflow (coming soon); network reconstruction

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 or by direct 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 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.

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.

There are three graphical compilation targets:

  1. Reaction graph
  2. Elemental species-reaction graph
  3. Regulatory graph

The graphs are exported to the XGMML format, which can be imported to Cytoscape (free download at cytoscape.org). We provide formatting files on GitHub (the rxncon2cytoscape file).

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:

  1. Bipartite Boolean model (Read more)
  2. Rule-based model

The Boolean model can be simulated with BoolNet, a freely available R package. We have provided a script for simulation here. The rule based model uses the BioNetGen language, and is prepared for simulation with NFsim.

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.

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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