Add-in for Excel

An SBtab add-in for Microsoft Excel, xlSBtab, can be downloaded from github. A screenshot can be found here.

Installation: A windows installer will be downloaded to the hard disk and can be started by a click. The prerequisites for using the add-in are:

  1. Windows Vista or higher
  2. Microsoft Excel 2010 or higher, 32 Bit
  3. Microsoft .NET Framework 4.5 (full) or higher (can be downloaded directly from Microsoft )
  4. Microsoft Visual Studio 2010 Tools for Office Runtime (VSTO) (can be downloaded directly from Microsoft)

After installation, the SBtab add-in will be automatically initialised upon Excel startup. The tools are accessible by choosing add-ins from the menu bar. The add-in enables users to upload and validate SBtab files. Furthermore, SBtab files can be exported to SBML (as long as they are valid and provide a model structure) and vice versa (see screenshot). If you experience any troubles installing or using xlSBtab, please contact us (Frank Bergmann (frank.bergmann@bioquant.uni-heidelberg.de) or Timo Lubitz (timo.lubitz@gmail.com)).

Python code

Python code for SBtab can be downloaded from github.

Documentation can be found here.

Python-SQlite interface

Single or collections of SBtab files can be automatically converted into an SQLite database, using the package sqlite_interface within the GitHub SBtab repository. This feature can be useful for developers that would like to allow users to upload their data in the form of SBtab into a web service, and using SQL to query the data using standard web development tools.

R code

The R project is a widespread and powerful software framework for statistical computing and graphics. We provide a simple interface that allows R users to import the SBtab python code into their R projects, manipulate SBtab objects, call Python functions from within the R environment. For this, we use the rPython library, which needs to be preinstalled to employ the provided code. The R files, which can be found in the SBtab repository on Github, exemplify how this can be done. SBtab objects can be created via the Python interface

  1. SBtab tables can be validated and the output stored as R variable
  2. SBtab tables can be edited (adding/removing rows, attributes, or columns) from within R
  3. SBtab tables can be converted to SBML and vice versa, where the output can be stored as R file objects

Alongside these rPython-based approaches, we also translated the creation of an SBtab file document (including one or more SBtabs) from Python directly into the R language. These example files are stored in the directory /R/ on github. We hope that these elucidations will help R programmers to integrate SBtab files and functionalities into their projects.

Matlab code

Matlab code for SBtab can be downloaded from github.

Documentation can be found here.

Definition of SBtab table types

Table defining the basic SBtab table types: definitions.tsv.


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