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README.md

xlSBtab - an SBtab Excel Add-in

This project hosts a basic Excel Add-in, for opening an SBML file within Excel and have it be converted to the SBtab format. Alternatively a file edited in the SBtab format can be validated and exported as SBML file.

Dependencies

For the program to work, you will need to have the following installed:

  • Windows Vista or higher
  • Microsoft Excel 2010 or higher
  • Microsoft .NET Framework 4.5 (full) or higher (can be downloaded directly from Microsoft )
  • Microsoft Visual Studio 2010 Tools for Office Runtime (VSTO) (can be downloaded directly from Microsoft)

Installation

After you installed the add-in, you will find a new tab called 'SBtab' in the Add-ins ribbon menu. On that tab, click settings to verify the python path, and the SBtab location. This is a crucial step: both paths have to be set to the installation directory of xlSBtab, which is usually either "C:\Program Files\xlSBtab" or "C:\Program Files (x86)\xlSBtab", depending on your system. The Python interpreter needs to be set to "...\xlSBtab\python\python.exe" and the SBtab scripts to "...\xlSBtab\SBtab\scripts".

The add in has four options:

SBtab options

  • Import SBML: imports an SBML file and replaces the contents of the current sheet with SBtab tables representing that file.
  • Export SBML: translates the tables of the current sheet back into an SBML file.
  • Validate: currently ensures only that the tables have the expected headers. It does not yet validate the entries in the table.
  • Settings: specify the path to the Python interpreter and the SBtab script directory.

Once a model is imported it will be displayed like in the example below (here BioModel 10 was imported):

SBtab of BioModel 10

License

This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.

Copyright (c) 2015, Frank T. Bergmann
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.