ddeemerpurdue / sbtab

SBtab - Table format for Systems Biology:

SBtab - Table format for Systems Biology

Python code and example files by Timo Lubitz, Elad Noor, Jens Hahn, Frank Bergmann (2018).

Data tables in the form of spreadsheets or delimited text files are the most utilised data format in Systems Biology. However, they are often not sufficiently structured and lack clear naming conventions that would be required for modelling. We propose the SBtab format as an attempt to establish an easy-to-use table format that is both flexible and clearly structured. It comprises defined table types for different kinds of data; syntax rules for usage of names, shortnames, and database identifiers used for annotation; and standardised formulae for reaction stoichiometries. Predefined table types can be used to define biochemical network models and the biochemical constants therein. The user can also define own table types, adjusting SBtab to other types of data.

The SBtab specification can be found on the SBtab homepage. The homepage also provides various information on example files, frequently asked questions, online tools, and tutorials.

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SBtab comes along with software tools which can be employed in 3 different ways:

1. In the online interface or as home server version
   

   

   You can use the software tools that come with SBtab in the convenient online interface on https://www.sbtab.net. The page is built with the Python web framework web2py.

   If you want to run the web2py application on your own home server, you can download it from this repository's directory SBtab/python/web_version. Change to this directory to find more information on the usage.

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2. As a Python3 package (pip installer)
   

   

   The tools can be employed as a Python3 package. It needs to be installed via pypi. Please type on your commandline
   
   

   sudo pip3 install sbtab

   You will then be able to import the SBtab library into your Python3 modules by adding

   import sbtab

   to them. See the code examples in this repository's directory SBtab/python. Also, you will find further information on the usage in the SBtab specification.

   Please note that the directory SBtab/pypi_installer only holds the files for the pip installer build up and is not required at all for users that want to employ SBtab.

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3. From the commandline (for experienced users)
   

   

   You can employ the SBtab commandline tools from the directory SBtab/python. To use this option, you will have to install the required packages on your own and put the Python modules to their according directory. Details on the usage of the commandline tools you can find in the directory SBtab/python.

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The SBtab repository consists of the following directories and contents:

R
SBtab interface for the language R. See directory for details on the usage.

definition table:
Default definitions of predefined SBtab table types.

excel:
Windows installer and source code for the excel add-in (courtesy of Frank T. Bergmann). Works for SBtab version 1.0 and the .xls format.

sbtab examples:
Example SBtab files. These files can also be found including explanatory words in the online SBtab Download Section

python:

• Source scripts and commandline Python3 modules, including a file and object validator, and a converter to and from SBML.
• Documentation:
  HTML pydoc documentation of the SBtab interface and source code.
• SQLite interface:
  Python interface for querying SQLite databases via SBtab (courtesy of Elad Noor).
• web2py:
  [Web2py](http://www.web2py.com) server files for the SBtab online tools. Can be run locally and offline if required.