Metadata-Version: 2.4
Name: sbtabpy
Version: 1.0.8
Summary: SBtab - Standardised Data Tables for Systems Biology
Author-email: Timo Lubitz <timo.lubitz@gmail.com>, Elad Noor <elad.noor@weizmann.ac.il>
License: MIT
Project-URL: Homepage, https://www.sbtab.net
Keywords: modelling,systems biology,standard format,data table
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: python-libsbml>=5.0
Requires-Dist: numpy>=2.0
Requires-Dist: scipy>=1.13
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Requires-Dist: pandas>=2.0
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Dynamic: license-file

SBtab: a Table format for Systems Biology
=========================================
Python code and example files by
Timo Lubitz, Elad Noor, Jens Hahn, Frank Bergmann (2018).

[![PyPI version](https://img.shields.io/pypi/v/sbtab)](https://pypi.org/project/sbtab/)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/sbtab)](https://pypi.org/project/sbtab/)
[![PyPI - Downloads](https://img.shields.io/pypi/dm/sbtab)](https://pypi.org/project/sbtab/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

Data tables in the form of spreadsheets or delimited text files are the most common data 
format in Systems Biology. However, they are often not sufficiently structured and lack 
clear naming conventions that would be required for modeling. 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 standardized formulae for reaction stoichiometries. Predefined table types can be
used to define biochemical network models and the biochemical constants therein. The users
can also define their own table types, adjusting SBtab to other types of data.

The SBtab specification can be found on the
[SBtab homepage](https://www.sbtab.net/sbtab/default/downloads.html#spec).
The homepage also provides various information on example files, frequently
asked questions, online tools, and tutorials.

Software tools
--------------

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

1. **SBtab online**

    You can use the software tools that come with SBtab in the convenient online interface:
    - [Validator](https://www.sbtab.net/sbtab/default/validator.html)
    - [SBML Converter](https://www.sbtab.net/sbtab/default/converter.html)
    - [Customize SBtab](https://www.sbtab.net/sbtab/default/def_files.html)
  
2. **Python package** (i.e., pip installer)
  
    The tools can be employed as a Python package. It needs to be installed via
    [pypi](https://pypi.org/project/sbtab/). Please type on your commandline:
    ```bash
      sudo pip install sbtab
    ```
    You will then be able to import the SBtab library into your Python modules by adding
    ```
      import sbtab
    ```
    to them. See the code examples in this repository's directory `/examples`.
  
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`.


Repository contents
-------------------
The SBtab repository consists of the following directories and contents:

- **Source Code `/src`**
  
  - Source scripts and commandline Python modules, including a file and object validator, and a converter to and from SBML.
  - SQLite interface: Python interface for querying SQLite databases via SBtab.

- **Unit Tests `/tests`**
  
  Some tests to ensure the correctness and functionality of the SBtab package.

- **Definition Table `/definitions_table`**

  Default definitions of predefined SBtab table types.

- **Example Files `/examples`**
  
  Example SBtab files. These files can also be found including explanatory words in the [online SBtab Download Section](https://www.sbtab.net/sbtab/default/downloads.html)

- **API documentation** `/api_documentation`
  
  HTML pydoc documentation of the SBtab interface and source code.
