.. sbmlxdf documentation master file, created by
   sphinx-quickstart on Fri Jul 23 16:09:30 2021.

.. image:: ./images/ccb_logo-2.0.1.png
   :scale: 10 %
   :align: right
   :target: https://www.cs.hhu.de/lehrstuehle-und-arbeitsgruppen/computational-cell-biology

Peter Schubert, Prof. Martin Lercher and the team of the
Institute of Computational Cell Biology,
Heinrich-Heine-University Duesseldorf, Germany

.. toctree::
   :maxdepth: 2
   :hidden:

   install
   tutorial
   scripts
   spreadsheet
   methods
   references

Welcome to sbmlxdf's documentation!
===================================

Convert between SBML and tabular structures
-------------------------------------------

.. image:: ./images/sbmlxdf.png
   :align: center

**sbmlxdf** is lightweight and transparent converter from
SBML to pandas Dataframes (sbml2df) and
from pandas Dataframes to SBML (df2sbml).

**sbmlxdf** supports, with few exceptions, all functionality of
**SBML L3V2 core** package [SBML_L3V2]_ and packages **Flux Balance
Constraints (fbc)** [SBML_fbc]_, **Groups (groups)** [SBML_groups]_
and **Distributions (distrib)** [SBML_distrib]_.

At the backend, **libSBML** API is used for accessing SBML data elements
[libsbml]_.

Benefits
--------

kinetic modelers with and without programming skills
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- overcome hesitation of creating own models in SBML
- have a tool for flexible kinetic modelling using spreadsheets
- inspect SBML models
- create/extend SBML models
- use latest SBML features
- generate ‘correct’ SBML models

Python programmers
~~~~~~~~~~~~~~~~~~
- get access to SBML model data via pandas DataFrames,
  e.g. for use in their optimizers
- can evaluate different model design strategies

Features
--------
- support of SBML L3V2 core [SBML_L3V2]_, including:

  - model history, miriamAnnotations, xmlAnnotations
  - units of measurement
  - local/global parameters
  - function definitions
  - Flux Balance Constraints package [SBML_fbc]_
  - Groups package [SBML_groups]_
  - Distributions package [SBML_distrib]_

.. note ::

   **sbmxdf** does not intent to support SBML packages related to graphical
   representations of network models. I.e. packages **Layout** and
   **Rendering** are not supported. Other released SBML packages as of July
   2021, see `package status <http://sbml.org/Documents/Specifications>`_
   i.e. **Hierarchical Model Composition**,
   **Multistate and Multicomponent Species** and **Qualitative Models** are
   not supported at the moment, but might be included in future versions.