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Deviser

Deviser stands for "Design Explorer and Viewer for Iterative SBML Enhancement of Representations". It is a code generator for defining and prototyping SBML Level 3 packages and code for use with libSBML.

   ⭐️ This is the repository for Deviser's code generation facility. The GUI is in a separate repository. ⭐️   

Authors: Sarah M. Keating and Frank T. Bergmann

Contributors: Matthew S. Gillman, Brett Olivier, Orod Razeghi, Lucian Smith & Mike Hucka
Repository: https://github.com/sbmlteam/deviser
Repository for GUI: https://github.com/sbmlteam/QtDeviser
Pivotal tracker: https://www.pivotaltracker.com/n/projects/977192
License: LGPL version 2.1 – see the file LICENSE for details

Background

Computation modeling has become crucial to biological research, and SBML (the Systems Biology Markup Language) has become the de facto standard open format for exchanging models between software tools in systems biology. SBML Level 3 has a modular structure, with as a core augmented with optional packages that add syntax and features. Development of new Level 3 packages is ongoing.

LibSBML is a free, open-source programming library to help developers read, write, manipulate, translate, and validate SBML files and data streams in their software systems. It is written in C++ and provides language bindings for other programming languages. Support for SBML Level 3 can be added to LibSBML by integrating the package-specific code and building with the package enabled.

Deviser facilitates the development of SBML Level 3 packages by enabling the creation of basic specifications, UML diagrams and code for integration with LibSBML.

Deviser is written in Python and is compatible with Python version 2.6 onwards.

Using Deviser

Deviser Edit GUI

The Deviser Edit tool allows you to quickly define an SBML Level 3 package. It then provides the following functionality

  1. Create and view a UML diagram.
  2. Generate the necessary libSBML code for the package.
  3. Generate TeX files and generate a PDF of a basic specification document for the package.
  4. Integrate and test the package with libSBML.

The Deviser Edit tool creates an XML description of the package that is used by the deviser code to generate the requested files. This XML description is exemplified in the samples directory.

Command Line Interface

There is command line version of the function that can be used to invoke Deviser on the XML file. This is the deviser.py file found in the generator directory.

deviser.py [--generate][--latex] input-file.xml    

This program will use a Deviser XML file, and generate either a C++ libSBML extension for it, or generate a LaTeX scaffold for its specification.

Full documentation is available in the docs directory.

Installation

The deviser release includes bundles/installer for each of the main operating systems.

Prerequisites

  1. A C++ compiler must be installed if you wish to compile the libSBML code generated.
  2. A pdflatex compiler must be installed if you wish to generate a PDF file from the TeX sources generated.

NOTE: These may already be available on your OS.

Microsoft Windows OS

A windows installation executable which installs the Deviser Edit tool (QtDeviser.exe), all the necessary Deviser files. Additionally it includes a Python interpreter and the sbmlpkgspec files for generating SBML Level 3 Package specifications.

Linux OS

A self-contained, binary installer is available that contains Deviser, DeviserEdit and the sbmlpkgspec modules. After installation DeviserEdit can be run from either a desktop icon or by calling the DeviserEdit.sh script in the installation directory. Deviser samples can be found in the deviser/samples subdirectory.

Mac OS X

A .dmg file is available containing the DeviserEdit Application that embeds the necessary Deviser and sbmlpkgspec files in addition to docs and samples directories.

Source archives

The source archives contain the Deviser code that can be used via the command line.

Other resources

Not all of the following are necessary as what is necessary depends on which operating system is being used and which Deviser functionality is required. These links are given as a quick reference.

Acknowledgments

The development of Deviser was supported in part by funding from the National Institute of General Medical Sciences (USA) under grant R01 GM070923 (principal investigator: Michael Hucka).

Copyright and license

Copyright (C) 2014-2018 jointly by the California Institute of Technology, Pasadena, CA, USA, EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK and the University of Heidelberg, Heidelberg, Germany

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or any later version.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder is on an "as is" basis, and the California Institute of Technology has no obligations to provide maintenance, support, updates, enhancements or modifications. In no event shall the California Institute of Technology be liable to any party for direct, indirect, special, incidental or consequential damages, including lost profits, arising out of the use of this software and its documentation, even if the California Institute of Technology has been advised of the possibility of such damage. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library in the file named "LICENSE" included with the software distribution.