scholarly journals Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology

2016 ◽  
Author(s):  
Kiri Choi ◽  
J. Kyle Medley ◽  
Caroline Cannistra ◽  
Matthias König ◽  
Lucian Smith ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Computational Models ◽  
Model Building ◽  
Stochastic Simulations ◽  
Superior Performance ◽  
Markup Language ◽  
Development Environment ◽  
Dimensional Parameter ◽  
Simulation Engine

AbstractIn this article, we present Tellurium, a powerful Python-based integrated environment designed for model building, analysis, simulation and reproducibility in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source integrated development environment (IDE) composed of multiple libraries, plugins, and specialized modules and methods. Tellurium ensures exchangeability and reproducibility of computational models by supporting SBML (Systems Biology Markup Language), SED-ML (Simulation Experiment Description Markup Language), the COMBINE archive, and SBOL (Synthetic Biology Open Language). Tellurium is a self-contained modeling platform which comes with a fully configured Python distribution independent of other local Python installations on the target machine. The main interface is based on the Spyder IDE which has a highly accessible user interface akin to MATLAB (https://www.mathworks.com/). Tellurium uses libRoadRunner as the default SBML simulation engine due to its superior performance, scalability and ease of integration. libRoadRunner supports deterministic simulations, stochastic simulations and steady state analyses. Tellurium also includes Antimony, a human-readable model definition language which can be converted to and from SBML. Other standard Python scientific libraries such as NumPy, SciPy, and matplotlib are included by default. Additionally, we include several user-friendly plugins and advanced modules for a wide-variety of applications, ranging from visualization tools to complex algorithms for bifurcation analysis and multi-dimensional parameter scanning. By combining multiple libraries, plugins, and modules into a single package, Tellurium provides a unified but extensible solution for biological modeling and simulation.

Systems biology markup language: Level 2 and beyond

2003 ◽  
Vol 31 (6) ◽  
pp. 1472-1473 ◽  
Author(s):  
A. Finney ◽  
M. Hucka
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Chemical Species ◽  
Biochemical Networks ◽  
Markup Language ◽  
Exchange Format ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Level 1 ◽  
Level 2

The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks. We continue developing SBML collaboratively with the modelling community to meet their evolving needs. The recently introduced SBML Level 2 includes several enhancements to the original Level 1, and features under development for SBML Level 3 include model composition, multistate chemical species and diagrams.

scholarly journals A standard-enabled workflow for synthetic biology

2017 ◽  
Vol 45 (3) ◽  
pp. 793-803 ◽  
Author(s):  
Chris J. Myers ◽  
Jacob Beal ◽  
Thomas E. Gorochowski ◽  
Hiroyuki Kuwahara ◽  
Curtis Madsen ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Markup Language ◽  
Design Tools ◽  
Data Standards ◽  
Data Repositories ◽  
Simulation Tools ◽  
Systems Biology Markup Language ◽  
Visualization Tools ◽  
Synthetic Biology Open Language

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

scholarly journals The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Andreas Dräger ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Translation Errors ◽  
Language Specification

AbstractComputational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

scholarly journals Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

2015 ◽  
Vol 12 (2) ◽  
pp. 731-901 ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Andreas Dräger ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Translation Errors ◽  
Level 2 ◽  
Cell Signaling Pathways

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

scholarly journals The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Andreas Dräger ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Design Changes ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Translation Errors

AbstractComputational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.

scholarly journals The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

2015 ◽  
Vol 12 (2) ◽  
pp. 382-549 ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
Sven Sahle ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Translation Errors ◽  
Language Specification

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

scholarly journals Designing and encoding models for synthetic biology

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Lukas Endler ◽  
Nicolas Rodriguez ◽  
Nick Juty ◽  
Vijayalakshmi Chelliah ◽  
Camille Laibe ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
System Design ◽  
Software Tools ◽  
Reaction Networks ◽  
Markup Language ◽  
Concomitant Increase ◽  
Relational Models ◽  
Gene Regulatory ◽  
Simulation Results

A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology ‘loop’.

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