scholarly journals PEtab—Interoperable specification of parameter estimation problems in systems biology

2021 ◽  
Vol 17 (1) ◽  
pp. e1008646 ◽  
Author(s):  
Leonard Schmiester ◽  
Yannik Schälte ◽  
Frank T. Bergmann ◽  
Tacio Camba ◽  
Erika Dudkin ◽  
...  
Keyword(s):  
Experimental Data ◽  
Parameter Estimation ◽  
Systems Biology ◽  
Model Simulation ◽  
Markup Language ◽  
Observation Model ◽  
Modeling Studies ◽  
Estimation Problems ◽  
Systems Biology Markup Language

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

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 SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

Computation ◽  
2014 ◽  
Vol 2 (4) ◽  
pp. 246-257 ◽  
Author(s):  
Alexander Dörr ◽  
Roland Keller ◽  
Andreas Zell ◽  
Andreas Dräger
Keyword(s):  
Parameter Estimation ◽  
Systems Biology ◽  
Model Simulation

scholarly journals cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

2020 ◽  
Vol 36 (8) ◽  
pp. 2620-2622 ◽  
Author(s):  
Irina Balaur ◽  
Ludovic Roy ◽  
Alexander Mazein ◽  
S Gökberk Karaca ◽  
Ugur Dogrusoz ◽  
...  
Keyword(s):  
Systems Biology ◽  
Web Service ◽  
Large Scale ◽  
Supplementary Information ◽  
Markup Language ◽  
File Format ◽  
Signalling Network ◽  
Lesser General Public License ◽  
Systems Biology Markup Language ◽  
General Public License

Abstract Motivation CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner’s proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. Results We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML. Availability and implementation The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively). Supplementary information Supplementary data are available at Bioinformatics online.

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

2007 ◽  
Author(s):  
Michael Hucka ◽  
Andrew Finney ◽  
Stefan Hoops ◽  
Sarah Keating ◽  
Nicolas Le Novere
Keyword(s):  
Systems Biology ◽  
Markup Language ◽  
Systems Biology Markup Language ◽  
Level 2

scholarly journals XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images

2019 ◽  
Vol 10 ◽  
Author(s):  
Kaito Ii ◽  
Kota Mashimo ◽  
Mitsunori Ozeki ◽  
Takahiro G. Yamada ◽  
Noriko Hiroi ◽  
...  
Keyword(s):  
Systems Biology ◽  
Language Models ◽  
Markup Language ◽  
Modeling Tool ◽  
Microscopic Images ◽  
Spatial Systems ◽  
Systems Biology Markup Language

scholarly journals Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

2007 ◽  
Vol 4 (3) ◽  
pp. 252-263 ◽  
Author(s):  
Allyson L. Lister ◽  
Matthew Pocock ◽  
Anil Wipat
Keyword(s):  
Systems Biology ◽  
Representative Sample ◽  
Model Development ◽  
Structural Knowledge ◽  
Markup Language ◽  
Web Ontology Language ◽  
Biological Models ◽  
Computational Approaches ◽  
Ontology Language ◽  
Systems Biology Markup Language

Abstract The creation of quantitative, simulatable, Systems Biology Markup Language (SBML) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the SBML schema document (XSD), the Systems Biology Ontology (SBO), and the “Structures and Facilities for Model Definition” document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language (OWL) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format OWL (MFO) performs both structural and constraint integration and can be reasoned over and validated. SBML Models are represented as individuals of OWL classes, resulting in a single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for SBML models into a single resource creates a new style of model development and checking.

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