Motivation: The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats.
Summary: Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format's inherent design, in addition to differences in functionality.
Availability And Implementation: Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/and JSim from http://physiome.org/jsim/.
Contact: lpsmith@u.washington.edu.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967103 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btt641 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE).
F1000Res
October 2023
Auckland Bioengineering Institute, University of Auckland, Auckland, 1010, New Zealand.
The Transformer-based approaches to solving natural language processing (NLP) tasks such as BERT and GPT are gaining popularity due to their ability to achieve high performance. These approaches benefit from using enormous data sizes to create pre-trained models and the ability to understand the context of words in a sentence. Their use in the information retrieval domain is thought to increase effectiveness and efficiency.
View Article and Find Full Text PDFSpecifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.
J Integr Bioinform
March 2023
Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.
View Article and Find Full Text PDFBioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res
July 2022
Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface.
View Article and Find Full Text PDFOne should assume that in silico experiments in systems biology are less susceptible to reproducibility issues than their wet-lab counterparts, because they are free from natural biological variations and their environment can be fully controlled. However, recent studies show that only half of the published mathematical models of biological systems can be reproduced without substantial effort. In this article we examine the potential causes for failed or cumbersome reproductions in a case study of a one-dimensional mathematical model of the atrioventricular node, which took us four months to reproduce.
View Article and Find Full Text PDFBioModels-15 years of sharing computational models in life science.
Nucleic Acids Res
January 2020
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!