ArticleBioinformatics (Oxford, England)2011
JSBML: a flexible Java library for working with SBML.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- EnzymeML: seamless data flow and modeling of enzymatic data.Nature methods · 2023Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- A compiler for biological networks on silicon chips.PLoS computational biology · 2020Article
- libsbmljs-Enabling web-based SBML tools.Bio Systems · 2020Article
- The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.Journal of integrative bioinformatics · 2019Article
- XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images.Frontiers in genetics · 2019Article
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression.PLoS computational biology · 2018Article
- Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.Bioinformatics (Oxford, England) · 2017Article
- ACRE: Absolute concentration robustness exploration in module-based combinatorial networks.Synthetic biology (Oxford, England) · 2017Article
- Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.Nucleic acids research · 2016Article
- The systems biology format converter.BMC bioinformatics · 2016Article
- Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.PLoS computational biology · 2016Article
- PSAMM: A Portable System for the Analysis of Metabolic Models.PLoS computational biology · 2016Article
- FlexFlux: combining metabolic flux and regulatory network analyses.BMC systems biology · 2015Article
- JSBML 1.0: providing a smorgasbord of options to encode systems biology models.Bioinformatics (Oxford, England) · 2015Article
- SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.BMC systems biology · 2015Article
- Pathways with PathWhiz.Nucleic acids research · 2015Article
- Reconstructing genome-scale metabolic models with merlin.Nucleic acids research · 2015Article
- Combining computational models, semantic annotations and simulation experiments in a graph database.Database : the journal of biological databases and curation · 2015Article
- An integrated network visualization framework towards metabolic engineering applications.BMC bioinformatics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
summaryThe specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. AVAILABILITY: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.