ArticleBMC bioinformatics2016
The systems biology format converter.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
14 citing papers in PubMed.
- SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences.Bioinformatics (Oxford, England) · 2025Article
- BioConvert: a comprehensive format converter for life sciences.NAR genomics and bioinformatics · 2023Article
- New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells.PLoS computational biology · 2023Article
- GraphML-SBGN bidirectional converter for metabolic networks.Journal of integrative bioinformatics · 2022Article
- A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.Neuroinformatics · 2022Article
- ODEbase: a repository of ODE systems for systems biology.Bioinformatics advances · 2022Article
- QSPcc reduces bottlenecks in computational model simulations.Communications biology · 2021Article
- SBML Level 3: an extensible format for the exchange and reuse of biological models.Molecular systems biology · 2020Review
- Closing the gap between formats for storing layout information in systems biology.Briefings in bioinformatics · 2020Article
- Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.Briefings in bioinformatics · 2019Review
- Harmonizing semantic annotations for computational models in biology.Briefings in bioinformatics · 2019Review
- Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.NPJ systems biology and applications · 2018Article
- Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).Standards in genomic sciences · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
backgroundInteroperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed independently, resulting in redundancy of efforts and lack of synergy.
resultsHere we present the System Biology Format Converter (SBFC), which provide a generic framework to potentially convert any format into another. The framework currently includes several converters translating between the following formats: SBML, BioPAX, SBGN-ML, Matlab, Octave, XPP, GPML, Dot, MDL and APM. This software is written in Java and can be used as a standalone executable or web service.
conclusionsThe SBFC framework is an evolving software project. Existing converters can be used and improved, and new converters can be easily added, making SBFC useful to both modellers and developers. The source code and documentation of the framework are freely available from the project web site.
Indexed as
Identifiers
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.