ArticleJournal of bioinformatics and computational biology2016
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
Article in Journal of bioinformatics and computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Verification and reproducible curation of the BioModels repository.PLoS computational biology · 2025Article
- Curating models from BioModels: Developing a workflow for creating OMEX files.bioRxiv : the preprint server for biology · 2024Article
- Article
- Adapting modeling and simulation credibility standards to computational systems biology.Journal of translational medicine · 2023Review
- A Practical Guide to Reproducible Modeling for Biochemical Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- PEtab-Interoperable specification of parameter estimation problems in systems biology.PLoS computational biology · 2021Article
- Best Practices for Making Reproducible Biochemical Models.Cell systems · 2020Review
- Recent advances in biomedical simulations: a manifesto for model engineering.F1000Research · 2019Review
- Tellurium: An extensible python-based modeling environment for systems and synthetic biology.Bio Systems · 2018Article
- Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.PLoS computational biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
motivationModel simulation exchange has been standardized with the Simulation Experiment Description Markup Language (SED-ML), but specialized software is needed to generate simulations in this format. Text-based languages allow researchers to create and modify experimental protocols quickly and easily, and export them to a common machine-readable format.
resultsphraSED-ML language allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and results) in a format easy to read and modify. The library can translate this script to SED-ML for use in other softwares. AVAILABILITY: phraSED-ML language specification, libphrasedml library, and source code are available under BSD license from http://phrasedml.sourceforge.net/ .
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.