ArticleBioinformatics advances2022
ODEbase: a repository of ODE systems for systems biology.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 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
2 citing papers in PubMed.
- Positive equilibria in mass action networks: geometry and bounds.Journal of mathematical biology · 2026Article
- Mathematical basis and toolchain for hierarchical optimization of biochemical networks.PLoS computational biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to biological questions. Qualitative methods analyze dynamical input systems as formal objects, in contrast to investigating only part of the state space, as is the case with numerical simulation. However, corresponding tools and libraries have a different set of requirements for their input data than their numerical counterparts. A common format used in mathematical modeling of biological processes is Systems Biology Markup Language (SBML). We illustrate that the use of SBML data in symbolic computation requires significant pre-processing, incorporating external biological and mathematical expertise. ODEbase provides suitable input data derived from established existing biomodels, covering in particular the BioModels database. Availability and implementation: ODEbase is available free of charge at https://odebase.org.
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.