ArticleBMC systems biology2016
Modelling with ANIMO: between fuzzy logic and differential equations.
Article in BMC systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Regulatory network-based model to simulate the biochemical regulation of chondrocytes in healthy and osteoarthritic environments.Scientific reports · 2022Article
- An ECHO of Cartilage:Frontiers in bioengineering and biotechnology · 2021Article
- Understanding the Mechanism of Cell Death in Gemcitabine Resistant Pancreatic Ductal Adenocarcinoma: A Systems Biology Approach.Current genomics · 2019Article
- DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks.BMC bioinformatics · 2019Article
- Computational Modeling and Reverse Engineering to Reveal Dominant Regulatory Interactions Controlling Osteochondral Differentiation: Potential for Regenerative Medicine.Frontiers in bioengineering and biotechnology · 2018Review
- Nitric Oxide Mediates Crosstalk between Interleukin 1β and WNT Signaling in Primary Human Chondrocytes by Reducing DKK1 and FRZB Expression.International journal of molecular sciences · 2017Article
- Simulation and visualization of multiple KEGG pathways using BioNSi.F1000Research · 2017Article
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Authors and funding
7 authors.
Funding
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Abstract
backgroundComputational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computational support and allow insight into the complex networks of signaling events occurring in living cells. ANIMO makes use of timed automata as an underlying model, thereby enabling analysis techniques from computer science like model checking. Biology experts are able to use ANIMO via a user interface specifically tailored for biological applications. In this paper we compare the use of ANIMO with some established formalisms on two case studies.
resultsANIMO is a powerful and user-friendly tool that can compete with existing continuous and discrete paradigms. We show this by presenting ANIMO models for two case studies: Drosophila melanogaster circadian clock, and signal transduction events downstream of TNF α and EGF in HT-29 human colon carcinoma cells. The models were originally developed with ODEs and fuzzy logic, respectively.
conclusionsTwo biological case studies that have been modeled with respectively ODE and fuzzy logic models can be conveniently modeled using ANIMO. The ANIMO models require less parameters than ODEs and are more precise than fuzzy logic. For this reason we position the modelling paradigm of ANIMO between ODEs and fuzzy logic.
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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.