ReviewBriefings in bioinformatics2021
A practical guide to mechanistic systems modeling in biology using a logic-based approach.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Recent applications of quantitative systems pharmacology and machine learning models across diseases.Journal of pharmacokinetics and pharmacodynamics · 2022Pooled it
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Digital twins to accelerate target identification and drug development for immune-mediated disorders.FEBS open bio · 2026Review
- Lactylation modulates immune infiltration in sepsis-induced acute respiratory distress syndrome: a multi-omics and machine learning study with experimental confirmation.European journal of medical research · 2025Article
- Constraint based modeling of drug induced metabolic changes in a cancer cell line.NPJ systems biology and applications · 2025Article
- Data-driven synthetic microbes for sustainable future.NPJ systems biology and applications · 2025Review
- PseudoCell: A Multivalued Logical Regulatory Network to Investigate Premature Senescence Dynamics and Heterogeneity.Aging medicine (Milton (N.S.W)) · 2025Article
- Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis.NPJ digital medicine · 2024Article
- Forum on immune digital twins: a meeting report.NPJ systems biology and applications · 2024Review
- Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.FEMS microbiology ecology · 2023Review
- Intervention Approaches in Studying the Response to Vitamin DNutrients · 2023Review
- Concepts of multi-level dynamical modelling: understanding mechanisms of squamous cell carcinoma development in Fanconi anemia.Frontiers in genetics · 2023Article
- A multiscale mechanistic model of human dendritic cells forFrontiers in immunology · 2023Article
- Building digital twins of the human immune system: toward a roadmap.NPJ digital medicine · 2022Review
- Boolean modelling as a logic-based dynamic approach in systems medicine.Computational and structural biotechnology journal · 2022Review
- Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map.Journal of personalized medicine · 2021Article
- Unsupervised logic-based mechanism inference for network-driven biological processes.PLoS computational biology · 2021Article
- The Need for Research-Grade Systems Modeling Technologies for Life Science Education.Trends in molecular medicine · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These models provide a means to analyze the dynamics of the systems they describe, and to study and interrogate their properties, and provide insights about the emerging behavior of the system in the presence of single or combined perturbations. Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps. The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting the appropriate modeling approach, constructing a model and simulating the model. To ensure broad accessibility of the protocol, we use a logical modeling framework, which presents a lower mathematical barrier of entry, and two easy-to-use and popular modeling software tools: Cell Collective and GINsim. The complete modeling workflow is applied to a well-studied and familiar biological process-the lac operon regulatory system. The protocol can be completed by users with little to no prior computational modeling experience approximately within 3 h.
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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.