ArticleFrontiers in physiology2018
BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks.
Article in Frontiers in physiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- From mechanistic models to artificial intelligence: exploring the potential of digital twins in geriatric oncology.Frontiers in artificial intelligence · 2026Article
- Path-based quantification of activation and repression in Boolean models using BooLEVARD.NPJ systems biology and applications · 2025Article
- Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial.Interface focus · 2025Article
- PseudoCell: A Multivalued Logical Regulatory Network to Investigate Premature Senescence Dynamics and Heterogeneity.Aging medicine (Milton (N.S.W)) · 2025Article
- Refining Boolean models with the partial most permissive scheme.Bioinformatics (Oxford, England) · 2025Article
- Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy.Briefings in bioinformatics · 2024Article
- MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps.Journal of integrative bioinformatics · 2024Article
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization.Frontiers in systems biology · 2023Article
- Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts.Computational and structural biotechnology journal · 2023Article
- Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach.PLoS computational biology · 2022Article
- An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.Nature methods · 2022Article
- Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes.iScience · 2021Article
- Boolean factor graph model for biological systems: the yeast cell-cycle network.BMC bioinformatics · 2021Article
- Logical modelling ofInterface focus · 2021Article
- In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer.International journal of molecular sciences · 2021Review
- Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Briefings in bioinformatics · 2021Review
- A logical network-based drug-screening platform for Alzheimer's disease representing pathological features of human brain organoids.Nature communications · 2021Article
- Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors.Frontiers in physiology · 2020Article
- Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction.Frontiers in physiology · 2020Article
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Abstract
Here we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations as building blocks for the development of integrated modeling software, or for the assembly of heterogeneous analysis workflows involving several complementary tools. Based on the definition of multi-valued logical models, bioLQM implements import and export facilities, notably for the recent SBML qual exchange format, as well as for formats used by several popular tools, facilitating the design of workflows combining these tools. Model modifications enable the definition of various perturbations, as well as model reduction, easing the analysis of large models. Another modification enables the study of multi-valued models with tools limited to the Boolean case. Finally, bioLQM provides a framework for the development of novel analysis tools. The current version implements various updating modes for model simulation (notably synchronous, asynchronous, and random asynchronous), as well as some static analysis features for the identification of attractors. The bioLQM software can be integrated into analysis workflows through command line and scripting interfaces. As a Java library, it further provides core data structures to the GINsim and EpiLog interactive tools, which supply graphical interfaces and additional analysis methods for cellular and multi-cellular qualitative models.
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