ArticlePLoS computational biology2020
Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
What it found
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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.
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Who cites it
67 citing papers in PubMed.
- A Comparison of Mechanisms Driving Lesion Outcomes During Lung Tumor and Tuberculosis Granuloma Formation.Bulletin of mathematical biology · 2026Article
- In silico models in oncology, neurology, and epidemiology: systems-level and multiscale perspectives.NPJ systems biology and applications · 2026Review
- Article
- TumorTwin: a Python framework for patient-specific digital twins in oncology.BMC medical informatics and decision making · 2026Article
- Article
- Overcoming vascular niche-mediated TKI resistance in acute myeloid leukemia through miR-126 inhibition.NPJ systems biology and applications · 2026Article
- Mathematical Oncology: How Modeling Is Transforming Clinical Decision-Making.Cancer research · 2025Review
- Astrocyte Reprogramming Drives Tumor Progression and Chemotherapy Resistance in Agent-Based Models of Breast Cancer Brain Metastases.Bulletin of mathematical biology · 2025Article
- Rethinking the seven-day treatment-free interval in T-cell engager therapy using agent-based modeling.bioRxiv : the preprint server for biology · 2025Article
- Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk.PLoS computational biology · 2025Article
- Article
- The role of environmentally mediated drug resistance in facilitating the spatial distribution of residual disease.Communications biology · 2025Article
- Using spatial statistics to infer game-theoretic interactions in an agent-based model of cancer cells.bioRxiv : the preprint server for biology · 2025Article
- Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk.bioRxiv : the preprint server for biology · 2025Article
- The adaptive state determines the impact of mutations on evolving populations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Validating the predictions of mathematical models describing tumor growth and treatment response.ArXiv · 2025Article
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- AMBER: A Modular Model for Tumor Growth, Vasculature and Radiation Response.Bulletin of mathematical biology · 2024Article
- Probability of early infection extinction depends linearly on the virus clearance rate.Royal Society open science · 2024Article
- Spatial interactions modulate tumor growth and immune infiltration.NPJ systems biology and applications · 2024Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
The Hybrid Automata Library (HAL) is a Java Library developed for use in mathematical oncology modeling. It is made of simple, efficient, generic components that can be used to model complex spatial systems. HAL's components can broadly be classified into: on- and off-lattice agent containers, finite difference diffusion fields, a GUI building system, and additional tools and utilities for computation and data collection. These components are designed to operate independently and are standardized to make them easy to interface with one another. As a demonstration of how modeling can be simplified using our approach, we have included a complete example of a hybrid model (a spatial model with interacting agent-based and PDE components). HAL is a useful asset for researchers who wish to build performant 1D, 2D and 3D hybrid models in Java, while not starting entirely from scratch. It is available on GitHub at https://github.com/MathOnco/HAL under the MIT License. HAL requires the Java JDK version 1.8 or later to compile and run the source code.
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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.