A parallelized cellular Potts model that enables simulations at tissue scale Article Swipe
Shabaz Sultan
,
Sapna Devi
,
Scott N. Mueller
,
Johannes Textor
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2312.09317
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2312.09317
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide use, CPM simulations are considered too computationally intensive for three-dimensional (3D) models at organ scale. CPMs have been difficult to parallelise because of their inherently sequential update scheme. Here, we present a Graphical Processing Unit (GPU)-based parallelisation scheme that preserves local update statistics and is up to 3-4 orders of magnitude faster than serial implementations. We show several examples where our scheme preserves simulation behaviors that are drastically altered by existing parallelisation methods. We use our framework to construct tissue-scale models of liver and lymph node environments containing millions of cells that are directly based on microscopy-imaged tissue structures. Thus, our GPU-based CPM framework enables in silico studies of multicellular systems of unprecedented scale.
Related Topics
Concepts
Computer science
Multicellular organism
Scale (ratio)
Scheme (mathematics)
Implementation
Node (physics)
In silico
Parallel computing
Distributed computing
Construct (python library)
Computational science
Biology
Mathematics
Cell
Physics
Programming language
Mathematical analysis
Quantum mechanics
Biochemistry
Gene
Genetics
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- http://arxiv.org/abs/2312.09317
- https://arxiv.org/pdf/2312.09317
- OA Status
- green
- Cited By
- 3
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4389911401
All OpenAlex metadata
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https://openalex.org/W4389911401Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.48550/arxiv.2312.09317Digital Object Identifier
- Title
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A parallelized cellular Potts model that enables simulations at tissue scaleWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
-
2023-12-14Full publication date if available
- Authors
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Shabaz Sultan, Sapna Devi, Scott N. Mueller, Johannes TextorList of authors in order
- Landing page
-
https://arxiv.org/abs/2312.09317Publisher landing page
- PDF URL
-
https://arxiv.org/pdf/2312.09317Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://arxiv.org/pdf/2312.09317Direct OA link when available
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Computer science, Multicellular organism, Scale (ratio), Scheme (mathematics), Implementation, Node (physics), In silico, Parallel computing, Distributed computing, Construct (python library), Computational science, Biology, Mathematics, Cell, Physics, Programming language, Mathematical analysis, Quantum mechanics, Biochemistry, Gene, GeneticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
3Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 2Per-year citation counts (last 5 years)
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.silico | 143 |
| abstract_inverted_index.tissue | 134 |
| abstract_inverted_index.tumour | 29 |
| abstract_inverted_index.update | 63, 78 |
| abstract_inverted_index.widely | 7 |
| abstract_inverted_index.Despite | 34 |
| abstract_inverted_index.altered | 105 |
| abstract_inverted_index.because | 58 |
| abstract_inverted_index.enables | 141 |
| abstract_inverted_index.present | 67 |
| abstract_inverted_index.ranging | 23 |
| abstract_inverted_index.scheme. | 64 |
| abstract_inverted_index.several | 94 |
| abstract_inverted_index.studies | 144 |
| abstract_inverted_index.systems | 12, 147 |
| abstract_inverted_index.Cellular | 1 |
| abstract_inverted_index.directly | 130 |
| abstract_inverted_index.examples | 95 |
| abstract_inverted_index.existing | 107 |
| abstract_inverted_index.methods. | 109 |
| abstract_inverted_index.millions | 125 |
| abstract_inverted_index.paradigm | 10 |
| abstract_inverted_index.GPU-based | 138 |
| abstract_inverted_index.Graphical | 69 |
| abstract_inverted_index.behaviors | 101 |
| abstract_inverted_index.construct | 115 |
| abstract_inverted_index.difficult | 55 |
| abstract_inverted_index.framework | 113, 140 |
| abstract_inverted_index.intensive | 44 |
| abstract_inverted_index.magnitude | 87 |
| abstract_inverted_index.preserves | 76, 99 |
| abstract_inverted_index.scenarios | 22 |
| abstract_inverted_index.Processing | 70 |
| abstract_inverted_index.considered | 41 |
| abstract_inverted_index.containing | 124 |
| abstract_inverted_index.inherently | 61 |
| abstract_inverted_index.migration. | 33 |
| abstract_inverted_index.sequential | 62 |
| abstract_inverted_index.simulation | 9, 100 |
| abstract_inverted_index.statistics | 79 |
| abstract_inverted_index.(GPU)-based | 72 |
| abstract_inverted_index.development | 26 |
| abstract_inverted_index.drastically | 104 |
| abstract_inverted_index.interacting | 14 |
| abstract_inverted_index.parallelise | 57 |
| abstract_inverted_index.simulations | 39 |
| abstract_inverted_index.structures. | 135 |
| abstract_inverted_index.environments | 123 |
| abstract_inverted_index.tissue-scale | 116 |
| abstract_inverted_index.multicellular | 146 |
| abstract_inverted_index.unprecedented | 149 |
| abstract_inverted_index.morphogenesis, | 28 |
| abstract_inverted_index.computationally | 43 |
| abstract_inverted_index.parallelisation | 73, 108 |
| abstract_inverted_index.implementations. | 91 |
| abstract_inverted_index.microscopy-imaged | 133 |
| abstract_inverted_index.three-dimensional | 46 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 4 |
| citation_normalized_percentile |