ArticleCellular and molecular bioengineering2011
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models.
Article in Cellular and molecular bioengineering, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 3 of them syntheses that pooled it.
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Who cites it
22 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Molecular Systems Architecture of Fibrotic Lung Microenvironment in Idiopathic Pulmonary Fibrosis.Cells · 2026Pooled it
- A molecular systems architecture of asthma.Frontiers in immunology · 2026Pooled it
- A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis.NPJ systems biology and applications · 2025Pooled it
- A molecular systems architecture of the mesenchymal stromal cell microenvironment.Stem cells (Dayton, Ohio) · 2025Article
- Attenuation of Aging-Related Oxidative Stress Pathways by Phytonutrients: A Computational Systems Biology Analysis.Nutrients · 2023Article
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- Molecular systems architecture of host-microbiome interactions in periodontitis.JADA foundational science · 2023Review
- Molecular Systems Architecture of Interactome in the Acute Myeloid Leukemia Microenvironment.Cancers · 2022Review
- A case for the reuse and adaptation of mechanistic computational models to study transplant immunology.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2020Review
- Modeling oxygen requirements in ischemic cardiomyocytes.The Journal of biological chemistry · 2017Article
- Pericytes of the neurovascular unit: key functions and signaling pathways.Nature neuroscience · 2016Review
- Challenges in horizontal model integration.BMC systems biology · 2016Article
- Integrating Multiscale Modeling with Drug Effects for Cancer Treatment.Cancer informatics · 2015Review
- Simulation environment and graphical visualization environment: a COPD use-case.Journal of translational medicine · 2014Article
- The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.BMC systems biology · 2013Article
- An online model composition tool for system biology models.BMC systems biology · 2013Article
- In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology.Biophysical journal · 2013Article
- Contribution of genome-wide association studies to scientific research: a pragmatic approach to evaluate their impact.PloS one · 2013Article
- Setting a research agenda for progressive multiple sclerosis: the International Collaborative on Progressive MS.Multiple sclerosis (Houndmills, Basingstoke, England) · 2012Review
- Combinatorial drug therapy for cancer in the post-genomic era.Nature biotechnology · 2012Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models' source codes to create a large monolithic model (computer program) that runs on a single computer. Such a larger model is difficult, if not impossible, to maintain given ongoing updates to the source codes of the smaller models. This paper describes a new system called CytoSolve that dynamically integrates computations of smaller models that can run in parallel across different machines without the need to merge the source codes of the individual models. This approach is demonstrated on the classic Epidermal Growth Factor Receptor (EGFR) model of Kholodenko. The EGFR model is split into four smaller models and each smaller model is distributed on a different machine. Results from four smaller models are dynamically integrated to generate identical results to the monolithic EGFR model running on a single machine. The overhead for parallel and dynamic computation is approximately twice that of a monolithic model running on a single machine. The CytoSolve approach provides a scalable method since smaller models may reside on any computer worldwide, where the source code of each model can be independently maintained and updated.
Identifiers
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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.