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Ten simple rules for creating reusable pathway models for computational analysis and visualization
2021
PLoS Computational Biology
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PLOS Computational Biology | https://doi.Citation: Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F, et al. (2021) Ten simple rules for creating reusable pathway models for computational ...
The rules range from reusability and dissemination (Rules 1, 9, and 10), intuitive visual concepts (Rules 2, 7, and 8), to enabling computational analysis (Rules 3 to 6). ...
Acknowledgments We would like to thank all WikiPathways contributors for their work creating pathway models, which has helped greatly in the development of these rules. ...
doi:10.1371/journal.pcbi.1009226
pmid:34411100
pmcid:PMC8375987
fatcat:kopq6o6hgfcbngrbu4bqi2ucie
Standardization of metabolic reaction databases and use in fluxomics
2021
Zenodo
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Denise Slenter in the Session/Class: Standardization of Metabolic reaction databases and use in fluxomics, taught on the second day of the 1st ELIXIR Fluxomics Training School 2021 (October 5, 2021). ...
Genet.
10:1203. doi: 10.3389/fgene.2019.01203
Fig 1-3 adapted from Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F,
et al. (2021) Ten simple rules for creating reusable pathway models for ...
computational
analysis and visualization. ...
doi:10.5281/zenodo.5772028
fatcat:umr5iti3kzghjb5wujb6fzyaem
Cell modeling with reusable agent-based formalisms
2006
Applied intelligence (Boston)
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Making use of the objectoriented (OO) paradigm, the Unified Modeling Language (UML) and Real-time Object-Oriented Modeling (ROOM) visual formalisms, and the Rational Rose RealTime (RRT) visual modeling ...
tool, we summarize a previously-described multi-step process for constructing top-down models of cells. ...
The combined action of multiple reaction rules over time results in the two metabolic pathways that are part of the simple example model, the glycolytic pathway and the TCA cycle. ...
doi:10.1007/s10489-006-6937-9
fatcat:vufokxeqxvbrxbrarklipw2g4y
OUP accepted manuscript
2018
Database: The Journal of Biological Databases and Curation
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Computational models in biology encode molecular and cell biological processes. Many of these models can be represented as biochemical reaction networks. ...
The large number and size of available models, however, require automated methods to support researchers in achieving their goals. ...
Acknowledgements The authors like to thank Faiz Muhammad Khan for the many fruitful discussions and Martin Scharm for helping with scripting issues. Conflict of interest. None declared. ...
doi:10.1093/database/bay051
pmid:29992320
pmcid:PMC6030809
fatcat:3qnywfjsezgmrdyz3s5cfs7ae4
Domain-Specific Languages For Agile Urban Policy Modelling
2013
ECMS 2013 Proceedings edited by: Webjorn Rekdalsbakken, Robin T. Bye, Houxiang Zhang
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aspects such as computational processes and computer-readable policy rules in the words of the domain expert. ...
We present a complete policy cycle that includes creating policy plans, securing stakeholders and public engagement, implementation, monitoring, and evaluating a particular policy model. ...
ACKNOWLEDGEMENT Research presented here is partly carried out within the project "urbanAPI" (Interactive Analysis, Simulation and Visualisation Tools for Urban Agile Policy Implementation), funded from ...
doi:10.7148/2013-0673
dblp:conf/ecms/KraemerLK13
fatcat:cdf3hgklk5dwjj6juokcwo3roi
Data Sharing: Convert Challenges into Opportunities
2017
Frontiers in Public Health
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The reuse of research data has the potential to avoid the duplication of data sets and to bring new views from multiple analysis of the same data set. ...
Initiatives for sharing research data are opportunities to increase the pace of knowledge discovery and scientific progress. ...
Make certain that the computer code is efficient and reproducible by following the ten simple rules for reproducible computational research laid out by Sandve et al. (31) . ...
doi:10.3389/fpubh.2017.00327
pmid:29270401
pmcid:PMC5723929
fatcat:phv7cwaiwzd3hnt5xwdqbteefq
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability
2018
Journal of Biomedical Semantics
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Interoperable and Reusable (i.e., FAIR). ...
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. ...
Acknowledgements We acknowledge the OBO Foundry consortium and OBO ontology developers for their support and collaborations. ...
doi:10.1186/s13326-017-0169-2
pmid:29329592
pmcid:PMC5765662
fatcat:5w3acqcqd5hnxphdq76ruqlrja
Ten simple rules to power drug discovery with data science
2020
PLoS Computational Biology
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Acknowledgments We would like to thank all members of the Computational Sciences Council at the Novartis Institutes for BioMedical Research for helpful input and feedback on the manuscript. ...
Both R and Python offer efficient ecosystems for data wrangling, modeling, and visualization: R as part of the tidyverse [14] and through independent packages like data.table [15] , mlr [16, 17] , ...
Tighter integration of data generation, engineering, and analysis functions also creates shared accountability and improves the impact of combined experimental and computational work supporting drug discovery ...
doi:10.1371/journal.pcbi.1008126
pmid:32853229
fatcat:k633mqpjlfdrzdzal5vbw662ce
Cell Modeling Using Agent-Based Formalisms
[chapter]
2004
Lecture Notes in Computer Science
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Making use of the object-oriented (OO) paradigm, the Unified Modeling Language (UML) and Real-time Object-Oriented Modeling (ROOM) visual formalisms, we describe a simple model that includes membranes ...
We demonstrate the validation of the model by comparison with Gepasi and comment on the reusability of model components. ...
The ROOM formalism David Harel, originator of the hierarchical state diagram formalism used in the Universal Modeling Language (UML) [10] , and an early proponent of visual formalisms in software analysis ...
doi:10.1007/978-3-540-24677-0_14
fatcat:idj7wtngmrbsviwso3sbrtzmla
Ten steps to investigate a cellular system with mathematical modeling
2021
PLoS Computational Biology
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In this article, we will focus on the generic modeling process and illustrate it with an example model of membrane lipid turnover. ...
Because of this complexity, mathematical modeling is increasingly used to simulate such systems and perform experiments in silico, many orders of magnitude faster than real experiments and often at a higher ...
Acknowledgments We would also like to thank Boris Slepchenko for the discussion and suggestions that greatly improved the manuscript. ...
doi:10.1371/journal.pcbi.1008921
pmid:33983922
fatcat:tt7qlwg67jeudnh26p4hptk5wm
Interactive Multiresolution Visualization of Cellular Network Processes
[article]
2019
biorxiv/medrxiv
pre-print
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Visualization plays a central role in the analysis of biochemical network processes to identify patterns that arise from model dynamics and perform model exploratory analysis. ...
PyViPR embeds network visualizations on Jupyter notebooks, thus facilitating integration with Python modeling, simulation, and analysis workflows. ...
workflows for model definition, visualization, and analysis. ...
doi:10.1101/659367
fatcat:bh57bwif2ndavkaz7ut2sxluhi
Dynamic Influence Networks for Rule-based Models
[article]
2017
arXiv
pre-print
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We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. ...
Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component ...
ACKNOWLEDGMENTS This work is funded by the DARPA Big Mechanism Program under ARO contracts W911NF-14-1-0367 and W911NF-14-1-0395. ...
arXiv:1711.00967v1
fatcat:wbigxsfybvei7fy2gy6ju5wnpq
Genome Scale Modeling in Systems Biology: Algorithms and Resources
2014
Current Genomics
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Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. ...
Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. ...
ACKNOWLEDGEMENTS We would like to thank all members of the laboratory of systems biology and bioinformatics (LBB) for their help during course of this study. ...
doi:10.2174/1389202915666140319002221
pmid:24822031
pmcid:PMC4009841
fatcat:xh7tgip2yfdq3fe2typ74jlfkq
Automated visualization of rule-based models
2017
PLoS Computational Biology
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and graph analysis, all of which are advances over the state of the art for rule-based models. ...
We expect that these tools will promote communication and analysis of rule-based models and their eventual integration into whole cell models. ...
Here, we show that a simple pathway representation can be achieved by formally compressing the rule-derived regulatory graph using user annotation and graph analysis. ...
doi:10.1371/journal.pcbi.1005857
pmid:29131816
pmcid:PMC5703574
fatcat:dqun2zkj4vgmrgxnpegd56bhha
The SPARC DRC: Building a Resource for the Autonomic Nervous System Community
2021
Frontiers in Physiology
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A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical ...
The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. ...
We would also like to acknowledge BioRxiv for hosting a preprint of this manuscript (Osanlouy et al., 2021) , and we thank Frontiers for its supportive preprint policy. ...
doi:10.3389/fphys.2021.693735
pmid:34248680
pmcid:PMC8265045
fatcat:nieiiwmbzjeqza3cj4zt2h7z2y
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