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Ten simple rules for creating reusable pathway models for computational analysis and visualization

Kristina Hanspers, Martina Kutmon, Susan L. Coort, Daniela Digles, Lauren J. Dupuis, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter (+6 others)
2021 PLoS Computational Biology  
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

Denise Slenter, Egon Willighagen
2021 Zenodo  
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

Ken Webb, Tony White
2006 Applied intelligence (Boston)  
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  
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

Michel Kraemer, David Ludlow, Zaheer Khan
2013 ECMS 2013 Proceedings edited by: Webjorn Rekdalsbakken, Robin T. Bye, Houxiang Zhang  
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

Ana Sofia Figueiredo
2017 Frontiers in Public Health  
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

Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong
2018 Journal of Biomedical Semantics  
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

Enrico Ferrero, Sophie Brachat, Jeremy L. Jenkins, Philippe Marc, Peter Skewes-Cox, Robert C. Altshuler, Caroline Gubser Keller, Audrey Kauffmann, Erik K. Sassaman, Jason M. Laramie, Birgit Schoeberl, Mark L. Borowsky (+2 others)
2020 PLoS Computational Biology  
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]

Ken Webb, Tony White
2004 Lecture Notes in Computer Science  
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

Jasia King, Kerbaï Saïd Eroumé, Roman Truckenmüller, Stefan Giselbrecht, Ann E. Cowan, Leslie Loew, Aurélie Carlier, Patricia M. Palagi
2021 PLoS Computational Biology  
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]

Oscar O. Ortega, Carlos F Lopez
2019 biorxiv/medrxiv   pre-print
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]

Angus G. Forbes, Andrew Burks, Kristine Lee, Xing Li, Pierre Boutillier, Jean Krivine, Walter Fontana
2017 arXiv   pre-print
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

Ali Najafi, Gholamreza Bidkhori, Joseph Bozorgmehr, Ina Koch, Ali Masoudi-Nejad
2014 Current Genomics  
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

John Arul Prakash Sekar, Jose-Juan Tapia, James R. Faeder, Jeffrey J. Saucerman
2017 PLoS Computational Biology  
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

Mahyar Osanlouy, Anita Bandrowski, Bernard de Bono, David Brooks, Antonino M. Cassarà, Richard Christie, Nazanin Ebrahimi, Tom Gillespie, Jeffrey S. Grethe, Leonardo A. Guercio, Maci Heal, Mabelle Lin (+9 others)
2021 Frontiers in Physiology  
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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