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The Practice of Archiving Model Code of Agent-Based Models

Marco A. Janssen
2017 Journal of Artificial Societies and Social Simulation  
To evaluate the concern over the reproducibility of computational science, we reviewed journal articles on agent-based models published between and and documented the public availability of source code  ...  There are big di erences among journals in the public availability of model code and so ware used.  ...  Acknowledgements The author would like to acknowledge the contributions of Allen Lee, Calvin Pritchard and Tejas Patel in developing the so ware for the metadata and Michael Barton for his feedback on  ... 
doi:10.18564/jasss.3317 fatcat:uzg2zzysafhqrbmos6zkyjo4y4

Introducing the eqasim pipeline: From raw data to agent-based transport simulation

Sebastian Hörl, Milos Balac
2021 Procedia Computer Science  
It therefore lays the foundation to achieve fully reproducible agent-based transport simulations.  ...  It therefore lays the foundation to achieve fully reproducible agent-based transport simulations.  ...  While car-sharing was probably one of the first emerging transport services to be investigated in detail using agent-based models [16, 4] , shared on-demand automated services ensured that agent-based  ... 
doi:10.1016/j.procs.2021.03.089 fatcat:ewknyp4sjjezhnf4abe7arkuqy

A meta-epidemiological assessment of transparency indicators of infectious disease models [article]

Emmanuel A. Zavalis, John Ioannidis
2022 medRxiv   pre-print
) were time series, 279 (20.9%) were spatiotemporal, 186 (13.9%) were agent-based and 25 (1.9%) contained multiple model types. 288 (21.5%) articles shared code, 332 (24.8%) shared data, 6 (0.4%) were  ...  On manual assessment, 5/6 articles identified as registered had indeed been registered. Transparency in infectious disease modelling is relatively low, especially for data and code sharing.  ...  Code sharing was more common in COVID-19 models and in agent-based models. Data sharing was more common in spatiotemporal and agent-based models and also depended substantially on the journal.  ... 
doi:10.1101/2022.04.11.22273744 fatcat:lvghfloen5eerlrsz7ft5vs2sy

A Computational Model Library for publishing model documentation and code

Nathan D. Rollins, C. Michael Barton, Sean Bergin, Marco A. Janssen, Allen Lee
2014 Environmental Modelling & Software  
The number of research projects using computational models has been steadily increasing but the resulting publications often lack model code and documentation which hinders replication, verification of  ...  Researchers can request that their models undergo a certification process that verifies that the model code successfully compiles and runs and that it follows documentation best practices.  ...  We also want to acknowledge the Center for Social Dynamics and Complexity, the Center for the Study of Institutional Diversity and the University Technology Office at ASU for their contributions to developing  ... 
doi:10.1016/j.envsoft.2014.06.022 fatcat:55l3ptnd6retfdlv3jpc4on2xu

Documenting, storing, and executing models in Ecology: A conceptual framework and real implementation in a global change monitoring program

Francisco J. Bonet, Ramón Pérez-Pérez, Blas M. Benito, Fábio Suzart de Albuquerque, Regino Zamora
2014 Environmental Modelling & Software  
We propose that it is time to address the problem of storing, documenting, and executing ecological models and analytical procedures.  ...  This is being used to document, share, and execute more than 200 models and analytical processes associated with a global change monitoring program that is being undertaken in the Sierra Nevada Mountains  ...  Acknowledgments This work has been done in the collaborative framework of the "Sierra Nevada Global Change Observatory" Project from the Environment Department of Andalusian Regional Government, the Sierra  ... 
doi:10.1016/j.envsoft.2013.10.027 fatcat:nlthxjhhubfvxpnffp7wjp4dwa

Integrative architecture elicitation for large computer based systems

P. Tabeling, B. Grone
2005 12th IEEE International Conference and Workshops on the Engineering of Computer-Based Systems (ECBS'05)  
This paper presents concepts and abstractions for integrative modeling, based on the Fundamental Modeling Concepts.  ...  Some information can be extracted and prepared by tools, but the majority is usually inside documents and the heads of the developers.  ...  Each functionality is typically represented as a single Generally, agents, storages and channels can each be derived by answering one of the following questions, based on the component's documentation:  ... 
doi:10.1109/ecbs.2005.46 dblp:conf/ecbs/TabelingG05 fatcat:d4mg4ac2dnefdlk5fxwzcx67vu

A semantic publish-subscribe coordination framework for IHE based cross-community health record exchange

Visara Urovi, Alex C. Olivieri, Stefano Bromuri, Nicoletta Fornara, Michael I. Schumacher
2013 ACM SIGAPP Applied Computing Review  
The framework models the interactions among the communities as a combination of the tuple centre agent communication model with the publish-subscribe paradigm and semantic web technologies.  ...  A set of autonomous agents and a set of distributed coordination rules are used to coordinate the agents in the search of specific health records.  ...  This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution.  ... 
doi:10.1145/2537728.2537732 fatcat:5qdg64ng5nag3j5lx3azy5b4oy

EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology

Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée, Pauline Ezanno, Mihaela Pertea
2019 PLoS Computational Biology  
The modelling language and simulation architecture both rely on the combination of advanced artificial intelligence methods (knowledge representation and multi-level agent-based simulation), allowing several  ...  modelling paradigms (from compartment- to individual-based models) at several scales (up to metapopulation).  ...  Acknowledgments We are very grateful to Thibaut Morel-Journel for his careful reading and relevant comments.  ... 
doi:10.1371/journal.pcbi.1007342 pmid:31518349 pmcid:PMC6760811 fatcat:aotghozenvgv3e5mmhhbhekms4

Indivo: a personally controlled health record for health information exchange and communication

Kenneth D Mandl, William W Simons, William CR Crawford, Jonathan M Abbett
2007 BMC Medical Informatics and Decision Making  
Indivo allows the ready integration of diverse sources of medical data under a patient's control through the use of standards-based communication protocols and APIs for connecting PCHRs to existing and  ...  Conclusion: The strict and transparent personal control model is designed to encourage widespread participation by patients, healthcare providers and institutions, thus creating the ecosystem for development  ...  Kohane, Nathan Finstein and Clark Freifeld of the Indivo team.  ... 
doi:10.1186/1472-6947-7-25 pmid:17850667 pmcid:PMC2048946 fatcat:3i6rbqksubbodfzfqrjyhejziq

Open Science, Replicability, and Transparency in Modelling [chapter]

Toby Prike
2021 Towards Bayesian Model-Based Demography  
In response to this, and as part of a broader open science movement, a variety of changes to research practice have started to be implemented, such as publicly sharing data, analysis code, and study materials  ...  This chapter outlines the relevance and applicability of these issues to computational modelling, highlighting the importance of good research practices for modelling endeavours, as well as the potential  ...  Additionally, if a computational model is informed by, or relies on, empirical findings to justify mechanisms and processes within the model (e.g., the decision making of agents within an agent-based model  ... 
doi:10.1007/978-3-030-83039-7_10 fatcat:dozkgdjpnjfnrmf5bkgzfvg3ca

Software engineering considerations for individual-based models

Glen E. Ropella, Steven F. Railsback, Stephen K. Jackson
2002 Natural Resources Modeling  
Software design is much more important for individual-based models (IBMs) than it is for conventional models, for three reasons.  ...  over the software as changes are implemented. (3) Develop multiple representations of the model and its software; diagrams and written descriptions of code aid design and understanding. (4) Use appropriate  ...  These thoughts were originally presented by the first author to the special symposium, Advancing the Individual-  ... 
doi:10.1216/nrm/1030539094 fatcat:ztwoty5j7va7deyj5nvo3rzy5y


2008 Natural Resource Modeling  
Software design is much more important for individual-based models (IBMs) than it is for conventional models, for three reasons.  ...  over the software as changes are implemented. (3) Develop multiple representations of the model and its software; diagrams and written descriptions of code aid design and understanding. (4) Use appropriate  ...  These thoughts were originally presented by the first author to the special symposium, Advancing the Individual-  ... 
doi:10.1111/j.1939-7445.2002.tb00077.x fatcat:btwy75ojjbgrpidp323wgfaj3q

A Methodology for Developing an Agent Systems Reference Architecture [chapter]

Duc N. Nguyen, Kyle Usbeck, William M. Mongan, Christopher T. Cannon, Robert N. Lass, Jeff Salvage, William C. Regli, Israel Mayk, Todd Urness
2011 Lecture Notes in Computer Science  
Rather than the traditional approach of studying existing systems, the documentation methodology relies on forensic software analysis of agent frameworks (i.e., APIs and libraries for constructing agent  ...  However, there is little, if any, consensus on how to create a reference architecture for agent-based systems.  ...  The Process View for Agent Mobility The Process view documents the runtime behavior of a functional concept based on a code snippets for each agent framework.  ... 
doi:10.1007/978-3-642-22636-6_11 fatcat:te4kah2m7nb2hmuidtlvx2i4y4

Data security services, solutions and standards for outsourcing

Kevin W. Hamlen, Bhavani Thuraisingham
2013 Computer Standards & Interfaces  
In particular, it discusses security issues pertaining to data-as-a-service and software-as-a-service models as well as supply chain security issues.  ...  Security of operation is therefore critical for effectively introducing and maintaining these business relationships without sacrificing product quality.  ...  We developed two types of cloud data managers, one based on semantic web data and the other based on relational data.  ... 
doi:10.1016/j.csi.2012.02.001 fatcat:h67wqqrezvg33nyxydnw7w6jhy

Survey of Agent-Based Simulations for Modelling COVID-19 Pandemic

Abdulla M. Alsharhan
2021 Advances in Science, Technology and Engineering Systems  
This paper aims to review published papers that discussed Agent-based simulation (ABS) for modelling the COVID-19 pandemic.  ...  Many modelers are using agent-based simulations to virtually examine the efficiency of these scenarios.  ...  The authors declare no conflicts of interest.  ... 
doi:10.25046/aj060250 fatcat:3itx3yh4hbgtrdyjisc5tegdyq
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