Literature DB >> 30191471

Issues in Reproducible Simulation Research.

B G Fitzpatrick1.   

Abstract

In recent years, serious concerns have arisen about reproducibility in science. Estimates of the cost of irreproducible preclinical studies range from 28 billion USD per year in the USA alone (Freedman et al. in PLoS Biol 13(6):e1002165, 2015) to over 200 billion USD per year worldwide (Chalmers and Glasziou in Lancet 374:86-89, 2009). The situation in the social sciences is not very different: Reproducibility in psychological research, for example, has been estimated to be below 50% as well (Open Science Collaboration in Science 349:6251, 2015). Less well studied is the issue of reproducibility of simulation research. A few replication studies of agent-based models, however, suggest the problem for computational modeling may be more severe than for laboratory experiments (Willensky and Rand in JASSS 10(4):2, 2007; Donkin et al. in Environ Model Softw 92:142-151, 2017; Bajracharya and Duboz in: Proceedings of the symposium on theory of modeling and simulation-DEVS integrative M&S symposium, pp 6-11, 2013). In this perspective, we discuss problems of reproducibility in agent-based simulations of life and social science problems, drawing on best practices research in computer science and in wet-lab experiment design and execution to suggest some ways to improve simulation research practice.

Entities:  

Keywords:  Agent-based models; Computational lab notebook; Simulation reproducibility; Test-driven development; Validation; Version control

Mesh:

Year:  2018        PMID: 30191471      PMCID: PMC6320709          DOI: 10.1007/s11538-018-0496-1

Source DB:  PubMed          Journal:  Bull Math Biol        ISSN: 0092-8240            Impact factor:   1.758


  9 in total

1.  Drug development: Raise standards for preclinical cancer research.

Authors:  C Glenn Begley; Lee M Ellis
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

2.  False-positive psychology: undisclosed flexibility in data collection and analysis allows presenting anything as significant.

Authors:  Joseph P Simmons; Leif D Nelson; Uri Simonsohn
Journal:  Psychol Sci       Date:  2011-10-17

Review 3.  Pattern-oriented modeling of agent-based complex systems: lessons from ecology.

Authors:  Volker Grimm; Eloy Revilla; Uta Berger; Florian Jeltsch; Wolf M Mooij; Steven F Railsback; Hans-Hermann Thulke; Jacob Weiner; Thorsten Wiegand; Donald L DeAngelis
Journal:  Science       Date:  2005-11-11       Impact factor: 47.728

Review 4.  Avoidable waste in the production and reporting of research evidence.

Authors:  Iain Chalmers; Paul Glasziou
Journal:  Lancet       Date:  2009-06-12       Impact factor: 79.321

5.  Believe it or not: how much can we rely on published data on potential drug targets?

Authors:  Florian Prinz; Thomas Schlange; Khusru Asadullah
Journal:  Nat Rev Drug Discov       Date:  2011-08-31       Impact factor: 84.694

Review 6.  Agent-based models in translational systems biology.

Authors:  Gary An; Qi Mi; Joyeeta Dutta-Moscato; Yoram Vodovotz
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2009 Sep-Oct

7.  The Economics of Reproducibility in Preclinical Research.

Authors:  Leonard P Freedman; Iain M Cockburn; Timothy S Simcoe
Journal:  PLoS Biol       Date:  2015-06-09       Impact factor: 8.029

8.  Optimization and Control of Agent-Based Models in Biology: A Perspective.

Authors:  G An; B G Fitzpatrick; S Christley; P Federico; A Kanarek; R Miller Neilan; M Oremland; R Salinas; R Laubenbacher; S Lenhart
Journal:  Bull Math Biol       Date:  2016-11-08       Impact factor: 1.758

9.  PSYCHOLOGY. Estimating the reproducibility of psychological science.

Authors: 
Journal:  Science       Date:  2015-08-28       Impact factor: 47.728

  9 in total
  3 in total

Review 1.  Computational models in systems biology: standards, dissemination, and best practices.

Authors:  Luis Sordo Vieira; Reinhard C Laubenbacher
Journal:  Curr Opin Biotechnol       Date:  2022-02-23       Impact factor: 10.279

2.  Appropriately Tuning Stochastic-Psychometric Properties of the Balloon Analog Risk Task.

Authors:  Simone Di Plinio; Mauro Pettorruso; Sjoerd J H Ebisch
Journal:  Front Psychol       Date:  2022-05-10

Review 3.  Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review.

Authors:  Sherli Koshy-Chenthittayil; Linda Archambault; Dhananjai Senthilkumar; Reinhard Laubenbacher; Pedro Mendes; Anna Dongari-Bagtzoglou
Journal:  Microorganisms       Date:  2021-02-17
  3 in total

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