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'One Size Does Not Fit All': A Roadmap of Purpose-Driven Mixed-Method Pathways for Sensitivity Analysis of Agent-Based Models

Arika Ligmann-Zielinska, Peer-Olaf Siebers, Nicholas Magliocca, Dawn C. Parker, Volker Grimm, Jing Du, Martin Cenek, Viktoriia Radchuk, Nazia N. Arbab, Sheng Li, Uta Berger, Rajiv Paudel (+4 others)
2020 Journal of Artificial Societies and Social Simulation  
We argue that no single SA method fits all ABMs and that di erent methods of SA should be used based on the overarching purpose of the model.  ...  Designing, implementing, and applying agent-based models (ABMs) requires a structured approach, part of which is a comprehensive analysis of the output to input variability in the form of uncertainty and  ...  Sensitivity Analysis Methods Used in ABM . In preparation for setting up a roadmap for purpose-driven mixed-method SA, we first discuss the SA methods identified in the ABM literature.  ... 
doi:10.18564/jasss.4201 fatcat:v3linogbsrar5kyuiz3gupvuf4

The 2019 Mathematical Oncology Roadmap

Russell C. Rockne, Andrea Hawkins-Daarud, Kristin R. Swanson, James P Sluka, James A. Glazier, Paul Macklin, David Hormuth, Angela M Jarrett, Ernesto Augutso Bueno da Fonseca Lima, J Oden, George Biros, Thomas E Yankeelov (+23 others)
2019 Physical Biology  
Mathematical Oncology-defined here simply as the use of mathematics in cancer research-complements and overlaps with a number of other fields that rely on mathematics as a core methodology.  ...  The dominant theme of this Roadmap is the personalization of medicine through mathematics, modelling, and simulation.  ...  Modeling radiation therapy Acknowledgements This work was supported in part by a pilot award from the NIH/NCI U54CA143970-05 (Physical Science Oncology Network (PSON)) "Cancer as a complex adaptive system  ... 
doi:10.1088/1478-3975/ab1a09 pmid:30991381 pmcid:PMC6655440 fatcat:sb4ms7zygngd3pp5xuxundp3gy

Systematic quantitative characterization of cellular responses induced by multiple signals

Ibrahim Al-Shyoukh, Fuqu Yu, Jiaying Feng, Karen Yan, Steven Dubinett, Chih-Ming Ho, Jeff S Shamma, Ren Sun
2011 BMC Systems Biology  
Results: We established and validated a data-driven mathematical approach to systematically characterize signalresponse relationships.  ...  The successful validation of identified combinations demonstrates the power of this approach. Moreover, the approach enables examining the efficacy of all lower order mixtures of the tested signals.  ...  Christopher Denny, Desmond Smith, Helen Brown, Elliot Landaw, and Henry Huang for critical reading of the manuscript; all Sun lab members for helpful discussions.  ... 
doi:10.1186/1752-0509-5-88 pmid:21624115 pmcid:PMC3138445 fatcat:du3szutk3zgqvp62myh643nviq

Big oil's biomass play

Cormac Sheridan
2007 Nature Biotechnology  
Cameron is a fellow of the American Institute of Medical and Biological Engineering and is on the editorial boards of Metabolic Engineering and Biomacromolecules. He serves on the  ...  In 1996 he was a guest professor in the Institute for Biotechnology at the Swiss Federal Institute of Technology in Zurich.  ...  Again, balancing enzymatic activities, removing limiting steps, and pruning unwanted reactions-all supported by comprehensive analysis and modeling-will be deployed for this purpose.  ... 
doi:10.1038/nbt1107-1201 pmid:17989660 fatcat:trpy2zkqorcznhfsv4b4uttupe

Energy systems modeling for twenty-first century energy challenges

Stefan Pfenninger, Adam Hawkes, James Keirstead
2014 Renewable & Sustainable Energy Reviews  
Energy systems models are important methods used to generate a range of insight and analysis on the supply and demand of energy.  ...  , power systems and electricity market models, and qualitative and mixed-methods scenarios.  ...  Acknowledgements Funding for this work was provided by the Grantham Institute for Climate Change and the European Institute of Innovation and Technology via its Climate-KIC program.  ... 
doi:10.1016/j.rser.2014.02.003 fatcat:64wnfq2eivb5vhj3sm2zk5u6iq

Applying metabolomics to cardiometabolic intervention studies and trials: past experiences and a roadmap for the future: Table 1

Naomi J Rankin, David Preiss, Paul Welsh, Naveed Sattar
2016 International Journal of Epidemiology  
of a new agent were unexpected, and thus help future drug development.  ...  On the basis of this review, and based on our research experience using clinically established biomarkers, we propose steps to more speedily advance this area of research towards potential clinical impact  ...  and statistical normalization methods, 9, 86 although this approach is only satisfactory for research (not clinical) purposes.  ... 
doi:10.1093/ije/dyw271 pmid:27789671 pmcid:PMC5100629 fatcat:aavj5smrt5gafprtccbr6zmgwm

Recent developments in parameter estimation and structure identification of biochemical and genomic systems

I-Chun Chou, Eberhard O. Voit
2009 Mathematical Biosciences  
Other methods targeted issues of data preprocessing, detection and amelioration of model redundancy, and model-free or model-based structure identification.  ...  The proposed methods mainly focused on various optimization algorithms, but also on support techniques, including methods for circumventing the time consuming numerical integration of systems of differential  ...  This work was supported in part by a National Heart, Lung and Blood Institute Proteomics Initiative  ... 
doi:10.1016/j.mbs.2009.03.002 pmid:19327372 pmcid:PMC2693292 fatcat:rqnk3f34w5g2xl4qcwicbnwtnm

Understanding Nanoparticle Toxicity to Direct a Safe-by-Design Approach in Cancer Nanomedicine

Jossana A. Damasco, Saisree Ravi, Joy D. Perez, Daniel E. Hagaman, Marites P. Melancon
2020 Nanomaterials  
Nanomedicine is a rapidly growing field that uses nanomaterials for the diagnosis, treatment and prevention of various diseases, including cancer.  ...  A special emphasis is put on the rational design to develop non-toxic/safe inorganic nanoparticle constructs to increase their viability as translatable nanomedicine for cancer therapies.  ...  Figure 5 . 5 A summarized general roadmap for implementing a model in the field of nanotoxicology. Figure 6 . 6 Data driven safe-by-design approach to tailor nanoparticle review for nanomedicine.  ... 
doi:10.3390/nano10112186 pmid:33147800 fatcat:ifnnqnpecne75d27huwko5gnb4

Toxicity Testing in the 21st Century: A Vision and a Strategy

Daniel Krewski, Daniel Acosta, Melvin Andersen, Henry Anderson, John C. Bailar, Kim Boekelheide, Robert Brent, Gail Charnley, Vivian G. Cheung, Sidney Green, Karl T. Kelsey, Nancy I. Kerkvliet (+11 others)
2010 Journal of Toxicology and Environmental Health. Part B, Critical Reviews  
Extrapolation of in vitro results to in vivo human blood and tissue concentrations would be based on pharmacokinetic models for the given exposure condition.  ...  Implementation of these strategies would result in a new toxicity testing paradigm firmly based on human biology.  ...  Phase I would focus on elucidating toxicity pathways; developing a data-storage, -access, and -management system; developing standard protocols for research methods and reporting; and planning a strategy  ... 
doi:10.1080/10937404.2010.483176 pmid:20574894 pmcid:PMC4410863 fatcat:v2wmp6tq4jbxxoztw3re2mwzfy

The International Exascale Software Project roadmap

Jack Dongarra, Pete Beckman, Terry Moore, Patrick Aerts, Giovanni Aloisio, Jean-Claude Andre, David Barkai, Jean-Yves Berthou, Taisuke Boku, Bertrand Braunschweig, Franck Cappello, Barbara Chapman (+53 others)
2011 The international journal of high performance computing applications  
Develop a coordinated software roadmap: The results of the group's analysis have been incorporated into a draft of a coordinated roadmap intended to help guide the open source scientific software infrastructure  ...  It seems clear that this completely uncoordinated development model will not provide the software needed to support the unprecedented parallelism required for peta/exascale computation on millions of cores  ...  Clearly all science areas and engineering areas that contain potential CDVs need something in all the software areas, but for the purposes of this exercise we tried to sort out areas of emphasis for each  ... 
doi:10.1177/1094342010391989 fatcat:twdszcjfxraijpsdcdacvpp6vm

Risk Assessment Model: Roadmap to Develop Kolkata into a Smart City

Sweta Saraff, Raman Kumar, Ayooshi Mitra, Sayantani Ghosh, Shrayana Ghosh, Sulagna Das
2020 EAI Endorsed Transactions on Smart Cities  
The current paper aims to focus on risk assessment based on the aggregation of various factors relevant to the prediction of disease transmission (RAAPDT).  ...  By customizing the risk assessment model for Kolkata, we will monitor the factors responsible for the growth and spread of diseases.  ...  Risk Assessment Model: Roadmap to Develop Kolkata into a Smart City Risk assessment based on aggregation of various factors relevant for prediction of disease transmission (RAAPDT) Several methods are  ... 
doi:10.4108/eai.5-10-2020.166545 fatcat:jrbpgcs6dvhorlj6mjzshne2pq

Developing a common approach for classifying building stock energy models

J. Langevin, J.L. Reyna, S. Ebrahimigharehbaghi, N. Sandberg, P. Fennell, C. Nägeli, J. Laverge, M. Delghust, É. Mata, M. Van Hove, J. Webster, F. Federico (+2 others)
2020 Renewable & Sustainable Energy Reviews  
Given these advancements, a new scheme for classifying building stock energy models is needed to facilitate communication of modeling approaches and the handling of important model dimensions.  ...  on Building Energy Epidemiology.  ...  Acknowledgments The authors gratefully acknowledge the strong support of Annex 70 from the International Energy Agency Energy in Buildings and Commu-  ... 
doi:10.1016/j.rser.2020.110276 fatcat:f6z3fu4lbjdvtb3i3s7lmp2mji

Mixtures research at NIEHS: An evolving program

Cynthia V. Rider, Danielle J. Carlin, Micheal J. DeVito, Claudia L. Thompson, Nigel J. Walker
2013 Toxicology  
A path forward for NIEHS mixtures research will be based on feedback from a Request for Information (RFI) designed to gather up-to-date views on the knowledge gaps and roadblocks to evaluating mixtures  ...  The National Institute of Environmental Health Sciences (NIEHS) has a rich history in evaluating the toxicity of mixtures.  ...  The content of this publication does not necessarily reflect the views or the policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations  ... 
doi:10.1016/j.tox.2012.10.017 pmid:23146757 pmcid:PMC4232209 fatcat:f73ol45z2jaajb3ez3zxv2b33e

Report on stocktaking results and initial impact assessment framework

Elina Griniece Silvia Vignetti
2019 Zenodo  
These ideas fed into the consultation phase (Work Package 4) to help structuring further work on a modular and comprehensive IA framework for the socio-economic impact assessment of research infrastructures  ...  This deliverable reports the results of the stocktaking exercise carried out in the framework of Work Package 3 - Impact assessment of RI: state of play and needs identification.  ...  For this reason, an over rigid and a one-size-fits-all approach is not advisable.  ... 
doi:10.5281/zenodo.3946371 fatcat:c3iz2rqgxffynpuz4d34c5on64

Review: Toxicometabolomics

Mounir Bouhifd, Thomas Hartung, Helena T. Hogberg, Andre Kleensang, Liang Zhao
2013 Journal of Applied Toxicology  
This might enable the deduction of underlying pathways of toxicity, which, in their entirety, form the Human Toxome, a key concept for implementing the vision of Toxicity Testing for the 21st century.  ...  This review summarizes the current state of metabolomics technologies and principles, their uses in toxicology and gives a thorough overview on metabolomics bioinformatics, pathway identification and quality  ...  Acknowledgments NIH transformative research grant 'Mapping the Human Toxome by Systems Toxicology' (RO1ES020750) and FDA grant 'DNTox-21c Identification of pathways of developmental neurotoxicity for high  ... 
doi:10.1002/jat.2874 pmid:23722930 pmcid:PMC3808515 fatcat:tczsmozyr5bdrh2i47xv4q745q
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