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A toolbox to find the best mechanistic model to predict the behavior of environmental systems

André G. van Turnhout, Robbert Kleerebezem, Timo J. Heimovaara
2016 Environmental Modelling & Software  
We thank you for your time and hope our paper is now fit to contribute to Environmental Modelling & Software. Sincerely yours, André van Turnhout  ...  toolbox to find the best mechanistic model to predict the behavior of environmental systems.  ...  Introduction It is challenging to make reliable predictions of the long-term behavior of environmental systems such as Municipal Solid Waste (MSW) landfills.  ... 
doi:10.1016/j.envsoft.2016.05.002 fatcat:oxliu4a4cbdqflae34hiqtnzma

Advancing Computational Toxicology in a Regulatory Setting: A Selected Review of the Accomplishments of Gilman D. Veith (1944–2013)

Steven P. Bradbury, Christine L. Russom, Patricia K. Schmieder, Terry W. Schultz, Robert Diderich, Charles M. Auer
2015 Applied In Vitro Toxicology  
was achieved by a focus on establishing a transparent, mechanistic understanding of the chemistry and biology underlying alternative experimental and mathematical models.  ...  Veith was a pioneer of the application of alternative methods, especially QSAR to industrial chemicals, which traditionally lacked the experimental data already available for pesticides and pharmaceuticals  ...  Apologies to the many other contributors to his 40 years of research in computational toxicology whom we did not capture in this review. The authors do wish to acknowledge the passing of James M.  ... 
doi:10.1089/aivt.2014.0002 fatcat:mj62aui6yzetdh3kg2rxvylb6e

LASSIM - a network inference toolbox for genome-wide mechanistic modeling [article]

Rasmus Magnusson, Guido Pio Mariotti, Mattias Kopsen, William Lovfors, Danuta R Gawel, Rebecka Jornsten, Jorg Linde, Torbjorn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang (+4 others)
2017 bioRxiv   pre-print
In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models with truly systems-level data.  ...  LASSIM models are built in two steps, where each step can integrate multiple data-types, and the method is implemented as a general-purpose toolbox using the PyGMo Python package to make the most of multicore  ...  This usage includes mathematical models for predictions of the cellular response to different stimuli, such as a change in environmental conditions or the presence of pathogens.  ... 
doi:10.1101/115477 fatcat:rr2yypesureofkygzhmcgzvdve

LASSIM—A network inference toolbox for genome-wide mechanistic modeling

Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R. Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E. M. Nordling, Elin Nyman, Sylvie Schulze, Colm E. Nestor, Huan Zhang (+5 others)
2017 PLoS Computational Biology  
In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines PLOS Computational Biology | https://doi.  ...  The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https:// gitlab.com  ...  This usage includes mathematical models for predictions of the cellular response to different stimuli, such as a change in environmental conditions or the presence of pathogens.  ... 
doi:10.1371/journal.pcbi.1005608 pmid:28640810 pmcid:PMC5501685 fatcat:giqo3ajbfjds5npgnecphvnfna

Design Methodologies and the Limits of the Engineering-Dominated Conception of Synthetic Biology

Tero Ijäs
2018 Acta Biotheoretica  
These two approaches take philosophically different stances to the design of biological systems.  ...  Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences.  ...  Not limited to a certain level of hierarchy. Allows system improvement in the absence of mechanistic detail. Environmental tuning of non-functional systems.  ... 
doi:10.1007/s10441-018-9338-7 pmid:30121875 fatcat:tcnj44gp65dhva2osyzxugic24

TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatry

Stefan Frässle, Eduardo A. Aponte, Saskia Bollmann, Kay H. Brodersen, Cao T. Do, Olivia K. Harrison, Samuel J. Harrison, Jakob Heinzle, Sandra Iglesias, Lars Kasper, Ekaterina I. Lomakina, Christoph Mathys (+9 others)
2021 Frontiers in Psychiatry  
Psychiatry faces fundamental challenges with regard to mechanistically guided differential diagnosis, as well as prediction of clinical trajectories and treatment response of individual patients.  ...  Here, we review the different tools within TAPAS and illustrate how these may help provide a deeper understanding of neural and cognitive mechanisms of disease, with the ultimate goal of establishing automatized  ...  neuromodulatory systems with generative modeling of neuroimaging or behavioral data.  ... 
doi:10.3389/fpsyt.2021.680811 pmid:34149484 pmcid:PMC8206497 fatcat:ichfqltpdbdfflh2ozfk4lduda

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

Osvaldo D. Kim, Miguel Rocha, Paulo Maia
2018 Frontiers in Microbiology  
Mathematical modeling is a key process to describe the behavior of biological networks.  ...  The aim is to establish a trade-off between the size of the model and the level of accuracy of the solutions.  ...  AUTHOR CONTRIBUTIONS All authors participated in the preparation of this work. OK had a major role in writing and editing the manuscript.  ... 
doi:10.3389/fmicb.2018.01690 pmid:30108559 pmcid:PMC6079213 fatcat:dgs2tzysijevdbza7sga3fzi2m

Mechanistic Modeling of Biochemical Systems Without A Priori Parameter Values Using the Design Space Toolbox v.3.0 [article]

Miguel A Valderrama-Gomez, Jason G Lomnitz, Rick A Fasani, Michael A Savageau
2020 bioRxiv   pre-print
Mechanistic models of biochemical systems provide a rigorous kinetics-based description of various biological phenomena.  ...  Here, we introduce the Design Space Toolbox v.3.0 (DST3), a software implementation of the Design Space formalism that enables mechanistic modeling of complex biological processes without requiring previous  ...  Introduction Mechanistic models have the advantage of being biologically realistic and the potential to rigorously define and predict biochemical phenotypes.  ... 
doi:10.1101/2020.01.30.927657 fatcat:ueiyv6wbtndvpayvpafjvncurq

Modelling Microcystis aeruginosa bloom dynamics in the Nakdong River by means of evolutionary computation and statistical approach

Kwang-Seuk Jeong, Dong-Kyun Kim, Peter Whigham, Gea-Jae Joo
2003 Ecological Modelling  
Blooms of M. aeruginosa occurred in summers when there were droughts. Using data from 1995 to 1998, GP and MLR were used to construct equation models for predicting the occurrence of M. aeruginosa .  ...  The lower Nakdong River exhibits reservoir-like ecological dynamics rather than riverine, and for this reason a previous river mechanistic model failed to describe uncertainty and complexity.  ...  This study was financially supported by the Institute of Environmental Technology and Industry (IETI) (project no. 01-10-99-01-A-1).  ... 
doi:10.1016/s0304-3800(02)00280-6 fatcat:rnwtxu4vtzbzbcub2msk54bsni

Energy Efficiency Analysis of the Refining Unit in Thermo-Mechanical Pulp Mill

Behnam Talebjedi, Timo Laukkanen, Henrik Holmberg, Esa Vakkilainen, Sanna Syri
2021 Energies  
A refining model is developed to analyses the refining process's energy efficiency based on the refining variables.  ...  A simulation model is obtained for longer-term refining energy analysis by further developing the MATLAB Thermo-Mechanical Pulping Simulink toolbox.  ...  Acknowledgments: We acknowledge having the opportunity to present our research at the 15th SDEWES Conference 2020 Cologne, Germany [32] .  ... 
doi:10.3390/en14061664 fatcat:lo6ekvf4djdy5fge2xe6kbksv4

Delineating genetic and familial risk for psychopathology in the ABCD study [article]

Clare E Palmer, Robert John Loughnan, Carolina Makowski, Wesley Thompson, Deanna Barch, Terry Jernigan, Anders M Dale, Chun C Fan
2020 medRxiv   pre-print
By including all genetic risk predictors in the same model, we were able to delineate unique behavioral associations across these measures.  ...  These findings provide important insight into the potential predictive utility of PRS and family history in early adolescence and suggest that they may be signaling differential, additive information that  ...  This is a multisite, longitudinal study designed to recruit more than 10,000 children age 9-10 and follow them over 10 years into early adulthood.  ... 
doi:10.1101/2020.09.08.20186908 fatcat:wj5asjhg4ncgldfaqfyf6zh4oq

TAPAS: an open-source software package for Translational Neuromodeling and Computational Psychiatry [article]

Stefan Frässle, Eduardo A Aponte, Saskia A Bollmann, Kay H Brodersen, Cao Tri Do, Olivia K Harrison, Samuel J Harrison, Jakob Heinzle, Sandra Iglesias, Lars Kasper, Ekaterina I Lomakina, Christoph Mathys (+9 others)
2021 bioRxiv   pre-print
Psychiatry faces fundamental challenges with regard to mechanistically guided differential diagnosis, as well as prediction of clinical trajectories and treatment response of individual patients.  ...  Here, we review the different tools within TAPAS and illustrate how these may help provide a deeper understanding of neural and cognitive mechanisms of disease, with the ultimate goal of establishing automatized  ...  neuromodulatory systems with generative modeling of neuroimaging or behavioral data.  ... 
doi:10.1101/2021.03.12.435091 fatcat:b6t53rzjdreqbgtid4kexcuw6q

Data-based mechanistic modeling, forecasting, and control

2001 IEEE Control Systems  
The authors would also like to thank all the past and present members of the Environmental Systems and Control Group in CRES at Lancaster University who have contributed to the research described in this  ...  Acknowledgments The authors are grateful to the United Kingdom Biotechnology and Biological Sciences Research Council for its support, through Research Grants 89/E06813 and 89/MMI09731, together with the  ...  or, in the case of environmental systems, even impossible to undertake.  ... 
doi:10.1109/37.954517 fatcat:cckvehpmkbbiph6dhuob7bulle

Mechanistic Modeling of Biochemical Systems Without a Priori Parameter Values Using the Design Space Toolbox v.3.0

Miguel A. Valderrama-Gomez, Jason G. Lomnitz, Rick A. Fasani, Michael A. Savageau
2020 Social Science Research Network  
A phenotype is defined in the context of a mechanistic mathematical model of a given biological system.  ...  Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0 iScience Article Miguel Á .  ...  In general, we are interested in the behavior of the system when knife-edge conditions are not satisfied, i.e., .  ... 
doi:10.2139/ssrn.3542578 fatcat:4nctzrjazbcapfnb5ljwpti5xm

Predictive power of cell-to-cell variability

Bochong Li, Lingchong You
2013 Quantitative Biology  
mechanisms, and how we can extract such information to gain a deeper understanding of biological systems.  ...  To this end, a major challenge is determining what aspects of variability bear significant biological meaning.  ...  Instead of finding the best point estimation of each parameter, a distribution of parameter values is obtained [60] .  ... 
doi:10.1007/s40484-013-0013-3 fatcat:ytzdboiwqzga5ki4ek7vdpdpa4
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