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Common Data Model for Neuroscience Data and Data Model Exchange

D. Gardner, K. H. Knuth, M. Abato, S. M. Erde, T. White, R. DeBellis, E. P. Gardner
2001 JAMIA Journal of the American Medical Informatics Association  
To mediate data exchange between disparate systems, the authors propose a set of XML-derived schema for describing not only data sets but data models.  ...  Each first-class component of the Common Data Model derives from one of five superclasses-site, data, reference, method, and model elements.  ...  to a range of domains and projects.  ... 
doi:10.1136/jamia.2001.0080017 pmid:11141510 pmcid:PMC134589 fatcat:zpbt3f46yfh6hdugpszjhhmjzi

A biopsychosocial formulation of pain communication

Thomas Hadjistavropoulos, Kenneth D. Craig, Steve Duck, Annmarie Cano, Liesbet Goubert, Philip L. Jackson, Jeffrey S. Mogil, Pierre Rainville, Michael J. L. Sullivan, Amanda C. de C. Williams, Tine Vervoort, Theresa Dever Fitzgerald
2011 Psychological bulletin  
neuroscience.  ...  We present a detailed framework for understanding the numerous and complicated interactions among psychological and social determinants of pain through examination of the process of pain communication.  ...  Conclusions and Directions for Future Research This article represents the most comprehensive description of a communications model of pain and the first formulation of the model that comprehensively incorporates  ... 
doi:10.1037/a0023876 pmid:21639605 fatcat:altv3chlpzcorazrvbnjegi7sy

Answering Schrödinger's question: A free-energy formulation

Maxwell James Désormeau Ramstead, Paul Benjamin Badcock, Karl John Friston
2018 Physics of Life Reviews  
The free-energy principle (FEP) is a formal model of neuronal processes that is widely recognised in neuroscience as a unifying theory of the brain and biobehaviour.  ...  More recently, however, it has been extended beyond the brain to explain the dynamics of living systems, and their unique capacity to avoid decay.  ...  We thank Jelle Bruineberg, Nabil Bouizegarene, Axel Constant, Michael Kirchhoff, Laurence Kirmayer, Noah Moss-Brender, Jonathan St-Onge, Samuel Veissière, Ishan Walpola, and Julian Xue, for helpful discussions  ... 
doi:10.1016/j.plrev.2017.09.001 pmid:29029962 pmcid:PMC5857288 fatcat:inhsfdidmvhhnigvb5ztumqiky

The hierarchically mechanistic mind: A free-energy formulation of the human psyche

Paul B. Badcock, Karl J. Friston, Maxwell J.D. Ramstead
2019 Physics of Life Reviews  
After leveraging the FEP to formally define the HMM across different spatiotemporal scales, we conclude by exploring its implications for theorising and research in the sciences of the mind and behaviour  ...  This theory synthesises the free-energy principle (FEP) in neuroscience with an evolutionary systems theory of psychology that explains our brains, minds, and behaviour by appealing to Tinbergen's four  ...  We are also indebted to Nicholas Allen, Luke Badcock, Axel Constant, Casper Hesp, Jakob Hohwy, Annemie Ploeger, and Samuel Veissière for their valuable discussions and comments on the earlier drafts.  ... 
doi:10.1016/j.plrev.2018.10.002 pmid:30704846 pmcid:PMC6941235 fatcat:hugpu5gi5nhpziv2hrljzft3yy

001 A Novel Model for the Assessment of Formulated Enzymatic Debriding Agents

Lei Shi, Justin Keen, Braham Shroot
2004 Wound Repair and Regeneration  
Department of Cell Biology and Neuroscience.  ...  HB107 has been evaluated for efficacy in a mouse incision model and for safety and efficacy in a pig burn wound model.  ...  The presence of activated b-catenin and c-myc in the epidermis of chronic wounds may serve as molecular markers of impaired healing and future targets for therapeutic intervention.  ... 
doi:10.1111/j.1067-1927.2004.0abstractb.x fatcat:beqi4durhveqpclqbtn44vqxlm

Action and behavior: a free-energy formulation

Karl J. Friston, Jean Daunizeau, James Kilner, Stefan J. Kiebel
2010 Biological cybernetics  
It is fairly easy to show that making inferences about the causes of sensory data can be cast as the minimization of a free-energy bound on the likelihood of sensory inputs, given an internal model of  ...  brain, starting from the fact that we exist: This fact places constraints on our interactions with the world, which have been studied for years in evolutionary biology and systems theory.  ...  Acknowledgements We would like to thank Neil Burgess and Florentin Wörgötter for very helpful reviews of a previous version of this work.  ... 
doi:10.1007/s00422-010-0364-z pmid:20148260 fatcat:mdaixqnztvgmbp57b7nx44hc3i

Reassembly and Interfacing Neural Models Registered on Biological Model Databases

Mihoko Otake, Toshihisa Takagi
2005 Genome Informatics Series  
GOURMET is not only a place for various simulation programs to meet and exchange the information they have, but also an editor of the input data, a viewer of the output data, a tool to make graphs and  ...  Model databases deal with such models and diverse data for building the models.  ... 
doi:10.11234/gi1990.16.2_76 fatcat:tnkl6kntjzg2tj3xzev5x6wrku

Ricochon: La tablette de Poitiers et une formule byzantine, tiree des Anecdotes graeco-byzantines de Yassiliev

A. Thumb
1903 Indogermanische Forschungen  
The value of neuroeconomics studies for social policy lies in the quality, replicability, and relevance of the research produced.  ...  This article identifies the ways in which this will occur, pitfalls of this approach, and areas where progress has already been made.  ...  These can usefully be incorporated into economic models through the common pathway of the brain.  ... 
doi:10.1515/if-1903-0110 fatcat:gs5kayz6r5dglpdbbpiviovpjq

Refining the Common Model of Cognition Through Large Neuroscience Data

Zoe Steine-Hanson, Natalie Koh, Andrea Stocco
2018 Procedia Computer Science  
into one common model.  ...  The Common Model of Cognition (CMC) is an effort to highlight the commonalities between multiple studies of human-like intelligent minds and cognition, and bring these architectures and functions together  ...  This allows more pathways for these two important modules to exchange and modify information.  ... 
doi:10.1016/j.procs.2018.11.026 fatcat:fafkcjo3ejd6zez45mxgrhyeia

OFN-Based Brain Function Modeling [chapter]

Piotr Prokopowicz, Dariusz Mikołajewski
2017 Studies in Fuzziness and Soft Computing  
A modeling approach may significantly help to explore the problem of weak understanding of the physiological and pathological central nervous system function in the most noninvasive and comprehensive way  ...  The aim of this chapter is to assess and discuss the extent to which possible opportunities concerning computational brain models based on fuzzy logic techniques may be exploited.  ...  exchange of models thanks to formats open to interconnection), but it may be hard to achieve.  ... 
doi:10.1007/978-3-319-59614-3_18 fatcat:ticbet54erbo3j4o3axavg37fy

Negotiating treatment preferences: Physicians' formulations of patients' stance

Anne Marie Dalby Landmark, Jan Svennevig, Pål Gulbrandsen
2016 Social Science and Medicine  
First, patient involvement can be seen as a general requirement and a goal that is common to all contemporary decision making models.  ...  Methodological implications and directions for future research Until recently, there has been a limited degree of exchange and interdisciplinary influence and contact between CA (and other observation  ... 
doi:10.1016/j.socscimed.2015.11.035 pmid:26699275 fatcat:ottnorgpfbaxvbvfcabshodseq

Workshop report: 1st INCF Workshop on Large-scale Modeling of the Nervous System

Mikael Djurfeldt, Mikael Djurfeldt, Anders Lansner
2007 Nature Precedings  
A model based on data from a lower level of organization, or formulated in terms of elements from multiple lower levels of organization, is not necessarily more realistic than data formulated and rooted  ...  data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. • The Invertebrate Brain Platform (IVB PF), which integrates experimental data, mathematical models,  ...  Models can be specified in NeuroML, making it possible to easily exchange models between simulators that use this standard.  ... 
doi:10.1038/npre.2007.262 fatcat:fref2h5qebelphhatefjl322py

Workshop report: 1st INCF Workshop on Large-scale Modeling of the Nervous System

Mikael Djurfeldt, Mikael Djurfeldt, Anders Lansner
2007 Nature Precedings  
A model based on data from a lower level of organization, or formulated in terms of elements from multiple lower levels of organization, is not necessarily more realistic than data formulated and rooted  ...  data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. • The Invertebrate Brain Platform (IVB PF), which integrates experimental data, mathematical models,  ...  Models can be specified in NeuroML, making it possible to easily exchange models between simulators that use this standard.  ... 
doi:10.1038/npre.2007.262.1 fatcat:z6zrci3wxfgtxnfxg32hmdwz3m

DUNEuro – A software toolbox for forward modeling in bioelectromagnetism [article]

Sophie Schrader, Andreas Westhoff, Maria Carla Piastra, Tuuli Miinalainen, Sampsa Pursiainen, Johannes Vorwerk, Heinrich Brinck, Carsten H. Wolters, Christian Engwer
2021 arXiv   pre-print
This paper presents DUNEuro, a free and open source C++ software toolbox for forward modeling in bioelectromagnetism.  ...  The user can choose between a variety of different source models that are implemented. The software's aim is to provide interfaces that are extendible and easy-to-use.  ...  SP and TM were supported by the Academy of Finland key project (305055) and TM also by the tenure track funding by Tampere University of Technology.  ... 
arXiv:1901.02874v4 fatcat:m7k23246urfarf3fu6m3xsptde

Towards Reproducible Descriptions of Neuronal Network Models

Eilen Nordlie, Marc-Oliver Gewaltig, Hans Ekkehard Plesser, Karl J. Friston
2009 PLoS Computational Biology  
But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing  ...  We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and softwaresharing, may lead to a deeper and more fruitful exchange  ...  Acknowledgments We would like to thank Markus Diesmann and Sven Schrader as well as three anonymous reviewers for stimulating feedback on earlier versions of the manuscript and Kittel Austvoll for help  ... 
doi:10.1371/journal.pcbi.1000456 pmid:19662159 pmcid:PMC2713426 fatcat:i3273wrl5vd3zhqal5ocvwub4i
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