Literature DB >> 27629590

Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience.

Robert A McDougal1, Thomas M Morse2, Ted Carnevale2, Luis Marenco2,3,4, Rixin Wang4,5, Michele Migliore2,6, Perry L Miller3,4,5, Gordon M Shepherd2, Michael L Hines2.   

Abstract

Neuron modeling may be said to have originated with the Hodgkin and Huxley action potential model in 1952 and Rall's models of integrative activity of dendrites in 1964. Over the ensuing decades, these approaches have led to a massive development of increasingly accurate and complex data-based models of neurons and neuronal circuits. ModelDB was founded in 1996 to support this new field and enhance the scientific credibility and utility of computational neuroscience models by providing a convenient venue for sharing them. It has grown to include over 1100 published models covering more than 130 research topics. It is actively curated and developed to help researchers discover and understand models of interest. ModelDB also provides mechanisms to assist running models both locally and remotely, and has a graphical tool that enables users to explore the anatomical and biophysical properties that are represented in a model. Each of its capabilities is undergoing continued refinement and improvement in response to user experience. Large research groups (Allen Brain Institute, EU Human Brain Project, etc.) are emerging that collect data across multiple scales and integrate that data into many complex models, presenting new challenges of scale. We end by predicting a future for neuroscience increasingly fueled by new technology and high performance computation, and increasingly in need of comprehensive user-friendly databases such as ModelDB to provide the means to integrate the data for deeper insights into brain function in health and disease.

Entities:  

Keywords:  Model analysis; Model discovery; Model sharing; Neuroinformatics; Reproducibility

Mesh:

Year:  2016        PMID: 27629590      PMCID: PMC5279891          DOI: 10.1007/s10827-016-0623-7

Source DB:  PubMed          Journal:  J Comput Neurosci        ISSN: 0929-5313            Impact factor:   1.621


  42 in total

1.  ModelDB: A Database to Support Computational Neuroscience.

Authors:  Michael L Hines; Thomas Morse; Michele Migliore; Nicholas T Carnevale; Gordon M Shepherd
Journal:  J Comput Neurosci       Date:  2004 Jul-Aug       Impact factor: 1.621

2.  The human brain project.

Authors:  Henry Markram
Journal:  Sci Am       Date:  2012-06       Impact factor: 2.142

3.  The CellML Model Repository.

Authors:  Catherine M Lloyd; James R Lawson; Peter J Hunter; Poul F Nielsen
Journal:  Bioinformatics       Date:  2008-07-25       Impact factor: 6.937

4.  ModelView for ModelDB: Online Presentation of Model Structure.

Authors:  Robert A McDougal; Thomas M Morse; Michael L Hines; Gordon M Shepherd
Journal:  Neuroinformatics       Date:  2015-10

5.  Cortical control of zona incerta.

Authors:  Péter Barthó; Andrea Slézia; Viktor Varga; Hajnalka Bokor; Didier Pinault; György Buzsáki; László Acsády
Journal:  J Neurosci       Date:  2007-02-14       Impact factor: 6.167

6.  Dynamic clamp: computer-generated conductances in real neurons.

Authors:  A A Sharp; M B O'Neil; L F Abbott; E Marder
Journal:  J Neurophysiol       Date:  1993-03       Impact factor: 2.714

7.  Optogenetics.

Authors:  Karl Deisseroth
Journal:  Nat Methods       Date:  2010-12-20       Impact factor: 28.547

Review 8.  Personalized medicine in psychiatry: problems and promises.

Authors:  Uzoezi Ozomaro; Claes Wahlestedt; Charles B Nemeroff
Journal:  BMC Med       Date:  2013-05-16       Impact factor: 8.775

9.  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

Authors:  Nicolas Le Novère; Benjamin Bornstein; Alexander Broicher; Mélanie Courtot; Marco Donizelli; Harish Dharuri; Lu Li; Herbert Sauro; Maria Schilstra; Bruce Shapiro; Jacky L Snoep; Michael Hucka
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  GeNN: a code generation framework for accelerated brain simulations.

Authors:  Esin Yavuz; James Turner; Thomas Nowotny
Journal:  Sci Rep       Date:  2016-01-07       Impact factor: 4.379

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  68 in total

1.  Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

Authors:  David B Stockton; Fidel Santamaria
Journal:  Neuroinformatics       Date:  2017-10

2.  A computational model of large conductance voltage and calcium activated potassium channels: implications for calcium dynamics and electrophysiology in detrusor smooth muscle cells.

Authors:  Suranjana Gupta; Rohit Manchanda
Journal:  J Comput Neurosci       Date:  2019-04-25       Impact factor: 1.621

3.  Outgrowing seizures in Childhood Absence Epilepsy: time delays and bistability.

Authors:  Yue Liu; John Milton; Sue Ann Campbell
Journal:  J Comput Neurosci       Date:  2019-02-09       Impact factor: 1.621

4.  Two Distinct Sets of Ca2+ and K+ Channels Are Activated at Different Membrane Potentials by the Climbing Fiber Synaptic Potential in Purkinje Neuron Dendrites.

Authors:  Karima Ait Ouares; Luiza Filipis; Alexandra Tzilivaki; Panayiota Poirazi; Marco Canepari
Journal:  J Neurosci       Date:  2019-01-10       Impact factor: 6.167

Review 5.  Tutorial: a computational framework for the design and optimization of peripheral neural interfaces.

Authors:  Simone Romeni; Giacomo Valle; Alberto Mazzoni; Silvestro Micera
Journal:  Nat Protoc       Date:  2020-09-28       Impact factor: 13.491

6.  T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells.

Authors:  Hermann Cuntz; Peter Jedlicka; Marcel Beining; Lucas Alberto Mongiat; Stephan Wolfgang Schwarzacher
Journal:  Elife       Date:  2017-11-22       Impact factor: 8.140

7.  Muscle Thickness and Curvature Influence Atrial Conduction Velocities.

Authors:  Simone Rossi; Stephen Gaeta; Boyce E Griffith; Craig S Henriquez
Journal:  Front Physiol       Date:  2018-10-29       Impact factor: 4.566

8.  Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Authors:  Natalie J Stanford; Martin Scharm; Paul D Dobson; Martin Golebiewski; Michael Hucka; Varun B Kothamachu; David Nickerson; Stuart Owen; Jürgen Pahle; Ulrike Wittig; Dagmar Waltemath; Carole Goble; Pedro Mendes; Jacky Snoep
Journal:  Methods Mol Biol       Date:  2019

9.  Paranoia as a deficit in non-social belief updating.

Authors:  Erin J Reed; Stefan Uddenberg; Praveen Suthaharan; Christoph D Mathys; Jane R Taylor; Stephanie Mary Groman; Philip R Corlett
Journal:  Elife       Date:  2020-05-26       Impact factor: 8.140

10.  Eupnea, tachypnea, and autoresuscitation in a closed-loop respiratory control model.

Authors:  Casey O Diekman; Peter J Thomas; Christopher G Wilson
Journal:  J Neurophysiol       Date:  2017-07-19       Impact factor: 2.714

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