Literature DB >> 8930855

ModelDB: an environment for running and storing computational models and their results applied to neuroscience.

B E Peterson1, M D Healy, P M Nadkarni, P L Miller, G M Shepherd.   

Abstract

Research groups within the Human Brain Project are developing technologies to help organize and make accessible the vast quantities of information being accumulated in the neurosciences. The goal of this work is to provide systems that enable this complex information from many diverse sources to be synthesized into a coherent theory of nervous system function. Our initial approach to this problem has been to create several small databases. While addressing the issues of each individual database, we are also considering how each might be incorporated into an integrated cluster of databases. In this paper, we describe a pilot project in which we construct a database of computational models of neuronal function. This database allows models to be created and run and their results reviewed through a World Wide Web interface. Because models encapsulate knowledge in a formal manner about how neuronal systems function, we also discuss how this database forms a natural center for our initial attempts at creating a cluster of related databases. General issues of database development in the context of the Web are also discussed.

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Year:  1996        PMID: 8930855      PMCID: PMC116323          DOI: 10.1136/jamia.1996.97084512

Source DB:  PubMed          Journal:  J Am Med Inform Assoc        ISSN: 1067-5027            Impact factor:   4.497


  13 in total

1.  Neuron simulations with SABER.

Authors:  N T Carnevale; T B Woolf; G M Shepherd
Journal:  J Neurosci Methods       Date:  1990-08       Impact factor: 2.390

Review 2.  The World Wide Web: a review of an emerging internet-based technology for the distribution of biomedical information.

Authors:  H J Lowe; E C Lomax; S E Polonkey
Journal:  J Am Med Inform Assoc       Date:  1996 Jan-Feb       Impact factor: 4.497

3.  A computer model of the cerebellar cortex of the frog.

Authors:  A Pellionisz; R Llinás; D H Perkel
Journal:  Neuroscience       Date:  1977       Impact factor: 3.590

4.  A program for simulation of nerve equations with branching geometries.

Authors:  M Hines
Journal:  Int J Biomed Comput       Date:  1989-03

5.  Theoretical reconstruction of field potentials and dendrodendritic synaptic interactions in olfactory bulb.

Authors:  W Rall; G M Shepherd
Journal:  J Neurophysiol       Date:  1968-11       Impact factor: 2.714

Review 6.  Visual feature integration and the temporal correlation hypothesis.

Authors:  W Singer; C M Gray
Journal:  Annu Rev Neurosci       Date:  1995       Impact factor: 12.449

7.  Motorneurons of different geometry and the size principle.

Authors:  R D Traub
Journal:  Biol Cybern       Date:  1977-02-07       Impact factor: 2.086

8.  Computer simulation of a dendrodendritic synaptic circuit for self- and lateral-inhibition in the olfactory bulb.

Authors:  G M Shepherd; R K Brayton
Journal:  Brain Res       Date:  1979-10-19       Impact factor: 3.252

9.  Distinguishing theoretical synaptic potentials computed for different soma-dendritic distributions of synaptic input.

Authors:  W Rall
Journal:  J Neurophysiol       Date:  1967-09       Impact factor: 2.714

10.  Logic operations are properties of computer-simulated interactions between excitable dendritic spines.

Authors:  G M Shepherd; R K Brayton
Journal:  Neuroscience       Date:  1987-04       Impact factor: 3.590

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  16 in total

1.  Neuronal database integration: the Senselab EAV data model.

Authors:  L Marenco; P Nadkarni; E Skoufos; G Shepherd; P Miller
Journal:  Proc AMIA Symp       Date:  1999

2.  Organization of heterogeneous scientific data using the EAV/CR representation.

Authors:  P M Nadkarni; L Marenco; R Chen; E Skoufos; G Shepherd; P Miller
Journal:  J Am Med Inform Assoc       Date:  1999 Nov-Dec       Impact factor: 4.497

3.  ModelDB: making models publicly accessible to support computational neuroscience.

Authors:  Michele Migliore; Thomas M Morse; Andrew P Davison; Luis Marenco; Gordon M Shepherd; Michael L Hines
Journal:  Neuroinformatics       Date:  2003

4.  SenseLab: new developments in disseminating neuroscience information.

Authors:  Chiquito J Crasto; Luis N Marenco; Nian Liu; Thomas M Morse; Kei-Hoi Cheung; Peter C Lai; Gautam Bahl; Peter Masiar; Hugo Y K Lam; Ernest Lim; Huajin Chen; Prakash Nadkarni; Michele Migliore; Perry L Miller; Gordon M Shepherd
Journal:  Brief Bioinform       Date:  2007-05-17       Impact factor: 11.622

5.  B-SPID: an object-relational database architecture to store, retrieve, and manipulate neuroimaging data.

Authors:  B Diallo; F Dolidon; J M Travere; B Mazoyer
Journal:  Hum Brain Mapp       Date:  1999       Impact factor: 5.038

6.  Optimizing computer models of corticospinal neurons to replicate in vitro dynamics.

Authors:  Samuel A Neymotin; Benjamin A Suter; Salvador Dura-Bernal; Gordon M G Shepherd; Michele Migliore; William W Lytton
Journal:  J Neurophysiol       Date:  2016-10-19       Impact factor: 2.714

Review 7.  Is realistic neuronal modeling realistic?

Authors:  Mara Almog; Alon Korngreen
Journal:  J Neurophysiol       Date:  2016-08-17       Impact factor: 2.714

8.  Reinforcement learning of two-joint virtual arm reaching in a computer model of sensorimotor cortex.

Authors:  Samuel A Neymotin; George L Chadderdon; Cliff C Kerr; Joseph T Francis; William W Lytton
Journal:  Neural Comput       Date:  2013-09-18       Impact factor: 2.026

Review 9.  Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience.

Authors:  Robert A McDougal; Thomas M Morse; Ted Carnevale; Luis Marenco; Rixin Wang; Michele Migliore; Perry L Miller; Gordon M Shepherd; Michael L Hines
Journal:  J Comput Neurosci       Date:  2016-09-15       Impact factor: 1.621

10.  Neuroinformatics: from bioinformatics to databasing the brain.

Authors:  Thomas M Morse
Journal:  Bioinform Biol Insights       Date:  2008-05-14
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