models on the web

Where are they and what do they have?

Moderator: tom_morse

Post Reply
tom_morse
Posts: 40
Joined: Wed May 18, 2005 10:23 pm
Location: Yale University School of Medicine
Contact:

models on the web

Post by tom_morse » Thu May 19, 2005 7:22 pm

ModelDB and Visiome Platform are two databases of neuronal and network models:

http://senselab.med.yale.edu/senselab/modeldb
http://www.visiome.org

Descriptions from their respective home pages:

ModelDB provides an accessible location for storing and efficiently retrieving computational neuron models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any language for any environment, though ModelDB has been initially constructed for use with NEURON and GENESIS. Model code can be viewed before downloading and browsers can be set to auto-launch the models.

Visiome Platform is the Neuroinformatics Search Service that provides access to mathematical models, experimental data, analysis libraries and related resources.

I invite investigators to post their computational neuroscience models, simulators, and tools URL's to this thread.

tom_morse
Posts: 40
Joined: Wed May 18, 2005 10:23 pm
Location: Yale University School of Medicine
Contact:

links to computational neuroscience models and methods

Post by tom_morse » Fri May 27, 2005 5:55 pm

Here are 10 URL's to models and methods from diverse fields in computational neuroscience:

C-C++:

1) Rat phrenic motor neuron (Amini et al 2004) Files available..
http://www.ece.rice.edu/~jwc/PMN/

Genesis:

2) Emergent properties of networks of biological signaling pathways (Bhalla, Iyengar 1999)
http://www.ncbs.res.in/downloads/index.html

3) Fast oscillations in inhibitory networks (Maex, De Schutter 2003)
4) Network model of the granular layer of the cerebellar cortex (Maex, De Schutter 1998)
http://www.tnb.ua.ac.be/models/models.shtml

5) Leech heart interneuron network model (Hill et al 2001, 2002)
http://calabreselx.biology.emory.edu/so ... l#netmodel

6) Spike timing detection in different forms of LTD (Doi et al 2005)
http://hawaii.naist.jp/~tomoka-d/doiJNS/index.html

Matlab:

7) Method of probabilistic principle surfaces (PPS) (Chang and Ghosh 2001)
http://www.lans.ece.utexas.edu/~lans/lans/

8) Neural model of two-interval discrimination (Machens et al 2005)
http://www.cshl.edu/labs/brody/Papers/

Neuron

9) CA1 Pyramidal Neuron: Synaptic Scaling (London, Segev 2001)
http://www.nature.com/neuro/journal/v4/ ... 853-S1.htm

10) Dendritica (Vetter et al 2001)
http://www.dendrite.org/software.html

These models and methods on the web have entries in ModelDB that point to them. If you have a published model or method on the web please let us know and we will make a link to it from ModelDB.

tom_morse
Posts: 40
Joined: Wed May 18, 2005 10:23 pm
Location: Yale University School of Medicine
Contact:

online database of neuronal, heart cell, and other models

Post by tom_morse » Thu Jan 12, 2006 1:35 pm

Here is another neuronal (and mostly heart) modeling site:
http://nsr.bioeng.washington.edu/PLN/Me ... portal_url

Post Reply