ModelView: online structural analysis of computational models (McDougal et al. 2015)

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Accession:154872
" ... To aid users, we have developed ModelView, a web application for NEURON models in ModelDB that presents a graphical view of model structure augmented with contextual information. Web presentation provides a rich, simulator-independent environment for interacting with graphs. The necessary data is generated by combining manual curation, text-mining the source code, querying ModelDB, and simulator introspection. ... With this tool, researchers can examine the structure of hundreds of models in ModelDB in a standardized presentation without installing any software, downloading the model, or reading model source code."
Reference:
1 . McDougal RA, Morse TM, Hines ML, Shepherd GM (2015) ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 13:459-70 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Methods;
Implementer(s): McDougal, Robert [robert.mcdougal at yale.edu];
/
modelview
analysis
presentation
readme.txt
modelview_how_to.txt
                            
ModelView on ModelDB: creating and running:

To install modelview:

To create modelview folder sign into indexer.med.yale.internal.
1) Run the below after cd'ing to the file shared ModelDB script folder:

hg clone https://tom_morse@bitbucket.org/ramcdougal/modelview

it will create the modelview folder among the other files and folders
in the modeldb home folder.

Run the same command
hg clone https://tom_morse@bitbucket.org/ramcdougal/modelview
in my home folder.  This will provide a place for the below mentioned sprinkle_json_gen.py
to take a copy of the json_gnerator.py to sprinkle into each of the expanded modeldb models

2) Note the neuronweb is from an early version Robert McDougal et
al.'s neuronweb.  The neuronweb folder in modeldb:
modeldb/modelview/neuronweb corresponds to the folder
neuronweb/JQUERYUITest in Robert's repository.

3) Download the nrntest repository from 
hg clone http://www.neuron.yale.edu/hg/nrntest
into the /home/tmm46 folder (doesn't need to be on modeldb)

The process involves

a) downloading the neuron code

cd /home/tmm46/nrntest/verify
(note there is a README here that explains how to run the nrn tester)
./senselabmodels.py

b) compiling the mod files
it's necessary to set export variables for example
export mdbtest=7.4
export standard=7.4
mkdir /home/tmm46/nrntest/verify/7.4
(and then you can run this command in the verify folder
sh verify.sh
(or ./verify.sh)

3) moving the json_generator into the model's top level folders and running
python json_gnerator.py accessionid:

This is done by 

First starting screen so that one can detach (ctrl-A, D) and reattach latter: type
"screen" and enter on the command line.  Secondly start vnc by entering "vncserver" on the command line.
Thirdly inform the shell to send X11 to the vncserver by typing
export DISPLAY="whatever_the_vncserver_program_said_was_display:was_number"
Finally:
cd'ing to ~/nrntest/verify and running
python sprinkle_json_gen.py
(wait some number of hours)

If it is desired to regenerate the accessionnum.json files then delete them all before hand:
rm /home/tmm46/nrntest/verify/7.4/*/*/*.json
(each of their existence prevents the sprinkle_json_gen.py script from creating them again on a model by model basis)

5) copying the accessionnum.json file into the 
modelview/modelview.html
folder

this can be done by typing the below in the nrntest/verify folder

cp 7.4/*/*/*json ~/senselab/Senselab/Web/ModelDB/modelview

(then the model visualizer is available in the browser with a url
senselab/modeldb/modelview/modelview.html#accessionnum)

7) setting the has_modelview true by editing the model which will then
activate the link to modelview (the updated showmodel.asp page
contains the proper link)

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