Help on How to Use Senselab's Model Database (ModelDB)

ModelDB has two collections of data, public and private. The public data is viewable by anyone on the web. The private data is only viewable by the creator (and senselab administrators).

It is recommended that this database is browsed with Netscape 6 or Internet Explorer 5 or above for full functionality.

More information is available at a help page for downloading and running models or read below information on how to submit models to modeldb.

Modelers may submit models either 1) directly via email to a ModelDB administrator or 2) interactively through a private account in our ModelDB database, or 3) effortlessly with a single form entry.

For direct submission merely attach a (compressed if possible) model file to an email. Describe the model in the body of the message. The ModelDB administrator enters your submission and works for you to refine your model entry and integrate it with senselab's other databases.

HOW TO SIGN UP FOR AN ACCOUNT:

Fill out the signup form to request an account that enables you to interactively enter a model.

USING AN ACCOUNT:

What an account allows you to do.
It allows you to add models to the database that are only viewable to yourself and senselab administrators. This can help you prepare a model for web publication. When ready request the ModelDB system administrator to change your model to public status. A ModelDB administrator will then verify the private model by checking that it reproduces one or more figures or results from the model's associated publication.

How to create a model in ModelDB (once you have an account).

Click on the Model List link from the ModelDB homepage. Then click on Create New. Fill in the form fields and press create (note: no form fields are required). Then click on edit and upload a model file to complete your entry. This two step process is necessary because field text data and binary file data can not be sent at the same time.

How to prepare a Neuron zip file for automatic download and run.

1) A directory should be created (with a meaningful name) and all the neuron model files and subdirectories should be placed there.
2) A file (called readme.txt, README, readme.html, or index.html) with specific information and instructions
on how to use the model should be placed in this directory.  This file is automatically loaded as the default
file viewed in the Model Files window of the model description page (ShowModel.asp).

3) In order to run the program from the web a mosinit.hoc file should be in the top level of this directory and should contain a command such as load_file("init.hoc") where init.hoc starts the neuron modeling session.
4) The directory should be zipped up. On unix systems an appropriate command for creating a zip file called ca1neuron.zip from a directory ca1nrn is
zip -r ca1neuron.zip ca1nrn
On windows systems with WinZip create a directory, ca1nrn, that contains all your Neuron files. Start Winzip. I find it easiest to run the wizard. After you enter the name of your new archieve (zip file) you can click on "add folders" and just select the folder with your model files. You can then close winzip. If you do not use the wizard then the model file directory you create must be the only directory at that level so that the wildcard add will work (there is no folder add).
5) The file can now be uploaded to ModelDB from the edit window once a model has been created.

How to find your private model in ModelDB.

First, login. Click on the list models sorted by ... model name link near the top of the ModelDB homepage. There is a pop-down list at the top of the page from which you should change from Current selection displays "all allowed" entries to "my private". Then click on the name of your private model to see the current detailed entries for that model in the show model page.

REFERENCES:

A freely available (after an easy registration) downloadable article has been published in the journal Neuroinformatics:
Migliore M, Morse TM, Davison, AP, Marenco L, Shepherd GM, Hines ML. ModelDB Making models publicly accessible to support computational neuroscience. Neuroinformatics 2003 1:135-139]

A book chapter on ModelDB:
Davison AP, Morse TM, Migliore M, Marenco L, Shepherd GM, and Hines ML. (2002). ModelDB: A Resource for Neuronal and Network Modeling. In: Neuroscience Databases: A Practical Guide. Ed. Rolf Kotter. Kluwer Academic Publishers, Dusseldorf, pp: 99-109.[amazon.com]