It is possible to use ModelDB by just clicking on links - learning your
way around intuitively (hopefully)! Please try this first.
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).
For full functionality, browse this database with Firefox 2, or Internet
Explorer 5 or above.
More information is available at
a help page for downloading and running models
or read below information on how to submit models to modeldb.
Models may be submitted in one of three ways:
Whichever way you choose, the model will remain private until you ask the ModelDB administrator to make it public.
While it is private, you can prepare it for web publication.
When you are satisfied that it is ready, request the ModelDB administrator to make it public.
- directly via
email to a ModelDB administrator. Attach a (compressed if possible) model file to the
email. Describe the model in the body of the message. The ModelDB administrator
will enter your submission and work for you to refine your model entry and
integrate it with senselab's other databases.
- a very easy entry form.
Here's a video tutorial to show you how:
- interactively through a private account in ModelDB.
If you plan to enter more than one model into ModelDB, you may want to sign up for an account.
This will make it easy for you to keep track of all private models that you created under that account.
WHY IS A ModelDB ACCOUNT USEFUL?
The reason to have an account is that once you are logged in,
ModelDB will show you a "Show my private models" link that will retrieve
all of the private models that you created while logged in.
Otherwise, if you do not have an account, you would have to remember the accession number and password
associated with each of your private models.
In order to take advantage of the top mentioned convenient listing feature, you must be logged in when you create the model entry.
Any model entries that you create while not logged in will not appear in your list of private models.
HOW TO SIGN UP FOR AN ACCOUNT:
USING AN ACCOUNT:
How to create a model entry in ModelDB (once you have an account):
Log into your account. Then click on "Create a private model under my account"
Fill in the form fields and press create (note: no form fields are
required). Then complete your entry by clicking on edit and uploading a model file.
This two step process is necessary because field text data and binary file data
can not be sent at the same time.
How to find your private model in ModelDB:
First, login. Click on the "Find models by ... model name" link
near the top of the ModelDB homepage.
This brings up a page with
"Current selection displays 'all allowed' entries" at the top,
where 'all allowed' is a pop-down list that you can click on to
select 'my private'. Then click on
the name of your private model.
HOW TO PREPARE A ZIP FILE FOR AUTOMATIC DOWNLOAD AND RUN
Web browsers can use NEURON as a "viewer" that automatically runs NEURON models downloaded
In principle, other simulation environments could also be enhanced so that
models written for them could run automatically when downloaded.
For this to work, the model source code must be properly "packaged."
The following procedure is for NEURON models.
- Create a directory that contains all the necessary neuron model files and subdirectories.
- In the same directory, put a file (called readme.txt, README, readme.html, or index.html)
that contains specific information and instructions
on how to use the model.
This is the file that ModelDB will display in the Model Files window of the model description page
- In order to run the program from the web, this directory must also contain a mosinit.hoc file.
mosinit.hoc should contain a command such as
load_file("init.hoc") where init.hoc starts the neuron modeling session. Invariably the command
load_file("nrngui.hoc") is included near the top of the mosinit.hoc file to display the NEURON main
menu and also to load frequently used libraries. If additional mod files are included in a subfolder, named for example
mod_files, then a command to compile these mod files
must be the first command in the mosinit.hoc file.
- Zip up the directory. On MAC OS X (do not use compress) and unix/linux systems an appropriate terminal window command
for creating a zip file called ca1neuron.zip from a directory ca1nrn would be
zip -r ca1neuron.zip ca1nrn
On MSWin systems with WinZip, create a directory called 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
You can also create your zip file on MSWin systems by right clicking in the Windows Explorer dialog box on the background of the right part of
the screen where your model files top level folder is displayed. Select create a compressed zip file from the pop-up menu. Change the name
of the newly created zip file to your top level folder name with a ".zip" file extension. Finish by dragging and dropping the top-level folder
onto the zip file name.
- The zip file is now ready to be uploaded to ModelDB.
Frequently Asked Questions (FAQ)
Can I make a model that is under review publicly available? Yes, we
can manually add the paper now with a citation that says
(in review) for the volume or year and either includes or omits the
journal name depending on your preference. If the paper is rejected
with no possibility of revisions we would have to make the model private. You can also use a read-only password (access code)
to allow reviewers or collaborators to see your model before it is made public. There is also a write access password that
you can assign to share with collaborators.
Once the model is made public can I change my model? It is not possible
for the modeler to directly change the model after it
is made public. The changes are emailed to a ModelDB Adminsitrator who
reviews (to keep the public models curated) and applies the suggested
changes. We invariably adopt the modelers suggestions, sometimes with
Hines ML, Morse T,
Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience.
J Comput Neurosci 17:7-11
M, Morse TM, Davison, AP, Marenco L, Shepherd GM, Hines ML. (2003) ModelDB: Making
models publicly accessible to support computational neuroscience.
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]
Email the ModelDB Administrator
to ask questions, suggest improvements,or send comments.
Last Modified: March 3rd, 2011