Help on How to Download and/or Run Models from Senselab's Model Database (ModelDB)
All locally stored models can
be downloaded as a single file by pressing the
"Download zip file" button. Some models can be run directly from the web page.
For these models there will be a button labeled "Auto-launch".
ModelDB models are associated with many simulators and simulation environments.
For some models the code is supplied externally and in these cases you will need to follow the links
to the web sites where the code is made available. If you have any trouble finding the code at these
external sites please email the ModelDB administrator which model (accession number) you were unable to find.
For models supplied internally in ModelDB, when you press the Download button, depending on your browser's settings, the file will
be downloaded to a previously choosen location (typically "Downloads" folder) or you will be asked to save the file in
a directory and, if you want, you can change the name of the file. Once the file is downloaded you can expand the zip
file with the unzip program that comes with your operating system (double clicking the zip file in windows explorer (mswin) or a finder window (mac)
will usually automatically invoke an unzip program). In general you will need to install a simulator or simulation environment and we provide below
additional instructions for NEURON, one of our most popular simulators:
If you do
not already have NEURON click here
to go to the download and install NEURON page.
Change directory (cd) to the directory that contains the mosinit.hoc file and if under unix
type nrnivmodl and press enter to compile the mechanism (.mod) files. If under windows run mknrndll to
compile the mod files. On the mac drag the model folder to the mknrndll application. Then the
model is ready to be run. A default way to run the model is given by the mosinit.hoc file
(which is executed on startup during Auto-Launch) and is executed by either double clicking on
the file (PC or MAC) or by typing nrngui mosinit.hoc on the command line (PC or unix). Check
the readme file for more information on running the model.
Start by clicking on the "Auto-Launch button". If
NEURON 5.1 or above
is installed on your PC the model will automatically download and start executing (if you
are using Internet Explorer) after you press return a couple of
times to confirm that this is what you
really want to do. Under Firefox and many other browsers when you click the auto-launch button, the browser will present you with a list of options.
Click the checkbox at the bottom that says always do this action and select to open an application (assuming that NEURON is installed).
Browse to the mos2nrn file (mos2nrn.exe in windows, mos2nrn in unix, or mos2nrn.app in MAC OS X) and select that
(under the directories c:/nrnXX/bin in windows, ~/neuron/nrn/i686/bin or /usr/local/nrn/i686/bin (i686 may be different on your platform, e.g. x86_64) in unix, or
the /Applications/NEURON-X.Y/ in MAC OS X).
Technical note: you will probably not need to but if you find a browser menu where you
would like to set a MIMEtype, use "application/mos2nrn" and Suffixes "nrnzip". You can enter "NEURON archive" under description but this
is for humans to read and unnecessary for function.Then press OK to close the boxes.
Historical note: mosinit is named for Mosaic initialization. Mosaic was an early (1993) internet browser.
Running models on your machine is inherently
insecure since models are able to execute any program or script
consistent with the permissions of the
user. We make a good faith effort at the ModelDB site to publicly provide
models that are associated with published papers and do not
knowingly provide models containing malicious or destructive
code, viruses, worms, etc. We take several steps to insure the
safety of running our publicly available models.
These include making a cursory examination
of each models code, test-running each model, and not
accepting anonymous models.
However if we were "hacked" our verified files
might be replaced with malicious ones.
Therefore please inform us if running a model
causes any kind of problem on your machine
so that we may remove the model as soon as possible from the database.
It is also possible for you to "audit" the auto-launched programs. The
auto-launched files are identical to the zip files except for having their name
and MIME type changed (this allows browsers to send them to a program
for execution rather than prompting to save them as a file).
Please do not hesitate to email the ModelDB Administrator
to ask questions, suggest improvements,or send comments.
Last Modified: March 12th 2013