ModelDB Help

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).

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

MODEL SUBMISSION:

Models may be submitted in one of three ways:

  1. 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.
  2. a very easy entry form. Here's a video tutorial to show you how:    
  3. interactively through a private account in ModelDB.
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 through repeated name, description and keyword edits, and uploading new versions of the zip file. When you are satisfied that it is ready, request the ModelDB administrator to make it public.

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.

ModelDB ACCOUNTS

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 (although there is a forgot my password reset on the login page).

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.
The members of the ModelDB group prefer the SubmitModel because it is so convenient (try that first).

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.

Frequently Asked Questions (FAQ)

  1. Can I make a model that is under review publicly available? No. You can however use a read-only password (access code) to allow reviewers or collaborators see your model before it is made public. There is also a write access password that you can assign to share with collaborators.
  2. 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 minor edits.

REFERENCES

McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. (2017) Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. J Comput Neurosci 42(1):1-10.

Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci 17:7-11

Migliore M, Morse TM, Davison, AP, Marenco L, Shepherd GM, Hines ML. (2003) ModelDB: Making models publicly accessible to support computational neuroscience. Neuroinformatics 1:135-139.

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]


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