ModelDB: Making Models Publicly Accessible to Support Computational Neuroscience

Abstract

Computational neuroscience as a scientific discipline must provide for the ready testing of published models by others in the field. Unfortunately this has rarely been fulfilled. When exact reproduction of a model simulation is achieved, it is often a long and difficult process. Too often, missing or typographically incorrect equations and parameter values have made it difficult to explore or build upon published models. Compounding this difficulty is the proliferation of platforms and operating systems that are incompatible with the author's original computing environment.Because of these problems, most models are never subjected to the rigorous testing by others in the field that is a hallmark of the scientific method. This not only impedes validation of a model, but also prevents a deeper understanding of its inner workings, especially through modification of the parameters. Furthermore, modular pieces of the model, e.g. ion channels or the morphology of a cell, cannot be reused to build new models and propel research forward.ModelDB (http://senselab.med.yale.edu/modeldb) is intended to address these issues (Peterson et al, 1996;Shepherd et al, 1998). ModelDB is a database of computational models, either classics in the field or published in recent years. It focuses on models for different types of neurons, and presently contains over 60 models for 15 neuron types. In addition to compartmental models, it contains models covering from ion channels and receptors through axons and dendrites through neurons to networks. Models can be accessed by author, model name, neuron type, concept, e.g. synaptic plasticity, pattern recognition, etc, or by simulation environment.ModelDB is a member of a major neuroscience database collection called SenseLab. Each SenseLab database has an easily extensible structure achieved through the EAV/CR (EntityAttribute-Value with Classes and Relationships) data schema , Miller et al 2001. ModelDB is integrated with NeuronDB (Marenco et al 1999), another SenseLab database that stores neuronal properties derived from the neuroscience literature (http:// senselab.med.yale.edu/senselab/NeuronDB). Use of the models is free to all. Contributing to the database is also open to all. Contributions are tested for quality-control purposes before being made public. Here we describe how to find, run, and submit models to ModelDB. Browsing ModelDBThe use of ModelDB typically starts with a computational neuroscientist who wishes to test the results of a simulation by a published model, and use that as a starting point for further research. Instead of recreating the model from scratch, the user goes to the ModelDB home page (Fig.1, top), to find the model by any of the various ways already mentioned. All the information about a model is shown on a single page (Fig.1, bottom), which also contains tools for finding related models in the database.The files required to run a simulation are stored in a compressed archive in zip format and can be browsed and/or downloaded (Fig.1, bottom, lower left column)...

Genotype–phenotype correlations in neonatal epilepsies caused by mutations in the voltage sensor of K v 7.2 potassium channel subunits

“…The I KM properties were implemented to fit the steady-state and kinetic values obtained in this work. The complete model and simulation files are available for public download under the ModelDB section of the Senselab database (http://senselab.med.yale.edu/modeldb/) (47).…”

A physiome standards-based model publication paradigm

“…MODELDB (http://senselab. med.yale.edu/modeldb/) is another excellent example and provides a generic Internet repository for the archiving of model implementations (Migliore et al 2003;Hines et al 2004). While such an approach to the distribution of a model implementation may provide an excellent reference implementation capable of accurately reproducing published results, it lacks the ability to easily document the development of the model implementation.…”

Interoperability of Neuroscience Modeling Software: Current Status and Future Directions

“…This at least would ensure that there is a complete and correct, although often hard to read, version of the system described in the paper. A first and encouraging project in this direction is the SenseLab's ModelDB database (http://senselab.med.yale.edu/senselab/modeldb/) (Migliore et al 2003) where researchers can submit their models once the publication is accepted. ModelDB already hosts a large number of models and is becoming a valued resource for researchers.…”