Standards and Guidelines for Multiscale Modeling
Multiscale modeling is a tool of critical importance for neuroscience. As computational modeling techniques become integrated with experimental neuroscience, more knowledge can be extracted from existing experimental data. Quantitative models assist in generating experimentally testable hypotheses and in selecting informative experiments. One major challenge in the field is that, because of a wide range of simulation tools being used in the community, it is unlikely that one laboratory can reproduce the results obtained by another group, even if the model is deposited in an openly accessible database. The absence of widely adopted standards for model description also hamper efforts to make existing programs more compatible, reduce opportunities for innovative software development and for benchmarking of existing simulators.
The INCF has started a project to develop a new standard markup language for model description. Based on lessons learned with previous efforts in computational neuroscience and in other fields like systems biology, a concerted effort is made to develop a well-defined but flexible syntax for a self-documenting markup language that will be easy to extend and that can form the basis for specific implementations covering a wide range of modeling scales. The initial effort focuses on describing a growing area of computational neuroscience, spiking networks. This language, called NineML (Network Interchange format for NEuroscience) is based on a layered approach: an abstraction layer allows a full mathematical description of the models, including events and state transitions, while the user layer contains parameter values for specific models.
To facilitate uptake of this new description language the INCF Task Force contains delegates from several relevant projects like the Blue Brain Project, GENESIS, KInNeSS, MOOSE, NEST, NeuroML, NEURON and PyNN.
The Task Force made the first official release of NineML in July 2011, at the workshop Emerging standards for network modeling at the CNS*2011 conference in Stockholm, Sweden. The official NineML web pages are located at the INCF Software Center.
