Finally: Network Modeling

Thu Sep 23 15:06:12 CEST 2010


After many struggles, a couple of rewrites from scratch of the discrete event system (DES), we recently got our first network model completely working. The spiker3 network which was already available as a low-level Heccer / DES test case, was converted to a high-level NDF model and then instantiated and run from SSP. Although it is a very simple test case with only one source and two target neurons, it proves that all low-level components are instantiated for correct simulation of this network model. Note that the model-container presents an abstraction of the model to DES making it transparant whether it is a network of multicompartmental neurons or of more abstract neuron models. I will equip SSP with a couple of network simulation templates (and likely will need to do some debugging here and there). But running network models with different stimulation protocols from a unix shell command line will now become easier than ever. Afterwards it will also become trivial to add commands for network models to the gshell.

From the technical point of view this means that the core functionality of the Neurospaces based simulation architecture has been finished. Documentation and tutorials still need to be developed, interfacing to the documentation system is on its way.

As a natural consequence, it is also time to revise the organization of GENESIS 3 development. In the past I have been the main contributor to the core of the code, but now, the core has been finished and only additions tangential to the existing functions are needed. Some of the these additions can be challenging (such as parallelization), but they will neither change the existing functionality nor interfaces. In other words, while I have been carrying Neurospaces and the core components of the architecture of GENESIS 3, now these components have been successfully finished. From here on development will focus on the GUI as an essential tool for tutorials, documentation and model publication. As a logical consequence, the role of each developer in this project needs to be revised too.

After a prototyping stage over the last year during which we integrated the (working) documentation system with the (prototype) GUI, the core design of the publication system is now in place. Build around sets of publication document snippets and an ontology for these snippets, we strongly believe we have all the essential ingredients to implement a extremely powerful GUI that integrates all of the Neurospaces software components with the documentation system. This will not only facilitate research simulation projects, it will also show the relationships between different projects (and their models). This system will help to accelerate knowledge production in a controlled manner. And that is why we are doing it.