GENESIS: Documentation

Heccer: A Numerical Solver

The optimization of a neuronal solver ultimately focuses on accuracy and performance. Transforming complex biological parameters into precomputed tables and optimizing for a high CPU cache hit ratio are the most important features for a good solver, and gives the solver a performance boost of about a factor four to six.

Heccer is a fast compartmental solver, that is based on hsolve of the GENESIS simulator. To find out more about the numerical principles implemented in Heccer see a small tutorial on numerical theory. The efficiency of Heccer is explained in Byte Code Compilation.

Heccer can be instantiated from C, or from Perl (or other scripting languages). It is also possible to link Heccer directly to Matlab. Heccer comes with Swig interface definitions, such that linking Heccer to any other technologies should be easy.

Adding new channel types to Heccer can be done using callouts. The callout mechanism allows for general user extensions that contribute a current or conductance at a particular time in a simulation. Heccer automatically integrates this contribution into the membrane potential. Check the tests of the callouts for more information (tests/code/callout1.c and tests/code/calloutInjector.c).

The source code of Heccer contains inline developer documentation. As yet, there is no stable API but the Swig interfaces for Heccer are not expected to change much. If you are interested in this, look at a simple example for driving Heccer from Perl, and another example with active channels and a calcium pool. Heccer is currently capable of simulating Purkinje cells (see the Purkinje Cell Model), and, at first evaluation, runs slightly faster than hsolve (It is difficult to assess why exactly: while the hsolve implementation is much more optimized than Heccer’s, the Heccer design is slightly better optimized than hsolve’s.).

Heccer Features

• Can be driven from C, Perl, SSP, and fetches the model parameters from the Model Container. The test specification in the Heccer package have examples of C-level tests (see the tests/code/ directory) and Perl-level tests (check the tests/glue/swig/perl/ directory). The SSP package defines many tests that integrate Heccer and the model-container.
• Computes the behaviour of single neurons.
• Integrates Hodgkin-Huxley-like channels.
• Integrates exponentially decaying calcium concentrations and Nernst potentials. Interfaces will be provided for more elaborate calcium models.
• Can operate in a “passive-only” mode, i.e. all channels in a model are ignored with exception of the synaptic channels.
• Tables to speed up computations, are dynamically generated and optimized.
• All parts of a model with the same kinetics automatically share tables.
• Computes the contribution of one channel type to the overall dendritic current, e.g. the contribution of all calcium channels or the contribution of all persistent calcium channels.
• Can serialize the current neuron state to an external stream for later resuming the simulation (or for multiple use).
• Generalizing the previous point, can be initialized from external sources.
• Can be used with or without the Model Container. To use Heccer without the Model Container, configure the module with the command line “./configure --without-neurospaces”. To use Heccer with the Model Container, the Model Container must be installed before Heccer is compiled.

Heccer has been validated with a Purkinje cell model and produces an exact match with hsolve (see the purkinje cell model and the Purkinje cell tutorial in the GENESIS simulator distribution). Heccer is constantly undergoing regression tests. Link to Regression Test Output. These tests give an idea of the functionality of Heccer as a compartmental solver.

Besides being open source, Heccer is also hypersource and Heccer Source Code is browsable.

Extending Heccer

• Adding new channel types to Heccer can be done using callouts. The callout mechanism allows for general user extensions that contribute a current or conductance at a particular time in a simulation. Heccer automatically integrates this contribution into the membrane potential. Check the tests of the callouts for more information (tests/code/callout1.c and tests/code/calloutInjector.c).