Time

This framework uses Evolutionary algorithms (EAs) to optimize Izhikevich model parameters. Models with up to 4-compartments can be tuned to reproduce experimentally recorded spike times.

Required libraries:

1. ECJ (Luke S, et al. (2015). "Ecj: A java-based evolutionary computation research system." Downloadable versions and documentation can be found at the following url: http://cs. gmu. edu/eclab/projects/ecj.)
2. Apache Commons Mathematics Library (http://commons.apache.org/proper/commons-math/)
3. CARLsim (Beyeler M, Carlson KD, Chou TS, Dutt N, Krichmar JL. (2015). A User-Friendly and Highly Optimized Library for the Creation of Neurobiologically Detailed Spiking Neural Networks. In International Joint Conference on Neural Networks.) http://www.socsci.uci.edu/~jkrichma/CARLsim/ (#3 is required only for multi-compartment models)

The following steps assume you are familiar with the required libraries above.

• Constraints are specified in JSON format under input/ directory
• Specify the .json file path in "primary_input" file (comma separated values. See "primary_input")
• Specify the number of compartments (up to 4), and their layout following the file path in primary_input e.g. 10_2_3,B4,3-000,1,0 will create a single compartment model using the constraints specified in input/10_2_3/B4/3-000.json. 10_2_3,B4,3-000,4,0,0,0,2 will create a 4-compartment model using the same constraints and additional dendritic constraints. {0,0,0,2} denotes the 4-compartment layout. index (0-based) represents a compartment, and the value represents the compartment which the index is connected to. 0 always represents soma (compartment-0). compartment-1 and compartment-2 (dendrites denoted by indices 1 and 2) are connected to soma. compartment-3 is connected to compartment-2
• The 2nd line in primary_input specifies which simulator to use. ("int" for Java-based ACM library, "ext" for CARLsim)
• Specify the ECJ parameters in .params file under input/ directory
• Once the modules are setup and input is specified, run src\ec\app\izhikevich\starter\ECJStarterV2.java (Or simply run startEA.sh)
• Outputs are generated under output/ directory
• Utility classes are available under src\ec\app\izhikevich\util package to read ECJ-generated output files
• .cpp files for simulating multi-compartment models using CARLsim are located under tuneIzh9p/

For more details and discussion of the modeling framework, please refer to the following article: Evolving simple models of diverse intrinsic dynamics in hippocampal neuron types. Frontiers in neuroinformatics. 2018 Mar 13;12:8. Venkadesh S, Komendantov AO, Listopad S, Scott EO, De Jong K, Krichmar JL, Ascoli GA. https://doi.org/10.3389/fninf.2018.00008

For comprehensive results (applied to hippocampal neuron types), refer to this article: Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity. PLOS Computational Biology. 2019 Oct 28. Venkadesh S, Komendantov AO, Wheeler DW, Hamilton DJ, Ascoli GA. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007462

For more details on simulating the models, please refer to this help page: http://hippocampome.org/