Use of GENESIS in Research

Earlier simulations that have been created with GENESIS range from a network model of piriform cortex with 4500 neurons containing simple model pyramidal cells (Wilson and Bower 1989, 1992) to a very detailed model of a cerebellar Purkinje cell that uses 4550 compartments and 8021 channels (De Schutter and Bower 1994a,b,c). Some notable recent network simulations are listed below. References for the papers are given in the list of research publications involving GENESIS.

Large Network Modeling

Although GENESIS continues to be widely used for single cell modeling, we have seen a dramatic increase in the number of publications that report the use of GENESIS for large network models in recent years. We believe that this trend is largely due to the availability of our libraries of ion channels and complete cell models. For example, we know of at least six research groups who have published the results of network simulations based on the GENESIS implementation of the Traub et al. (1991) CA3 pyramidal cell model (Murphy and Kairiss 1997; Jaboori, Sampat and Sayegh 1995; Jackson, Patterson and Cauller 1996; Hasselmo, Wyble and Wallenstein 1996; Menschik and Finkel 1998; Yang et al. 2002).

These are some of the notable large-scale network GENESIS simulations (many with parallel GENESIS, and some with over 10,000 cells) that were published during the last few years. (See the list of Research publications using GENESIS for the full references.)

Biochemical Kinetics Modeling

The development of the GENESIS library for modeling biochemical kinetics and its graphical interface Kinetikit (Bhalla and Iyengar,1999) has extended the use of GENESIS into the study of intracellular biochemical signaling mechanisms. A database of chemical kinetics models has also been established, which uses the Kinetikit tool in GENESIS for validation of the resulting models (Sivakumaran, et al., 2003). Driven by our users, we anticipate continued expansion of GENESIS as a tool for cellular and molecular level modeling. In fact, 17 of the 103 GENESIS-related papers published from the begining of 2004 through June 2007 (16.5%) used Kinetikit.

Click here to see a list of research publications involving GENESIS

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