GENESIS Tutorial 2 - single cell modeling

Exercises

• Examine the file ~/.simrc - note the SIMPATH statements
• Read the GENESIS Modeling Tutorial "Building a cell the easy way". If necessary, read the previous section on "Making realistic neural compartments".
• Examine the files in Tutorials/cells/simplecell: simplecell.g, cell.p, protodefs.g - optionally, graphics.g
• Copy the simplecell directory to a place of your own and do the suggested exercises in the Tutorial:
  • Add a muscarinic K channel to produce spike frequency adaptation
  • Modify simplecell in other ways - add more dendrite compartments or add channels taken from genesis/neurokit/prototypes/traub91chan.g.
• Run the Tutorials/cells/simplecell2 version of the model. Then use Neurokit to edit the channels and modify the channel activation taus to make it fire more slowly, without causing it to stop firing. The cells/cell-tuning directory has additional tools for fitting channel parameters to current and voltage clamp data.
• Do the exercise in Tutorials/exercies/traubcell. First use the unix "less" command (or a file browser) to read the README file, then examine the scripts. Run traubcell.g and use "showfield" and "showmsg" to explore the model. Later, when you are familiar with the GENESIS commands to create GUIs, create a graphics.g file to run traubcell from the GUI and plot Vm for the soma and apical_14 compartments.

Additional exercises or projects

Suggested reading in BoG

• Chapt. 7 - Ion Channels and Bursting Neurons
  • V and Ca activated channels
  • Case study of genesis/Scripts/burster model
  • Neurokit experiments with genesis/Scripts/traub91
• Chapt. 19 (1st ed: 18) - Implementing Other Types of Channels (Use of tabchannels)
• Chapt. 16 (1st ed: 15) - Cell Construction with the Cell Reader
• Chapt. 17 (1st ed: 16) - Building a Cell With Neurokit
• Chapt. 20 (1st ed: 19) - Last part: using hsolve

Project suggestion

Pick an intresting neuron for which (ideally):

• There is no GENESIS model
• Important channels have been identified
• Some voltage clamp data is available
• Some current clamp data is available

THEN

• Make simplifed morphology ("ball and stick" or "reduced morpholgy")
• Implement channels
  • starting from scratch, or
  • modifying existing GENESIS channels (from genesis/Scripts/neurokit/prototypes, or from one of the cells in Tutorials/cells)
• Perform parameter seach
  • manually using variations of the scripts in Tutorials/cells/cell-tuning (or with Neurokit)
  • automatically (see Reference Manual "Parameter Search Library")

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