How to do voltage clamp mode?

• Set the capacitance to infinity and control the clamped voltage by adjusting the initial voltage value

How to vary population size?

• vary = {'popName','size',[1 10 100]};

How to vary inclusion of mechanisms without changing model qualitatively (e.g., for use with compilation)?

• To prevent recompiles when using compile_flag=1, include all mechanisms and vary the conductance from 0

How to change a parameter midway through a simulation?

• The way to achieve this is to define the parameter as a function of time.
• Example: (leak current turns on at t=50ms)

  eqns='dV/dt=10+@current+gl(t)*(V+65); {iNa,iK}; gl(t)=0*(t<50)+.8*(t>50)';
  dsPlot(dsSimulate(eqns));

• see issue #62

How to vary a specific mechanism's parameter when the parameter name is shared by multiple mechanisms?

• Use {'popX.mechY','param',values} in the vary cell array

How to change default figure size?

• see issue #113 discussion. One way is to add code like this to the startup.m file:

  w = 800;
  h = 600;
  monitors = get(0,'MonitorPositions');
  x = 0.5*(monitors(1,3)-w);
  y = 0.5*(monitors(1,4)-h);
  set(0, 'DefaultFigurePosition',[x y w h]);

How to get data from the calculation functions called by the plot functions (e.g. peak frequency from peak power)?

• All calc functions used in the plot function can be independently called to get results stored in the desired fields
• Analysis results should be obtained using the calc functions (i.e., not the plot functions)
• If the calc function is called first and the fields are present in data, then dsPlot() uses the values in the field without re-analyzing the data.
• see issue #56

How to monitor spikes?

• DynaSim now records the previous 2 spike times whenever the spike monitor is on (e.g., using: monitor V.spikes(thresh)). Spike times can be accessed using the reserved variables "tspike" for the parent population, "tspike_pre" for presynaptic spike times, and "tspike_post" for postsynaptic spike times (equivalent to "tspike" in this case). tspike has dimensions [buffer_size x num_cells]; therefore, operations like summation can be performed on functions of spike times like this: sum(f(t-tspike)) where f is some function that, in this case, has a single argument that is the elapsed time since the previous spike.

monitor VAR.spikes(#)
monitor VAR.spikes(threshold)
monitor VAR.spikes(threshold,#)
monitor VAR.spikes(#,#)
monitor VAR.spikes(threshold,buffer_size)

How to store user data?

• Store data in the 'userdata' option in dsSimulate call. The data is stored studyinfo.base_simulator_options.userdata (available on dev branch as of 8/24/18).

How to create refractory periods?

• Refractory periods can be implemented using the reserved variable "tspike" (which is a buffer containing the spike times for the previous two spikes); tspike is recorded any time that spikes are monitored

  LIF={
      'dV/dt=(-70-V+R*I)/10; V(0)=reset'
      'if(any(t<tspike+tabs,1))(V=reset)'   % <-- hold V=reset throughout the absolute refractory period.
      'monitor V.spikes(thresh)'
      'tabs=10; thresh=-55; reset=-75; R=9; I=10'
       };
  data=dsSimulate(LIF);

How do I automate logging into the cluster?

• Use expect in BASH:
  • http://sharadchhetri.com/2010/12/07/how-to-use-expect-in-bash-script/
  • http://stackoverflow.com/questions/4780893/use-expect-in-bash-script-to-provide-password-to-ssh-command
• KDE users can benefit from ksshaskpass, which uses KDE's kwallet to encrypt the user-password combination

How do I set my Matlab or Octave version on the cluster?

• Edit your bash profile ~/.bash_profile in the SCC (all nodes will see that environment):

  • For Matlab add: module load matlab/2017b (example for using Matlab 2017b, adjust it to your preference!)
  • For Octave (current stable version, Octave 4.2.1, requires centos7 nodes) add:

  module use /share/module/centos7
  module load octave/4.2.1

• Note: These tips are for the Boston University cluster but are likely applicable to many Linux clusters.

• For more help, see the online BU SCC cluster support

How do I access persistent nodes (i.e. not a login node)?

• The way to access centos7 nodes manually is by adding the directive -l centos7=TRUE, so you can connect to a node like this: qrsh -l centos7=TRUE
• DynaSim manages that for you transparently when submitting loop batches (although it remains to be ported to array and array_one_file, see issue #249).