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xml_tutorial.xml
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xml_tutorial.xml
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<?xml version="1.0" ?>
<!--Welcome to the tutorial of Optimizer's configuration xml. In the following lines you can see the settings used for the simplified CA1 piramidal cell,
and I'm going to use this example to explain the various options in the configuration file.-->
<settings>
<simulator>
<!--This indicates which simulator was used, and the value can be Neuron or External-->
Neuron
</simulator>
<f_tol>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</f_tol>
<max_evaluation>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
200.0
</max_evaluation>
<spike_window>
<!--Error function parameter, sets the window size for excluding spikes. Default value is 1ms*input_freq/1000.'-->
5.0
</spike_window>
<evo_strat>
<!--Name of the selected algorithm.'-->
Classical EO
</evo_strat>
<seed>
<!--Seed for the random number generator.'-->
1234.0
</seed>
<m_gauss>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</m_gauss>
<run_controll_vrest>
<!--Initial voltage value. Used only if simulator is not External'-->
-65.0
</run_controll_vrest>
<starting_points>
<!--Algorithm parameter, either None, which indicates that there are no given starting points,
or a list of floating point values (e.g: [0,1,2,3,4] one value for each parameter)
or a list of lists (this is only suported by algorithms from the inspyred package).
We highly recommend to use the GUI if you want to specify starting points as the graphical interface has error handling).'-->
None
</starting_points>
<cooling_rate>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</cooling_rate>
<pop_size>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
300.0
</pop_size>
<adjusted_params>
<!--The selected model parameters for optimization. It must be a list containing strings.
The string can be either "section channel channel parameter" format or "section parameter" depending on what you try to optimize.
If you defined a user function and gave the names of the parameters, then those names must be listed here.'-->
['soma H_CA1pyr_prox gmax_H_CA1pyr_prox', 'soma CaN gmax_CaN', 'soma CaL gmax_CaL', 'soma K_AHP gmax_K_AHP', 'soma K_C_1D gmax_K_C_1D', 'soma K_M gmax_K_M', 'soma K_A_prox gmax_K_A_prox', 'soma K_DR gmax_K_DR', 'soma Na_soma gmax_Na_soma']
</adjusted_params>
<param_vals>
<!--Depreceted-->
[0, 0, 0, 0, 0, 0, 0, 0, 0]
</param_vals>
<run_controll_tstop>
<!--Length of the simulation in ms. Used only if simulator is not External.'-->
1000.0
</run_controll_tstop>
<num_inputs>
<!--Algorithm parameter, must be equal to the number of optimization parameters (length of the list given at <adjusted_params>).'-->
9
</num_inputs>
<stim_sec>
<!--Name of the stimulated section. Used only if simulator is not External.'-->
soma
</stim_sec>
<spike_thres>
<!--Error function parameter, used to detect spikes. Default value is 0.0.'-->
-10.0
</spike_thres>
<boundaries>
<!--Algorithm parameter, describing parameter boundaries. It must take a form of [[min_parameter1,...,min_parameterN],[max_parameter1,...,max_parameterN]].'-->
[[0.0001, 0.0001, 0.0001, 9.9999999999999995e-07, 0.0001, 0.0001, 0.001, 0.001, 0.001], [0.01, 0.10000000000000001, 0.10000000000000001, 0.01, 0.10000000000000001, 0.10000000000000001, 1.0, 1.0, 1.0]]
</boundaries>
<stim_pos>
<!--Stimulation position inside the stimulated section. Used only if simulator is not External.'-->
0.5
</stim_pos>
<dwell>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</dwell>
<input_size>
<!--Number of traces in the input file.'-->
1
</input_size>
<type>
<!--Input type. Can be ['voltage'] or ['current'].'-->
['voltage']
</type>
<x_tol>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</x_tol>
<feats>
<!--Names of the selected error function separated by a comma and a space.'-->
Spike Count, Averaged Squared Error II, Latency to 1st Spike, AP Overshoot, AHP Depth, AP Width
</feats>
<input_length>
<!--Length of the input trace(s) in ms.'-->
1000
</input_length>
<sim_command>
<!--The command which runs the external simulator or this "" which indicates that an internal simulator is used (only is available Neuron at the moment).'-->
""
</sim_command>
<init_temp>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</init_temp>
<schedule>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</schedule>
<stim_dur>
<!--Duration of stimulation in ms. Only present if internal simulator is used.'-->
600.0
</stim_dur>
<run_controll_dt>
<!--Integration step size.'-->
0.05
</run_controll_dt>
<run_controll_sec>
<!--Name of the section where the recording takes place.'-->
soma
</run_controll_sec>
<input_cont_t>
<!--Input file contains time or not. Depreceted (Optimizer autodetects the format via regex).'-->
False
</input_cont_t>
<start_time_stamp>
<!--Time stamp of start.'-->
1395931694.17
</start_time_stamp>
<model_spec_dir>
<!--Special directory which contains the results of calling nrnivmodl on the mod files.'-->
/home/kali/neuron/optimizer/szabolcsnak/ca1pc_simple/mod_files
</model_spec_dir>
<acc>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</acc>
<std_gauss>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</std_gauss>
<run_controll_record>
<!--Parameter to record. Either i or v for current or voltage recordings. Not present when External simulator is used.'-->
v
</run_controll_record>
<stim_type>
<!--Stimulation type. Either IClamp or VClamp. Not present when External simulator is used.'-->
IClamp
</stim_type>
<stim_del>
<!--Length of the stimuli delay in ms. Not present when External simulator is used.'-->
200.0
</stim_del>
<stim_amp>
<!--Amplitude of the stimuli in the form of a list (one entry for every input trace) or a list containing the path as string of the stimulation file. Not present when External simulator is used.'-->
[0.20000000000000001]
</stim_amp>
<input_dir>
<!--Path to the input file.'-->
/home/kali/neuron/optimizer/szabolcsnak/ca1pc_simple/Vinj48_2c_1.dat
</input_dir>
<input_freq>
<!--Sampling frequency of input trace(s) in Hz'-->
5000
</input_freq>
<input_scale>
<!--Scale of the input. Can be V, mV, uV or uA, nA, pA. Other values will result in an error.'-->
V
</input_scale>
<u_fun_string>
<!--User function in a form of a string or this "" which indicates that no function is used (default).
We highly recommend using the GUI to if user function is needed.'-->
""
</u_fun_string>
<mutation_rate>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
0.25
</mutation_rate>
<weights>
<!--Erro function parameter. The values of this list are assigned to the selected error functions as weights in the given order.
The list must contain a number of floating values equal to the number of functions specified in <feats>'-->
[0.40000000000000002, 0.20000000000000001, 0.10000000000000001, 0.10000000000000001, 0.10000000000000001, 0.10000000000000001]
</weights>
<model_path>
<!--Path to the model file.'-->
/home/kali/neuron/optimizer/szabolcsnak/ca1pc_simple/ca1pc_model.hoc
</model_path>
<final_temp>
<!--Algorithm parameter, either None, which indicates that the algorithm in use doesn't require this parameter,
or some floating point value.'-->
None
</final_temp>
<run_controll_pos>
<!--Position inside the section, where the recording tkes place.'-->
0.5
</run_controll_pos>
<base_dir>
<!--Path to bbase directory where the results will be generated.'-->
/home/kali/neuron/optimizer/szabolcsnak/ca1pc_simple
</base_dir>
</settings>