AlphaSynapse is broken (at least in some version) #582
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Problem is with the |
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so this code: x = xolotl;
x.add('compartment','AB','A',0.0628)
x.AB.add('prinz/NaV','gbar',1000);
x.AB.add('prinz/CaT','gbar',25);
x.AB.add('prinz/CaS','gbar',60);
x.AB.add('prinz/ACurrent','gbar',500);
x.AB.add('prinz/KCa','gbar',50);
x.AB.add('prinz/Kd','gbar',1000);
x.AB.add('prinz/HCurrent','gbar',.1);
x.AB.add('prinz/CalciumMech');
x.add('compartment','LP','A',0.0628)
x.LP.add('prinz/NaV','gbar',1000);
x.LP.add('prinz/Kd','gbar',1000);
x.connect('AB','LP','AlphaSynapse')
x.LP.AlphaSynapseAB.gmax = 20;
x.plot()works for me, and generates this output
@smbaca can i ask which version of xolotl you're using? what does did you install via the toolbox, or did you download via git and install? I may have to bring the toolbox up to date. |
sg-s
changed the title
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> xolotl.version
v21.5.9
I installed with the Toolbox. I know that if I install the BlackBoxNeuron toolbox I get a lot more errors running the code until I place the BlackBox folder further down in the MATLAB path.
smb
… On Jul 17, 2022, at 3:17 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
so this code:
x = xolotl;
x.add('compartment','AB','A',0.0628)
x.AB.add('prinz/NaV','gbar',1000);
x.AB.add('prinz/CaT','gbar',25);
x.AB.add('prinz/CaS','gbar',60);
x.AB.add('prinz/ACurrent','gbar',500);
x.AB.add('prinz/KCa','gbar',50);
x.AB.add('prinz/Kd','gbar',1000);
x.AB.add('prinz/HCurrent','gbar',.1);
x.AB.add('prinz/CalciumMech');
x.add('compartment','LP','A',0.0628)
x.LP.add('prinz/NaV','gbar',1000);
x.LP.add('prinz/Kd','gbar',1000);
x.connect('AB','LP','AlphaSynapse')
x.LP.AlphaSynapseAB.gmax = 20;
x.plot()
works for me, and generates this output
<https://user-images.githubusercontent.com/6005346/179421406-6e95d33e-e116-4106-be72-66016b0662f7.png>
@smbaca <https://github.com/smbaca> can i ask which version of xolotl you're using? what does xolotl.version tell you?
did you install via the toolbox, or did you download via git and install? I may have to bring the toolbox up to date.
—
Reply to this email directly, view it on GitHub <#582 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAVXMEQGV7GKYTDNB7MJDALVURL4BANCNFSM52Z3IRUA>.
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Uninstalled all the Toolbox versions and used git. Took me a bit to realize I needed to rebuild the cache but now I have v22.7.17 and the code below runs properly.
…-smb
On Jul 17, 2022, at 3:17 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
so this code:
x = xolotl;
x.add('compartment','AB','A',0.0628)
x.AB.add('prinz/NaV','gbar',1000);
x.AB.add('prinz/CaT','gbar',25);
x.AB.add('prinz/CaS','gbar',60);
x.AB.add('prinz/ACurrent','gbar',500);
x.AB.add('prinz/KCa','gbar',50);
x.AB.add('prinz/Kd','gbar',1000);
x.AB.add('prinz/HCurrent','gbar',.1);
x.AB.add('prinz/CalciumMech');
x.add('compartment','LP','A',0.0628)
x.LP.add('prinz/NaV','gbar',1000);
x.LP.add('prinz/Kd','gbar',1000);
x.connect('AB','LP','AlphaSynapse')
x.LP.AlphaSynapseAB.gmax = 20;
x.plot()
works for me, and generates this output
<https://user-images.githubusercontent.com/6005346/179421406-6e95d33e-e116-4106-be72-66016b0662f7.png>
@smbaca <https://github.com/smbaca> can i ask which version of xolotl you're using? what does xolotl.version tell you?
did you install via the toolbox, or did you download via git and install? I may have to bring the toolbox up to date.
—
Reply to this email directly, view it on GitHub <#582 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAVXMEQGV7GKYTDNB7MJDALVURL4BANCNFSM52Z3IRUA>.
You are receiving this because you were mentioned.
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you don't need to install BlackBoxNeuron and xolotl -- they're redundant in some sense because BlackBoxNeuron includes xolotl. Maybe an older version of the synapse was shadowing the newer version? anyway glad it's working now. i'll build a new release but it looks like this is resolved. |
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Please go through the following steps before you file an issue that documents a problem or a potential bug and please check each item as you do so:
xolotl.cleanupand my error persistscpplab.rebuildCacheand my error persistsInformation
Please provide the following information:
Operating System
MAC 12.4 '9.12.0.1975300 (R2022a) Update 3'
Output of "version" command in MATLAB
Output of "mex.getCompilerConfigurations('C++')" in MATLAB
CompilerConfiguration with properties:
Bug reports
Please replace this section with:
I am trying to run through the xolotl self-tests. Everything ran ok except most conductances failed to compile. I then went to the docs page to try to compile and setup a simple cell and network with the following:
What you expected to happen
I expected it to work as demonstrated in the how to documents.
What actually happened
To see the complete error I changed the self.verbosity to -v instead of -silent in the compile.m. The error is below.
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