sg-s
commented
2 years ago Problem is with the AlphaSynapse component
Closed smbaca closed 2 years ago
sg-s
commented
2 years ago Problem is with the AlphaSynapse component
sg-s
commented
2 years ago 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 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.
smbaca
commented
2 years ago 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 https://github.com/sg-s/xolotl/issues/582#issuecomment-1186592294, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAVXMEQGV7GKYTDNB7MJDALVURL4BANCNFSM52Z3IRUA. You are receiving this because you were mentioned.
smbaca
commented
2 years ago 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 https://github.com/sg-s/xolotl/issues/582#issuecomment-1186592294, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAVXMEQGV7GKYTDNB7MJDALVURL4BANCNFSM52Z3IRUA. You are receiving this because you were mentioned.
sg-s
commented
2 years ago 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.
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.