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Stephen Larson
@slarson
Sorry; the link didn’t come through earlier @gsarma @brijeshmodi12 @m4-miranda
Folks who couldn’t attend; if you don’t have the first two badges yet; suggest to check them out and try to earn them
Stephen Larson
@slarson
Hi @/all — since the last session we have a new badge for you to earn! https://www.badgelist.com/OpenWorm/Muscle-Model-Explorer This is a more advanced badge than the last two, and has a pre-requisite that you must have completed the first two! Earning this will get you closer to being able to hack on some cell models. Happy badging & good luck.
Stephen Larson
@slarson
@m4-miranda @miladjafary @theodinspire @brijeshmodi12 any luck earning the earlier badges?
Marc Miranda
@m4-miranda
Will get to the new badge as soon as I can
Brijesh Modi
@brijeshmodi12
I will resume the work once I am settled in Frankfurt
Neil Shah
@shah-n
For the muscle model explorer, I am receiving an error when loading channel files. The ca_boyle channel has an h gate without the time_course and steady_state attributes.
Eric T Cormack
@theodinspire
Looks like vacation is getting in the way. I'll give it another go next week
Stephen Larson
@slarson
@siddhant-bansal welcome!
siddhant-bansal
@siddhant-bansal
Hello Everyone!
Stephen Larson
@slarson
@shah-n Can you post the error as an issue at https://github.com/openworm/muscle_model/issues/new ?
And mention it in here? Thanks :)
Stephen Larson
@slarson
@shah-n I’m curious what steps you are following and if it is different than what is in the notebook?
Neil Shah
@shah-n
I have posted the error - openworm/muscle_model#61
@slarson I copied the source code from the notebook to a .py file and then ran the file at the command prompt.
Marc Miranda
@m4-miranda
Submitted evidence for the badge
Gopal Sarma
@gsarma
This message was deleted
Gopal Sarma
@gsarma

Hi all, I’m running into some problems running muscle_model. Here is what I am seeing:

pynml-channelanalysis -temperature 34 -minV -55 -maxV 80 -duration 600 -clampBaseVoltage -55 -clampDuration 580 -stepTargetVoltage 10 -erev 50 ./ca_boyle.channel.nml
Traceback (most recent call last):
File "/Users/gopalsarma/anaconda/bin/pynml-channelanalysis", line 9, in <module>
load_entry_point('pyNeuroML==0.2.2', 'console_scripts', 'pynml-channelanalysis')()
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/init.py", line 558, in load_entry_point
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/init.py", line 2682, in load_entry_point
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/init.py", line 2355, in load
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/setuptools-17.1.1-py2.7.egg/pkg_resources/init.py", line 2361, in resolve
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/pyNeuroML-0.2.2-py2.7.egg/pyneuroml/analysis/NML2ChannelAnalysis.py", line 21, in <module>
import matplotlib.pyplot as plt
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 27, in <module>
import matplotlib.colorbar
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py", line 34, in <module>
import matplotlib.collections as collections
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/collections.py", line 27, in <module>
import matplotlib.backend_bases as backend_bases
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 56, in <module>
import matplotlib.textpath as textpath
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py", line 22, in <module>
from matplotlib.mathtext import MathTextParser
File "/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/mathtext.py", line 63, in <module>
import matplotlib._png as _png
ImportError: dlopen(/Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/_png.so, 2): Library not loaded: @loader_path/../../../libpng15.15.dylib
Referenced from: /Users/gopalsarma/anaconda/lib/python2.7/site-packages/matplotlib/_png.so
Reason: image not found

I’m not sure if this error log is helpful, because there were others along the way that I addressed and the errors keep changing.
Appreciate any help!
Stephen Larson
@slarson
@gsarma 'pip install matplotlib' ? What version do you have?
Gopal Sarma
@gsarma

@slarson unfortunately, I don’t think that’s the issue, it’s definitely installed, unless it’s with the version. I have 1.4.3. In case it is helpful, this particuarly set of error messages came about after I had reinstalled lxml2 after getting this error:
http://stackoverflow.com/questions/23172384/lxml-runtime-error-reason-incompatible-library-version-etree-so-requires-vers

The matplotlib error wasn’t there before I re-installed lxml2.

Gopal Sarma
@gsarma

Sorry all, I realize that was probably a completely unhelpful set of error messages without any context. Unfortunately, muscle_model has always given me problems and it’s never been easy to get it running on my machine. Not sure if there are any general issues that people are aware of.

I’m running Mac OS X 11.6 and am using Anacoda. I was initially using Enthought, but some strange issues kept cropping up with virtualenv and it ended being that the only workaround was to use conda envs instead.

Marc Miranda
@m4-miranda
I had an issue running muscle_model on my Ubuntu system with anaconda too. Don't remember the exact error log, but I switched to a different system with only conda, and it worked with no issues
Stephen Larson
@slarson
@gsarma I’m thinking your anaconda environment may not be working. Can you reinstall it or update it? I’m also curious what happens if you grab the source for matplotlib and try running the tests: http://matplotlib.org/devel/testing.html
Gopal Sarma
@gsarma
This message was deleted
This message was deleted
Ok, looks like updating anacoda may have done the trick! These are the plots I’m seeing:
Screen Shot 2016-10-08 at 11.31.21 AM.png
Screen Shot 2016-10-08 at 11.31.23 AM.png
Stephen Larson
@slarson
@gsarma nice! Looks submittable for the badge! :)
Gopal Sarma
@gsarma
Done!
Stephen Larson
@slarson
Well played :)
Gopal Sarma
@gsarma
The badge system is a terrific idea. Hats off to @cheelee and others for making this happen!
Stephen Larson
@slarson
@gsarma Nice! I’ll add you as a badgemaker admin in case you get inspired to produce one — possibly a good accompaniment to the walkthrough? :)
Gopal Sarma
@gsarma
@slarson thanks, I appreciate it! I definitely think a badge would make a good companion to the walkthrough. Let me think about what we could do along the lines of the muscle_model builder or the GitHub best practices badge.
Stephen Larson
@slarson
@gsarma Cool :) You’ve been added.
Chee Wai Lee
@cheelee
@gsarma Glad you like it!
Stephen Larson
@slarson
@gsarma @m4-miranda @miladjafary @VahidGh @theodinspire FYI: There is a new next-level muscle model badge to earn: https://www.badgelist.com/OpenWorm/Muscle-Model-Hacker - -Thanks to @shah-n for the help in putting it together.
Neil Shah
@shah-n
@slarson Thanks for the opportunity to work on it.
krisdamato
@krisdamato
Does mm require python 2.7? I'm using 3.5/Windows/Anaconda and I'm running into difficulties when I run setup.py. Seems that it doesn't like Python 2.7 style print statements
Padraig Gleeson
@pgleeson
@krisdamato pyNeuroML is tested with Python 3 so installing that (e.g. with pip install) should be sufficient to getting the muscle model running. It's not been tried out much on Windows though...
Marc Miranda
@m4-miranda
Hi, is this still active?
I'm trying to install muscle_model
Getting back to this now, done with grad
I installed as per the muscle model explorer badge, but don't get an output after the last step
No errors are thrown either
marc@marc-Pavilion:~/Documents/Projects/openWorm/muscle_model/NeuroML2$ pynml-channelanalysis -temperature 34 -minV -55 -maxV 80 -duration 600 -clampBaseVoltage -55 -clampDuration 580 -stepTargetVoltage 10 -erev 50 ./ca_boyle.channel.nml pyNeuroML >>> pyNeuroML >>> Analysing channels from files: ['./ca_boyle.channel.nml'] pyNeuroML >>>
Stephen Larson
@slarson
@m4-miranda we have migrated this channel over into Slack. Please join us over there by filling out this form and follow the invite link at the end. Please repost in the muscle_model channel over there. Thanks!