These are chat archives for openworm/ChannelWorm

23rd
Aug 2015
Travis Jacobs
@travs
Aug 23 2015 15:58
Hey @/all the hackathon agenda is over here
@cheelee hey Chee Wai, here's the plugin we're currently using in ChannelWorm
Gopal Sarma
@gsarma
Aug 23 2015 16:09
Hi guys, I have to leave in 1 hour, and thought I would spend some time on curation for ChannelWorm.
Can someone give me instructions for how to get started on that?
Chee Wai Lee
@cheelee
Aug 23 2015 16:09
@travs you have a tutorial for curation for ChannelWorm correct?
Milad Jafary
@miladjafary
Aug 23 2015 16:10
@gsarma HI
What you need? do you want to know to how run the app ?
Travis Jacobs
@travs
Aug 23 2015 16:12
@cheelee Yup! @gsarma Let me grab the link for the instructions, one sec
Chee Wai Lee
@cheelee
Aug 23 2015 16:12
@travs Thanks for that django-pytest link ... I had been working on the assumption pytest will just work out of the box with django! Apparently I'm mistaken!
Gopal Sarma
@gsarma
Aug 23 2015 16:13
@miladjafary yes, but also I've never done curation for ChannelWorm before, so I don't really know what needs to be done.
Milad Jafary
@miladjafary
Aug 23 2015 16:13
@gsarma runing the app is easy . just clone the ChannelWorm in you computer.
summerworm
@sumwor
Aug 23 2015 16:13
hi! I think ion channel is something I have some experience with, I am working in a electrophysiology lab and working on a G-protein coupled ion channel in rat's brain
Gopal Sarma
@gsarma
Aug 23 2015 16:14
I have ChannelWorm- is there not a web link? I remember using that at some point.
Milad Jafary
@miladjafary
Aug 23 2015 16:14
@gsarma the ./manage.py runserver
Travis Jacobs
@travs
Aug 23 2015 16:14
@gsarma Ok, the docs are not synced to readthedocs, I'll work on that now, but the main page for instructions is over here: https://github.com/openworm/ChannelWorm/blob/dev/docs/walkthrough.md
Stephen Larson
@slarson
Aug 23 2015 16:14
@sumwor awesome -- which ion channel?
Chee Wai Lee
@cheelee
Aug 23 2015 16:15
@sumwor nice! I think the folks are trying to curate ion channel data into our databases now. You might find that interesting.
Travis Jacobs
@travs
Aug 23 2015 16:15
@gsarma Link to channelworm webapp: http://channelwormdjango-channelworm.rhcloud.com/
Milad Jafary
@miladjafary
Aug 23 2015 16:15
@gsarma you should run the django built in web server
@gsarma as @travs link you can use live channelworm app
but if you wan't run it locally follow the instruction : https://docs.djangoproject.com/en/1.8/intro/tutorial01/#the-development-server
Gopal Sarma
@gsarma
Aug 23 2015 16:18
I registered an account but it is not letting me sign in. Should I receive a confirmation email?
Milad Jafary
@miladjafary
Aug 23 2015 16:18
no it dosen't need
please give me your username
Gopal Sarma
@gsarma
Aug 23 2015 16:19
gopalworm
Milad Jafary
@miladjafary
Aug 23 2015 16:19
let me check
Gopal Sarma
@gsarma
Aug 23 2015 16:19
thank you
Milad Jafary
@miladjafary
Aug 23 2015 16:20
@gsarma please try agin
Gopal Sarma
@gsarma
Aug 23 2015 16:20
@miladjafary great, it works!
Ok, I am looking at the spreadsheet and it looks like Elkes et al. 1997 hasn't been entered yet
Chee Wai Lee
@cheelee
Aug 23 2015 16:22
@travs django-pytest is working great for my own little examples with the django tutorial, thanks! Now I can finally get some progress going on getting real tests in.
Travis Jacobs
@travs
Aug 23 2015 16:24
@gsarma Ok glad it's working! And yes, that one has not been entered yet
Gopal Sarma
@gsarma
Aug 23 2015 16:26
Screen Shot 2015-08-23 at 12.23.04 PM.png
I'm not quite sure what points I should be selecting in the final step for this one.
Travis Jacobs
@travs
Aug 23 2015 16:26
@cheelee Radical! Yeah that's a good plugin from what I've seen
Gopal Sarma
@gsarma
Aug 23 2015 16:26
Do I just select as many points as possible at regular intervals?
Ah, ok I see that this is covered in the curation guide. Thanks.
Travis Jacobs
@travs
Aug 23 2015 16:28
@gsarma Haha, ok, yes you got it!
Milad Jafary
@miladjafary
Aug 23 2015 16:29
@gsarma could you give me the guid
Stephen Larson
@slarson
Aug 23 2015 16:30
@miladjafary I think he's referring to this: https://github.com/openworm/ChannelWorm/blob/dev/docs/walkthrough.md
@sumwor you may also want to visit the webapp here: http://channelwormdjango-channelworm.rhcloud.com/ and create an account to check out what's going on over there :)
Milad Jafary
@miladjafary
Aug 23 2015 16:31
@slarson thank you for link
summerworm
@sumwor
Aug 23 2015 16:34
ok I will @slarson
Milad Jafary
@miladjafary
Aug 23 2015 16:34
@sumwor hi
i can help you about app
Gopal Sarma
@gsarma
Aug 23 2015 16:39
Does this look reasonable?
Screen Shot 2015-08-23 at 12.39.10 PM.png
summerworm
@sumwor
Aug 23 2015 16:40
@miladjafary If you mean the http://channelwormdjango-channelworm.rhcloud.com/ yeah definitely I can use some help, the website won't let me sign in
Gopal Sarma
@gsarma
Aug 23 2015 16:44
Oh, no! I think this was probably supposed to be digitized as multiple files, is that correct?
@travs @miladjafary can you take a look at the figure I digitized? Also, what do I do with this data once it's been entered?
When I click on "Edit" in the ChannelWorm interface, it doesn't seem that there is a field for uploading the digitized plots.
Milad Jafary
@miladjafary
Aug 23 2015 16:51
@sumwor please give me you username
@gsarma are you in digitizting process?
Gopal Sarma
@gsarma
Aug 23 2015 16:53
@miladjafary I digitized one plot, but I think it is probably supposed to be multiple plots.
I uploaded the figure a few messages ago- do you see it in gitter?
Milad Jafary
@miladjafary
Aug 23 2015 16:53
@sumwor please try to sign in
agin
@gsarma you can define multiple plot by using "Manage Dataset" menu
Gopal Sarma
@gsarma
Aug 23 2015 16:56
Yes, I understand that. I just wanted to first verify that this is supposed to consist of multiple plots.
Also, the instructions don't state where this data should go once it's been digitized.
Also, Figures 1, 2, and 3 seem to be broken on the instructions.
Milad Jafary
@miladjafary
Aug 23 2015 16:59
@gsarma you can save you dataset through "view data" button in the "ToolBox"
panel
when you click on it one diaglog is open
and you can see your data set
summerworm
@sumwor
Aug 23 2015 17:01
ok I can sign in now, thank you @miladjafary
Milad Jafary
@miladjafary
Aug 23 2015 17:01
by clicking on Save button your dataset can be saved for your figure
Gopal Sarma
@gsarma
Aug 23 2015 17:01
@miladjafary yes, I understand how to enter and save the data. I have two questions. The first is the following- is a plot of this kind supposed to be a single data set or multiple datasets?
Milad Jafary
@miladjafary
Aug 23 2015 17:01
@sumwor welcom
Gopal Sarma
@gsarma
Aug 23 2015 17:01
The second is- once we have saved the data to our computer, where does it go?
It doesn't look like we upload it to the ChannelWorm interface.
Milad Jafary
@miladjafary
Aug 23 2015 17:02
@gsarma about your second questions
, the dataset save in sqllight and save in server
you can access it by clicking in "Series" link in
for each row
Gopal Sarma
@gsarma
Aug 23 2015 17:03
Ah, ok, I was looking at ion channels and not ion channel models. Thank you for the clarification.
@gsarma welcome. but i can't help you about your first questions. :D
Gopal Sarma
@gsarma
Aug 23 2015 17:05
@miladjafary @travs @slarson Unfortunately I need to leave now. Now that I understand how this works, I will continue with some more curation on my own time. I may email you guys for some clarification if anything arises. I still am not clear about how many time series figure 4A from Elkes et al. 1997 consists of. If someone can clarify this for me, I will finish this plot later.
Thank you everyone. Enjoy the rest of the hackathon!
Milad Jafary
@miladjafary
Aug 23 2015 17:06
@gsarma let me know if you need help ;)
bye
Travis Jacobs
@travs
Aug 23 2015 17:14
@gsarma Ok, and that looks good! The broken images in the guide are due to viewing it on github, instead of RTD (getting it back on rtd soon).
I'm not sure what figure that is (it's not showing in the django app for me for some reason), but I can tell it's time series from the image, so it should have a different dataset for each line.
@gsarma If you think the instructions can do with clarification in any way, please do add to them, since they are still in the early stages
@gsarma Ok just read your comment and it's figure 4A. It should be 5 datasets. The caption is somewhat unclear about this, but the 5 stimulations are for 5 different lengths, being 100ms, 200ms...500ms
Chee Wai Lee
@cheelee
Aug 23 2015 17:20
@travs ok, got my personal trial tests to work with empty django databases. I can finally attempt database fixtures, and extend those to the tests we need to do for ChannelWorm. Is there a good initially-populated starting point I can use for a ChannelWorm test?
Travis Jacobs
@travs
Aug 23 2015 17:20
@gsarma So all of the time series would include that huge increase from 0-100ms, but would just dive at different times (100ms, 200ms, etc)
@cheelee Hey that's great! You could connect to the sql database which has all of the data synced over from the live web app; is this what you're looking for?
That should be in channelworm/db.sqlite3
@cheelee Also, you can play around with that db by doing ./manage.py shell if you want something hands-on. This is how I like to start my tests :)
Chee Wai Lee
@cheelee
Aug 23 2015 17:27
@travs I'm looking for a good starting point where test data is concerned, so the tests on the 4 basic db operations are realistic and is reflective of production use-cases in our code.
@travs I can take a look at channelworm/db.sqlite3 and go from there! Thanks!
Travis Jacobs
@travs
Aug 23 2015 17:33
@cheelee No sweat! The code in conftest.py may be a good guide to grabbing data interactively as well. Let me know how it goes! :)
Chee Wai Lee
@cheelee
Aug 23 2015 17:34
@travs will do! I was just looking at it! And it sure looks like my idea of conditionally generating cProfiles via pytest may just be possible as a pytest plugin!
Milad Jafary
@miladjafary
Aug 23 2015 17:34
@travs the Figure 1 and 2 are broken in digitiztion guid https://github.com/openworm/ChannelWorm/blob/dev/docs/walkthrough.md
Stephen Larson
@slarson
Aug 23 2015 17:35
@miladjafary I'm looking into seeing if I can fix that actually :)
Milad Jafary
@miladjafary
Aug 23 2015 17:35
@slarson thank you :d
Shreejoy Tripathy
@stripathy
Aug 23 2015 17:42
Hello all, I can't contribute much today, but I'm happy to continue curating plots in the future
Stephen Larson
@slarson
Aug 23 2015 17:50
@stripathy no worries, Shreejoy! Thanks for saying hi :)
@miladjafary images are back on the walkthrough: https://github.com/openworm/ChannelWorm/blob/dev/docs/walkthrough.md
still working on getting this into readthedocs
Milad Jafary
@miladjafary
Aug 23 2015 17:54
@slarson great :d Image help me better understand :D
Travis Jacobs
@travs
Aug 23 2015 17:57
@slarson Ok thank you for fixing those!
Travis Jacobs
@travs
Aug 23 2015 18:03
Alright @/all, just about to jump back into the hangout now. See you there!