These are chat archives for openworm/ChannelWorm

12th
Jul 2015
Chee Wai Lee
@cheelee
Jul 12 2015 06:32
@VahidGh Thanks again for the link to the paper. I think I have a better layman's idea about what we are trying to achieve from a science-simulation perspective. Let me try to summarize it here, and if you guys have any clarifying comments that'd be great! Overall we are trying to figure out how the worm actually moves, with the Boyle et.al. 2007 paper providing a model for how the muscle cells are connected, and how the intercell gaps facilitate the flow of electrical currents (via the propagation equations). The work in ChannelWorm is to provide this model with accurate parameters that describe the action potentials between each different types of ion channels in these intercell gaps ... is that a reasonable layman's description/interpretation of the problem?
Travis Jacobs
@travs
Jul 12 2015 15:02
Hi @/all, we're over here starting the hackathon. Hope to see you there! :)
Milad Jafary
@miladjafary
Jul 12 2015 15:16
Hi @/all
Travis Jacobs
@travs
Jul 12 2015 15:17
Hey ! :)
Milad Jafary
@miladjafary
Jul 12 2015 15:17
@travs did you see new Experiment dashboard?
Travis Jacobs
@travs
Jul 12 2015 15:20
@miladjafary checking it out now
Chee Wai Lee
@cheelee
Jul 12 2015 15:21
So the password I got from @travs to access the interface the last time no longer works. Is this expected
?
Milad Jafary
@miladjafary
Jul 12 2015 15:22
@cheelee did you registerd?
Chee Wai Lee
@cheelee
Jul 12 2015 15:23
yah I did the last time, got in and played around with it with the gang 2 days ago.
Travis Jacobs
@travs
Jul 12 2015 15:23
@miladjafary Where is the new UI stuff exactly?
click on Add Experiemnt
@cheelee now you can login
@cheelee please check it out now
Travis Jacobs
@travs
Jul 12 2015 15:25
@miladjafary ohh! I see now
Chee Wai Lee
@cheelee
Jul 12 2015 15:25
oh, that's a different site from what I had been using.
Travis Jacobs
@travs
Jul 12 2015 15:25
@miladjafary This is awesome
Milad Jafary
@miladjafary
Jul 12 2015 15:25
@travs Good :d
Chee Wai Lee
@cheelee
Jul 12 2015 15:25
@miladjafary ok that link works perfectly, doesn't even require I paste the generated password.
Milad Jafary
@miladjafary
Jul 12 2015 15:25
I hope to usefull
Travis Jacobs
@travs
Jul 12 2015 15:26
@miladjafary I think the workflow is much more clear with this interface. Thanks for these changes :)
Milad Jafary
@miladjafary
Jul 12 2015 15:26
@cheelee if you want do data entry you need login first
Travis Jacobs
@travs
Jul 12 2015 15:26
@VahidGh Does this mean we can freeze the version and push to dev for now?
Milad Jafary
@miladjafary
Jul 12 2015 15:26
@travs welcome :d
Chee Wai Lee
@cheelee
Jul 12 2015 15:28
@miladjafary The second link just gives me the login screen, so permission denied.
@miladjafary I don't plan to, thanks! My interest has been in the workflow and how the data fits in with the rest of the project. And as soon as you guys start doing real data entry, I'm gonna have to stop messing around with it.
Milad Jafary
@miladjafary
Jul 12 2015 15:28
@cheelee you can't login ?
@cheelee now you can .
@cheelee please check it out again :d
you permission was wrong
Chee Wai Lee
@cheelee
Jul 12 2015 15:31
@miladjafary Nope, still the login screen.
ah, let me try again thanks!
Milad Jafary
@miladjafary
Jul 12 2015 15:32
@cheelee OK. NOP!
Chee Wai Lee
@cheelee
Jul 12 2015 15:32
Milad Jafary
@miladjafary
Jul 12 2015 15:33
@cheelee yes . it's work beacause it's public page
Chee Wai Lee
@cheelee
Jul 12 2015 15:34
@miladjafary gotcha! It is not a big deal if I cannot access the restricted page.
The public page gives me a good idea of what to expect.
Milad Jafary
@miladjafary
Jul 12 2015 15:37
@cheelee ok
@cheelee i send you usename and password in private chat :d
Chee Wai Lee
@cheelee
Jul 12 2015 15:40
awesome trying again
Yup, am in.
Milad Jafary
@miladjafary
Jul 12 2015 15:41
OK :D
Shreejoy Tripathy
@stripathy
Jul 12 2015 15:57
@VahidGh @cheelee can I get my username and password reset for the channelworm app?
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:00
@stripathy, you can not login?!
Chee Wai Lee
@cheelee
Jul 12 2015 16:01
@miladjafary can help you with that, @stripathy . He just helped me! hehe
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:01
@VahidGh no... i think i forgot my password
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:02
@travs Yeah, we just need some changes on the OpenShift side to read from dev version, as we need to push changes frequently these days
Chee Wai Lee
@cheelee
Jul 12 2015 16:03
@VahidGh Something went wrong with my login too. @miladjafary had to reset it for me.
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:03
@miladjafary can I get some help resetting my password?
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:04
@travs, do you have problem with login too?
I had no problem!
Travis Jacobs
@travs
Jul 12 2015 16:09
@VahidGh Yes I am having trouble too :(
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:13
I'm in the app now, @VahidGh helped me reset my password =)
@travs should I try curating a paper from start to finish?
and take notes as i go?
Travis Jacobs
@travs
Jul 12 2015 16:14
@stripathy If you did that it would be a great help! :)
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:14
@travs sounds good
Travis Jacobs
@travs
Jul 12 2015 16:14
Do you have a link to the google doc? That may be the best place to make notes
@stripathy
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:15
@travs, that's odd! let me reset yours too
Will check new changes!
Travis Jacobs
@travs
Jul 12 2015 16:16
@VahidGh Ok thanks!
@stripathy There's that but also this one
Travis Jacobs
@travs
Jul 12 2015 16:16
Yes exactly
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:18
Would you try again
I reset the pass to "zaq1"
Travis Jacobs
@travs
Jul 12 2015 16:19
@VahidGh not working for me :(
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:21
without double quotes? :D
Milad Jafary
@miladjafary
Jul 12 2015 16:21
@stripathy sorry for delay
yes i can reset your password
do you want it?
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:21
@miladjafary I did chabge
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:21
@miladjafary no i'm ok, @VahidGh just did it for me
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:22
*change
Travis Jacobs
@travs
Jul 12 2015 16:22
@VahidGh Haha, of course :)
Milad Jafary
@miladjafary
Jul 12 2015 16:22
@stripathy great :d
@VahidGh OK
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:27
@VahidGh does the current webapp interface allow editing information that I just added?
like, editing an existing reference?
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:28
Yes, in Action column you can see edit button
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:29
ok, thanks
where is the action column?
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:30
You should go back to the experiment page
from left-side menu
This is still not available while creating new one
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:31
ok i see - all this does is allow me to edit the comments on that
i can't go back and do any more editing of the reference
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:32
Sorry, If you want edit a reference you should click the references
We have a plan to merge adding reference while creating a new experiment
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:33
there's no "action" button under the references page
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:33
Action column, edit button :D
Travis Jacobs
@travs
Jul 12 2015 16:34
I can only see the very beginning of the action column
@VahidGh The problem @stripathy is having may be because he cannot horizontally scroll in his browser. I am unable to do so for some reason
@VahidGh The problem @stripathy may be because he cannot horizontally scroll in his browser. I am unable to do so for some reason
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:36
@travs is correct
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:36
Would you please post a screen capture here?
Maybe the problem is with using Safari!
Travis Jacobs
@travs
Jul 12 2015 16:38
I am using chrome
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:39
i'm using safari
Travis Jacobs
@travs
Jul 12 2015 16:39
Trying to upload a gif here; not sure if it will animate :\
channelworm.gif
Oh cool!
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:42
@travs, this is due to resolution. Bootstrap should act responsive here, let me check
@miladjafary
Would you try again
Travis Jacobs
@travs
Jul 12 2015 16:47
@VahidGh Right. I think if box-primary in the html was wrapping its contents it would work this way
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:47
@travs I did some changes, I guess it's OK now
Travis Jacobs
@travs
Jul 12 2015 16:48
@VahidGh Awesome; works perfect now
What did you change?
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:49
@VahidGh still not ok for me in safari, fine in chrome
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:49
The problem was with CSS Style in the table
@stripathy, oh, Does what you see the same as Travis' screenshot?
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:52
yes
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:54
I did the change in references, now I applied this in other lists (in case you were checking experiments)
Would you refresh your page and try again
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:55
sure
no - same problem as before in safari
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:56
@miladjafary, what do you think?
Milad Jafary
@miladjafary
Jul 12 2015 16:57
@VahidGh yes. you should add "table-responsive" to the div that container of table
@stripathy please press CTRL+F5
Travis Jacobs
@travs
Jul 12 2015 16:57
@/all Hey guys, in about 15 minutes let's jump back in the video chat and give some updates!
Shreejoy Tripathy
@stripathy
Jul 12 2015 16:58
@VahidGh thanks! that works!
Vahid Ghayoomie
@VahidGh
Jul 12 2015 16:58
@stripathy, great
@travs please you too check it reference page
Travis Jacobs
@travs
Jul 12 2015 17:04
@miladjafary Works for me ! :)
Vahid Ghayoomie
@VahidGh
Jul 12 2015 17:07
@miladjafary, Previous problem was due to Style="..."which I think was platform/version dependent
Milad Jafary
@miladjafary
Jul 12 2015 17:08
@VahidGh Would you please explain more :d
Vahid Ghayoomie
@VahidGh
Jul 12 2015 17:09
@miladjafary, check this commit: VahidGh/ChannelWorm@d284a71
I thought Bootstrap has built-in responsive tables
Milad Jafary
@miladjafary
Jul 12 2015 17:11
yes of course :d
Stephen Larson
@slarson
Jul 12 2015 17:47
@stripathy ok, these are the issues related to data collection right now: https://waffle.io/VahidGh/ChannelWorm?milestone=Collect%20and%20digitize%20channel%20data
Not sure if you have seen these yet
Shreejoy Tripathy
@stripathy
Jul 12 2015 17:48
@slarson yeah, saw this
so, I think i'm saying, add an issue for "convert 7 I/V curves to neuroML2" or something like that
Stephen Larson
@slarson
Jul 12 2015 17:54
@stripathy makes sense — right now there are some lower level issues similar to that over here: https://waffle.io/VahidGh/ChannelWorm?milestone=Optimize%20an%20ion%20channel%20model%20to%20pass%20validation
I think the reason that doesn’t exist is because doing it for one channel is still getting sorted, though I just saw more results from @VahidGh today that look like he’s getting this working well
@VahidGh I would love to know what process is working for you these days for doing those optimization, after the investigations you have been doing
Shreejoy Tripathy
@stripathy
Jul 12 2015 17:59
alright, thanks @slarson
Vahid Ghayoomie
@VahidGh
Jul 12 2015 18:00
@stripathy, @slarson yeah, this week I'm going to finish a sample one
as you can see in the graphs we have from this channel
I started working on SLO-2
I'm working mainly on I/V and G/Gmax-V for Cl- and Ca- dependent activation
I could do some fit on the I/V plot and get voltage-dependent activation
And going to integrate this with Ion-dependent activation as mentioned in two separate references
This is the main reference, which is confirmed in this one:
Vahid Ghayoomie
@VahidGh
Jul 12 2015 18:05
That this channel depends on both Cl and Ca for activation
SLO-2-sim-IV.png
This is the fit using CWfitter, that This week I hope I can complete to generate the Modalator module for exporting the results to NeuroML2 format
Milad Jafary
@miladjafary
Jul 12 2015 18:11
@VahidGh can we finalizing CWfitter ?
Vahid Ghayoomie
@VahidGh
Jul 12 2015 18:14
The good thing when starting from scratch to the end is that while going through the whole process, new changes come with new challenges
When a primary version done, we can starting test and improve cycles
@miladjafary, Yeah, now have to integrate this with UI
Vahid Ghayoomie
@VahidGh
Jul 12 2015 21:05

@VahidGh Thanks again for the link to the paper. I think I have a better layman's idea about what we are trying to achieve from a science-simulation perspective. Let me try to summarize it here, and if you guys have any clarifying comments that'd be great! Overall we are trying to figure out how the worm actually moves, with the Boyle et.al. 2007 paper providing a model for how the muscle cells are connected, and how the intercell gaps facilitate the flow of electrical currents (via the propagation equations). The work in ChannelWorm is to provide this model with accurate parameters that describe the action potentials between each different types of ion channels in these intercell gaps ... is that a reasonable layman's description/interpretation of the problem?

@cheelee, Sorry, I didn't notice you commented. Actually, the aim of the muscle-model sub-project is what you described, and we have models for the Boyle&Cohen paper right now, and working on improvement. Then. this is going to be integrated with models from motor neurons, etc. Motor neurons, and other type of neurons have also their own ion channels, so in CW we are working to model those channels in different cells for the overall integration and optimization (e.g in C302 project). And finally model some overall behavior like movement.