These are chat archives for openworm/ChannelWorm

30th
Jun 2015
Shreejoy Tripathy
@stripathy
Jun 30 2015 15:43
@VahidGh or @travs can you spell out what you need from me? I don't have the specific data you're looking for in NeuroElectro, but if you tell me what you want, I can probably help find it for you very quickly
Vahid Ghayoomie
@VahidGh
Jun 30 2015 17:29
@stripathy, We need structured data related to ion channel kinetics as much as possible. One such a dataset is Channelpedia, but I was curious if we can find similar data in the NeuroElectro project.
Shreejoy Tripathy
@stripathy
Jun 30 2015 18:34
@VahidGH data = ?
like... traces?
send me a couple examples of what you're hoping to find
Vahid Ghayoomie
@VahidGh
Jun 30 2015 18:46
@stripathy, e.g. for ion channel Kv1.1 in some cell type in some organism: Conductance= 10 ps, V_half activation= 20 mv, activation tau= 25 ms, activation scale = 15 mv, etc
Shreejoy Tripathy
@stripathy
Jun 30 2015 18:48
ahh - ok, so this is the non-patch clamp channels data
Vahid Ghayoomie
@VahidGh
Jun 30 2015 18:48
This is patch-clamp data but not for C. elegans :D
Shreejoy Tripathy
@stripathy
Jun 30 2015 18:50
no, but the distinction is that you do'nt want to mine figures/activation curves for this data, right? you just want the summary measurements?
Vahid Ghayoomie
@VahidGh
Jun 30 2015 18:51
We hope to apply the best match of saying Kv1.1-8 in mammalians for example to Kv1 in C. elegans based on the structure.
Shreejoy Tripathy
@stripathy
Jun 30 2015 18:52
ok cool
@VahidGh what happened with the curation interface that you me and @travs were talkign about last week?
Vahid Ghayoomie
@VahidGh
Jun 30 2015 19:20
@stripathy, We had some heavy changes in our data model. Also imported information about ion channels we had in a spreadsheet to the DB. Needs some user management, in order to add contribution info and separate the curation UI and some better separation of fields (patch-clamp parameters, experiment condition, etc) in UI.
@miladjafary and I are working to finish these by the end of this week.
Vahid Ghayoomie
@VahidGh
Jun 30 2015 19:30
Meanwhile I was working on the digitization format we should consider for a typical patch-clamp figure.
Now we support two types of digitization for some figure like the one in #46
As we don't know which line belongs to which holding potential
Vahid Ghayoomie
@VahidGh
Jun 30 2015 19:35
We could digitize each curve manually in a separate file (or dataset in the digitizer) and then fit them to the the best match of some trace while simulating
Or digitize the whole figure by the automatic digitization feature of the digitizer (which is much easier) and find some method to fit simulated curves to all these points
I did some work to both approaches
Shreejoy Tripathy
@stripathy
Jun 30 2015 19:37
@VahidGh hmm... my suggestion as before is to start simple - and just focus on IV curve extraction for now
i think digitizing the I/T or V/T curves is harder for the issues you just raised
Vahid Ghayoomie
@VahidGh
Jun 30 2015 19:38
Certainly the first one is more accurate but harder for digitization
@stripathy, we have had this discussion before
With just an I/V curve for steady state current we will lose info about inactivation
Shreejoy Tripathy
@stripathy
Jun 30 2015 19:41
that's true
Vahid Ghayoomie
@VahidGh
Jun 30 2015 19:42
And I think we have no choice other than considering at least either I/t ot V/t
BTW, now we have the possibility for analyzing I/t and V/t curves
Just needs some more effort (took me about 10 mins for digitizing with the first approach) for each article we are going through
Shreejoy Tripathy
@stripathy
Jun 30 2015 19:46
ok