Camelia, the Perl 6 bug

IRC log for #bioclipse, 2013-04-18

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All times shown according to UTC.

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08:42 hybridivy hi egonw and jonalv
08:43 jonalv hi hybridivy
08:43 hybridivy im interested in gsoc idea of Integration of WikiPathways Visualization with PathVisio into Bioclipse
08:43 jonalv cool
08:43 hybridivy i have been checking out bioclipse code with help of egonw
08:43 jonalv aha
08:44 jonalv egonw asked me if I could be a mentor just the other day
08:44 hybridivy and as a start up thing i have made a basic gpml viewer
08:44 hybridivy The code is @ https://github.com/Sravanth​iSinha/bioclipse.pathvisio ,
08:44 hybridivy code does: https://github.com/SravanthiSinha/bioclips​e.pathvisio/blob/master/pvinbioclipse.png
08:45 jonalv so I am reading and learning about the gsoc process
08:46 jonalv hybridivy: that looks very interesting
08:46 hybridivy jonalv : thanks
08:46 hybridivy :)
08:47 jonalv Are those things written for SWT?
08:47 egonw hybridivy: now would be a good time to discuss what the expected outcome of the project should be
08:47 jonalv or is it Swing below perhaps?
08:48 hybridivy egonw :yes
08:49 jonalv ah seems it's awt actually :)
08:53 jonalv I will be online a few more minutes then I have to run and will be back about 2 or 2.5 hours later
08:53 hybridivy so, i have to implement whole thing in swt?
08:53 jonalv no I don't think so
08:53 jonalv these bridges have worked well before
08:54 jonalv if I recall correctly the JMol plugin in Bioclipse uses a bridge
08:54 jonalv that might have been to Swing though
08:55 jonalv so it should be fine
08:55 hybridivy jonalv: ok great
08:56 hybridivy jonalv: so as per the project idea ,event propagation mechanism has to be done so that when users select protein and metabolites, Bioclipse will automatically visualize 2D or 3D structural information about those molecules .
08:56 hybridivy jonalv and egonw : right ?
08:56 jonalv that sounds like a useful feature yea
08:57 jonalv Gpox: What's the status of the jmol view?
08:57 hybridivy jonalv : the project idea is at http://nrnb.org/gsoc/ , idea 15
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09:00 jonalv hybridivy: visualizing 2D structures at selection should be easy. That is a good first step. As for 3d I think we only have an editor so far and no view. So it takes a bit more effort to build that view as well but it shouldn't be so complicated I hope.
09:01 jonalv Gpox, egonw: Do any of you remember about the status of the jmol view. I seem to recall it not being ready but I might be wrong...
09:01 jonalv hi sravanthisinha
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09:02 jonalv hybridivy: welcome back. What was the last message you got from me?
09:02 hybridivy jonalv: sorry was disconnected, did i miss anythng
09:03 hybridivy i wrote , jonalv : the project idea is at http://nrnb.org/gsoc/ , idea 15
09:03 jonalv I wrote: hybridivy: visualizing 2D structures at selection should be easy. That is a good first step. As for 3d I think we only have an editor so far and no view. So it takes a bit more effort to build that view as well but it shouldn't be so complicated I hope.
09:04 jonalv hybridivy: also, if you want to look back at this later have a look at http://colabti.org/irclogge​r/irclogger_logs/bioclipse
09:04 hybridivy jonalv: thanks
09:08 hybridivy i think , i am missing out something - how do i visualise 3d structural information about a metbolite or protein
09:09 jonalv as of now Bioclipse can open 3d coordinates of molecules which are stored in files.
09:09 jonalv This is done in the Jmol editor
09:10 hybridivy yes so using jmol and jchempaint plugins i should do visualisation based on the metabolite selected
09:10 egonw practically: by sending around a selection event
09:10 egonw "selection event" that's a key term here
09:10 egonw existing Jmol and JChemPaint "views" will then automatically visualize this
09:11 jonalv However, I am not sure one wants to open a new editor when selecting a metabolite. Bur rather use a view
09:11 hybridivy egonw : ok great
09:11 egonw yes, view better than editor
09:11 jonalv An eclipse view differs from and Eclipse editor
09:12 hybridivy ok i have cretaed a editor so far, i will look into more details about the view part
09:14 hybridivy jonalv and egonw : any more suggestions on the idea ?
09:15 hybridivy or tips on how to go about the idea?
09:15 jonalv there is a 2d view in Bioclipse. A good milestone is to visualize selected metabolite as 2d in it
09:15 egonw hybridivy: write down the goals
09:15 jonalv the take 3d as next step
09:16 egonw e.g. is "visualizing" the goal, or perhaps really "editing"...
09:16 egonw what formats will you support
09:16 egonw -> GPML, perhaps other input formats?
09:16 egonw will you implement 2D and 3D viz?
09:16 egonw how will that be done...
09:16 egonw write up these things first now...
09:16 egonw that's more important right now than more ideas
09:19 hybridivy ok, sure will note down things :)
09:19 hybridivy egonw  and jonalv :thanks
09:19 jonalv I need to run, I will be back probably 2 hours from now
09:19 jonalv later o/
09:19 egonw and hybridivy: also write down how you will keep jonalv updated on things...
09:20 egonw e.g. using a blog where you will write at least once a week what you that...
09:20 egonw and/or other communication channels
09:22 hybridivy egonw : i think i need little more investigation on the idea
09:22 hybridivy will do it and get back to you :)
09:24 hybridivy egonw : so by 2d visualisation you mean the same visulaisation which is carried down in pathvisio right
09:24 hybridivy ?
09:24 egonw well, visualization of what
09:24 egonw make that clear in your writing
09:25 egonw there is viz of the pathway
09:25 egonw and of the pathway components, like metabolites
09:25 egonw and geness too
09:25 egonw e.g. there is a "View" for DNA/RNA/Protein sequences too
09:26 hybridivy Visualizing experimental data on pathways, by coloring the genes.  which is done is pathvisio
09:26 egonw ah, well, that's a whole other thing indeed
09:26 hybridivy ok
09:27 egonw I would suggest that as additional thing you can do
09:27 hybridivy ok , so what do i have to visualise now?
09:27 egonw as optional goal
09:27 egonw depends on what you want...
09:27 egonw turn it around
09:27 egonw it's your project, what would you do?
09:28 egonw and what do you think is realistic
09:28 hybridivy btw where is the "view " for dna/rna?
09:28 hybridivy biolcipse or you meant in pathvisio?
09:28 egonw in Bioclipse
09:28 hybridivy ok
09:28 egonw mom, let me find a ref for that
09:30 egonw http://wiki.bioclipse.net/in​dex.php?title=Biojava_plugin
09:30 egonw screenshot, down the bottom
09:30 egonw a PDB is visualized there
09:30 egonw with 3D on the right
09:30 egonw sequence middle bottom
09:32 hybridivy egonw :yes thanks a ton
09:40 hybridivy egonw:  I  will be back probably in an hour.
09:40 egonw ok
09:40 egonw good luck with the writing!
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10:46 egonw hi olass
10:59 olass hi
10:59 zarah ni hao olass
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11:17 jonalv olass: do you remember the status of the jmol view?
11:17 olass nope
11:19 jonalv I seem to recall it not working. But I wonder what could have been the problem. If the Google summer project want to visualize 3d structures in a view I sot of wonder how much work that would be
11:19 jonalv I am pretty sure the sdf editor can show 3d structures now so I suppose it's should be pretty easy to do it in a view as well?
11:19 jonalv olass: or what do you think?
11:27 olass jmol view has always been able to visualize 3d structures
11:27 olass that is its purpose
11:27 olass but it might be that it needs updates
11:27 olass you'll have to test
11:28 jonalv olass: I donut think there is a jmol view
11:28 olass ok...
11:28 olass sounds easy to get one
11:28 jonalv Bioclispe 1 had one but I think there was a lack of round tuts
11:28 jonalv *tuits
11:28 jonalv when we came to Bioclipse 2
11:29 olass ok
11:29 jonalv I seem to recall some hack for converting between cdk molecules and jmol molecules that stopped working
11:29 jonalv but yea I agree. I think it should be easy now. Probably was not at some point in time
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12:31 egonw jonalv: I spoke with Bob at he ACS meeting...
12:31 egonw we looked a bit at updating Jmol in Bioclipse
12:31 egonw and he told me how to do it...
12:31 egonw what APIs changed etc
12:31 egonw I plan to make this update in the near future
12:31 egonw there is cool new viz stuff in the newer Jmol versions
12:31 jonalv egonw++ cool
12:31 egonw e.g. for docking
12:38 olass sounds nice!
13:16 egonw yeah, it looked great
13:17 egonw olass: is there code to download a very specific PDB entry?
13:17 egonw I know there is code to do a search...
13:17 egonw but I could not quickly find a method that given a PDB code just returns that one
13:17 egonw like for !CRN
13:17 egonw like for 1CRN
13:20 olass egonw: I think it should be
13:20 egonw ok, I'll look better than :)
13:21 olass ws.queryPDB("1CRN")
13:21 olass oh, maybe it doesn't do that
13:21 egonw yeah, but that does a search and returns a list
13:21 olass ah
13:22 olass hmm, there should be one… just don't remember
13:22 olass you could look in old gists!
13:22 egonw we should have a book(let)
13:24 egonw seriously, if *we* do not remember all functionality available...
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14:02 hybridivy hi jonalv
14:03 jonalv hybridivy: hi I am in a telephone conference for the moment so I am probably gonna be slightly laggy in answering :)
14:03 hybridivy jonalv: i will catch you little later
14:03 hybridivy :)
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