Perl 6 - the future is here, just unevenly distributed

IRC log for #bioclipse, 2014-05-12

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All times shown according to UTC.

Time Nick Message
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09:18 jonalv egonw: did we have some way of listing BSL scriptis? Something online?
09:19 commitbot joined #bioclipse
09:19 commitbot [bioclipse.bioinformatics] goglepox closed pull request #2: Added BioJava DOIs (develop...1-dev-bioJavaDOIs) http://git.io/MrMhLw
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09:21 egonw jonalv: myexperiment
09:21 egonw but that code needs fixing
09:22 jonalv egonw: seems you have plenty of scripts there
09:22 egonw yes, quite a few
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09:22 commitbot [bioclipse.core] goglepox pushed 2 new commits to develop: http://git.io/rgBrfw
09:22 commitbot bioclipse.core/develop 47e982a Egon Willighagen: Added support for the new non-integer gist identifiers
09:22 commitbot bioclipse.core/develop c865750 Arvid Berg: Merge pull request #53 from egonw/5-dev-gistUpdate...
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09:22 jonalv egonw: do you have some favourits that you can suggest for the publication?
09:24 egonw http://www.myexperiment.org/workflows/3701.html
09:25 egonw and we could extend this one: http://www.myexperiment.org/workflows/930.html
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09:25 commitbot [bioclipse.core] goglepox pushed 3 new commits to develop: http://git.io/42hh_Q
09:25 commitbot bioclipse.core/develop 7a33be8 Egon Willighagen: Implemented a PythonConsole
09:25 commitbot bioclipse.core/develop b064348 Egon Willighagen: Now properly lists the managers when you hit TAB
09:25 commitbot bioclipse.core/develop 482405c Arvid Berg: Merge pull request #54 from egonw/6-dev-pythonConsole...
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09:26 jonalv egonw: do we have a groovy editor?
09:27 egonw no, don't think so
09:27 jonalv egonw: so, how do I run that?
09:27 egonw copy/paste :)
09:27 jonalv I see
09:27 egonw should not be too hard to fix, I guess
09:29 jonalv egonw: hm, this script has some prerequisits?
09:29 egonw which of the two?
09:29 jonalv the first one
09:30 egonw 3701?
09:30 jonalv yea
09:31 egonw well, it needs these managers: opsin, cdk, chemspider, bioclipse, inchi, ui
09:31 jonalv / download all GPML files for a species, and save those in /WikiPathways/data/
09:31 egonw ah, yes, you need data...
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09:32 egonw mom, looking up exact download URL
09:33 egonw http://wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=gpml&tag=Curation:AnalysisCollection
09:33 zarah egonw's link is also http://tinyurl.com/koe9l9y
09:33 egonw for homo sapiens
09:35 egonw left this as comment on myExperiment too
09:36 egonw there is a wikipathways manager, but not so functional yet, and at least doesn't automate this (yet)
09:38 jonalv egonw: I tested the other script. It\s not working out of the box either
09:38 egonw well, that script is 5 years old!
09:39 jonalv wow
09:39 jonalv 5 years?
09:39 jonalv yiekes
09:39 egonw yes, it's not just me whom is getting old :)
09:41 jonalv egonw: it seems like that online service at http://toposome.chemistry.drexel.edu don’t wanna play
09:42 egonw "@egonwillighagen What is the state of CDKTaverna and BioClipse integration for Taverna 2.5..? Any plans?" -> https://twitter.com/soilandreyes/status/465788282601627648
09:42 egonw jonalv: yeah, we need to ping Rajarshi
09:43 jonalv okey, or maybe there are other nice scripts? :)
09:44 egonw well, we need to decide what we want to tell
09:45 egonw what arguments we want to make...
09:45 egonw I'd guess:
09:45 egonw 1. we don't care what script/programming language you prefer
09:46 egonw 2. hell, you can even combine them (at least you can run a JavaScript file; should check the same for python and groovy)
09:46 jonalv egonw: number 927 finds no hits it seems
09:46 egonw (I guess I fix them all then :)
09:46 egonw (I guess I fixed them all then :)
09:46 jonalv egonw: did you get tab completion to work for Python as well?
09:47 egonw at least for listing all the managers
09:47 egonw not sure for methods...
09:47 jonalv okey
09:47 egonw qsar.TAB works too
09:47 egonw but not on Java classes...
09:47 jonalv well, I am thinking we shuld ahve editors for all three languages, with run buttons and probably with Ctrl+Etner functionality for running a row
09:48 jonalv or for running what is selected
09:48 egonw that is:
09:48 egonw inchiObj = inchi.generate(opsin.parseIUPACName("methane"))
09:48 egonw inchiObj.TAB
09:48 jonalv zaetnick: do you have code for doing that for R? Maybe we can borrow some stuff from you?
09:48 egonw that second does *not* list the methods on that InChI class
09:48 jonalv egonw: okey, guess we should look into that too then
09:48 egonw jonalv: +1 on editors
09:49 egonw 3. each programming language has gems... Groovy is great for XML parsing, for example
09:50 egonw 4. you can mix domain specific things like it's 1999
09:50 egonw 5. you can script the GUI
09:52 jonalv egonw: can you think of a usefull example of scripting the GUI?
10:00 egonw as a matter of fact...
10:00 egonw what about taking the Open Source Malaria compounds, run OpenTox or local toxicity predictions on that, and visualize results on the structure?
10:01 egonw better even, have the script do a few simple derivatives on sites that are too toxic, and suggest a modification, lowering the toxicity?
10:09 zaetnick jonalv: doing what, tab completion?
10:15 egonw jonalv: but we should be a bit ambitious... let's just list whatever we think needed to make this a great paper. and then we'll figure out what can be done and what not
10:15 egonw jonalv: importantly, we need a shortlist what was already published in the Bioclipse 2 paper
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10:43 jonalv zaetnick: not tab completion but running things from the editor in the console
10:43 jonalv egonw: yea
10:44 zaetnick jonalv: yes, there would be not much use of the editor otherwise :)
10:44 jonalv exactly...
10:46 jonalv egonw: sounds interesting. Can you write such a script?
10:46 jonalv egonw: suggesting modification might be a bit over the top though or?
10:47 egonw not sure... just needs a shortlist of reasonable modifications, and then just calculating the improvement
10:48 zaetnick jonalv: the code is in net.bioclipse.r.ui.handlers and net.bioclipse.r.ui.util
10:49 jonalv zaetnick: cool, is this avilable to test run from the update site by the way?
10:52 zaetnick jonalv: not sure what you mean
10:53 jonalv zaetnick: can I testrun this R console?
10:54 * jonalv tries
10:54 zaetnick this functionality is released long ago
10:57 jonalv zaetnick: is there a short command for runnign current line in the R Console?
10:58 jonalv zaetnick: such as Ctrl + Enter perhaps?
10:59 zaetnick jonalv: not yet, if I remember correct we have it on the “wish list”
11:00 jonalv okey
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