Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-16

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All times shown according to UTC.

Time Nick Message
04:56 egonw joined #bioclipse
05:03 samuell joined #bioclipse
05:22 egonw hi samuell
05:31 samuell hello egonw
07:11 Gpox joined #bioclipse
07:15 egonw hi Gpox
07:16 Gpox hi egonw
08:34 torbenh3 joined #bioclipse
08:35 egonw hi torbenh3
08:35 torbenh3 hi
08:35 zarah hello torbenh3, you fantastic person you
08:36 torbenh3 heh ? :)
08:36 egonw torbenh3: zarah is our friendly boy
08:36 egonw zarah: aren't you?
08:36 zarah egonw: are you talking to *me*?
08:37 egonw ok, mostly friendly :)
08:37 torbenh3 :)
08:39 torbenh3 i want to help my brother with simulating biological processes (like carbon cycle) ... breaking it down to isotopes. i am trying to determine how much existing molecular dynamics stuff can help me with automating the calculation of reaction rates.
08:39 egonw MD alone is not going to help you here, AFAIK
08:39 egonw I think most computation like this is a mix of QM and MD
08:42 egonw samuell: did you ever write up that paper review for the UUCJC ?
08:42 torbenh3 egonw: but you think its possible ?
08:42 samuell egonw: No ... :/
08:42 egonw yeah, I think people have done it... but on a large scale? dunno ...
08:43 samuell (UUCJC really was a bit too much for my schedule, I realize)
08:43 egonw torbenh3: I think that is mostly done with systems biology approaches
08:43 egonw where they calculate fluxes
08:43 samuell egonw, torbenh3: I don't think so
08:44 samuell Or well, sorry, I might now follow ...
08:44 samuell (Never mind)
08:44 torbenh3 egonw: thats what i want. i just want fluxes in the end. just breaking it down to fluxes of isotopes.
08:45 torbenh3 but basically i need the different rate constants for reactions of C^14 O_2  and C^13 O_2
08:46 samuell ... but I think most systems biology approaches use previously calculated reaction rates, and instead focus on simulating how the system behaves when connecting things together, that regulates each other etc ...
08:46 samuell (but I might be wrong)
08:47 egonw samuell: you said something about SBML and Eclipse/Bioclipse... what was that again?
08:47 egonw torbenh3: Bioclipse does not have plugins for this kind of systems biology yet... but eager to see such an extension
08:48 samuell There is a nice systems biology simulation package that is built to be easy to implement: FERN, but I don't know if has the right functionality
08:48 samuell I thinkt it might need pre-calculated reaction rates
08:49 samuell ( http://www.bio.ifi.lmu.de/FERN )
08:49 zarah samuell's link is also http://tinyurl.com/3axdyqd
08:49 torbenh3 egonw: i am actually a python guy. i was just looking for some people who know something about bio/chem informatics. so i found you guys :)
08:49 egonw fair :)
08:50 egonw actually... should be trivial to script Bioclipse with python, using the Jython implementation...
08:50 torbenh3 i basically already built a simulation core which you feed reactions (and rates), and then it builds up the ode system.
08:51 egonw not sure about embedding python code in bioclipse plugins though
08:52 samuell torbenh3: Calculating reaction rates is really a hard problem, AFAIK
08:52 egonw indeed
08:52 samuell Only experimental data seems to be good enough at the moment ... is my impression
08:52 egonw very limited data available on that
08:52 egonw most not Open, I guess
08:52 torbenh3 there is probably no data on isotopic reactions.
08:53 samuell People are looking forward though to the day when you can connect molecular dynamics to systems biology software, for automatic calculation of rates
08:53 torbenh3 i already figured that getting reaction rates for transport proteins is pretty hard, too
08:53 samuell ... but it might be worth looking into of course :)
08:53 samuell Ok
08:55 torbenh3 hmm... so whats the hard thing of finding the reaction rate of H20 <-> H+ + OH-   ?
08:56 * torbenh3 doesnt really know much about chemistry and biology (apart from school stuff and physics)
08:57 egonw you have to calculate the energies of all chemical structures and of any intermediate state...
08:57 egonw the only way to do that accurately is using QM
08:57 egonw but that scales very badly compared to the number of atoms
08:57 torbenh3 but there are QM packages.
08:57 egonw there are a few indeed...
08:58 egonw but using them is not trivial
08:58 egonw you can ask on http://blueobelisk.shapado.com/ about how to calculate a reaction path using Open/free QM tools...
08:58 zarah egonw's link is also http://tinyurl.com/yj67n5a
08:58 egonw but enzymatic reactions is way beyond the scope of QM tools
08:59 samuell egonw: Any open source tools similar to Gaussian?
08:59 egonw so, people approximate by using a mixed QM/MD approach
08:59 egonw samuell: see e.g. http://blueobelisk.shapado.com/ques​tions/how-can-i-do-the-most-accurat​e-geometry-optimization-on-ubuntu
08:59 zarah egonw's link is also http://tinyurl.com/38bcq8u
08:59 egonw but those approximations, well... they approximate...
09:00 egonw and without experimental data, you do not know well how accurate those approximations are...
09:00 torbenh3 egonw: yeah. i am not looking for enzymatic reactions right now.
09:00 egonw bbl
09:03 samuell torbenh3: Yeah, sounds more like metabolic reactions / pathways
09:05 samuell (That's a good search term for googling :) )
09:06 samuell Ah ... but, the metabolic reactions involve enzymes as well though ...
09:07 samuell It's all the time enzymes that do the "editing" of the small metabolites (molecules going through metabolism / carbon cycle etc)
16:21 egonw joined #bioclipse
17:00 egonw joined #bioclipse
18:01 egonw joined #bioclipse
19:03 egonw joined #bioclipse
19:04 egonw hi samuell
19:05 samuell hello egonw
19:07 egonw neat screencast!
19:07 egonw very well done!
19:08 samuell Thx :)
19:09 samuell Had to redo quite a numer of times ... ^^
19:09 egonw :)
19:11 egonw samuell: your 'Install Instructions' URL seems faulty: http://code.google.com/p/s​mwrdfio/w/edit/InstallAll
19:11 zarah egonw's link is also http://tinyurl.com/3xhra8y
19:11 egonw gives me a general google code page
19:12 egonw when I am not logged in on google
19:12 samuell Ah ... it's the edit link ! *doh* ... thanks!
19:12 samuell Will fix
19:12 egonw and when I am, I get a 'Forbidden'
19:12 samuell Fixed!
19:12 samuell No ...
19:13 samuell Now!
19:13 samuell http://code.google.com/p/smwrdfio/wiki/InstallAll
19:13 zarah samuell's link is also http://tinyurl.com/2uo387o
19:13 egonw you just want more hits ... :)
19:13 egonw ok, that looks better
19:13 samuell Heh :)
19:13 egonw is this the Ubuntu install guide?
19:14 samuell Yes, should be general enough for most OSs though, except the patching, which is Linux specific
19:15 samuell Was thinking of an install screencast for windows ... but that will take a bit of time, so dont know when ...
19:15 samuell Have some bugfixing to do as well :(
19:15 samuell :/ I mean
19:16 egonw that install tutorial does not install the RDFa extension, correct?
19:16 egonw http://www.mediawiki.org/wiki/Extension:RDFa
19:16 zarah egonw's link is also http://tinyurl.com/lpxuap
19:16 egonw did you see my second blog of today, about the Firefox extension?
19:25 samuell Haven't read yet ... will do so!
19:26 samuell Cool! :) (SPARQL)
19:27 egonw indeed :)
19:28 egonw and slowly everything comes together :)
20:03 samuell True
20:07 egonw writing up my notebook item on installing semantic mediawiki
20:08 egonw btw, cool FOAF stuff: http://foaf-visualizer.org/?uri=http://w​ww.joergkurtwegner.eu/foaf.xml&amp;hl=en
20:08 zarah egonw's link is also http://tinyurl.com/2wmc2m6
20:08 egonw would be cool to create such a page based on a wiki page ;)
20:12 egonw ok, semantic wiki set up...
20:13 egonw grmph...
20:14 egonw samuell: how did you install SemMW 1.5?
20:15 samuell There is a svn checkout snippet at http://semantic-mediawiki.org/wiki/Help:Download
20:15 zarah samuell's link is also http://tinyurl.com/3x6kvu8
20:15 samuell And then some steps and snippets at http://semantic-mediawiki.​org/wiki/Help:Installation
20:15 zarah samuell's link is also http://tinyurl.com/lac94p
20:15 egonw 1.4 is not going to work?
20:16 samuell You basically place the extension as wikifolder/extension/SemanticMediaWiki , adds some include lines to LocalSettings.php, and goes to the SMW Admin -page to initiaize db tables
20:17 samuell (The instructions in the link are somewhat verbose :/ )
20:18 samuell egonw: I don't think so
20:18 samuell There were a lot of changes in 1.5, they say
20:18 samuell Have a 1.4 already?
20:19 egonw yes, I had
20:19 egonw that's what comes with Lucid
20:19 samuell Ah
20:30 egonw ok, this needs more much detail...
20:30 egonw I think I got SMW 1.5 installed now
20:30 egonw but not sure
20:30 egonw this is too complicated... :(
20:30 egonw ok, going offline now

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