Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-23

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All times shown according to UTC.

Time Nick Message
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08:12 edrin hi
08:12 edrin hi egonw
08:13 edrin reading all your interesting and straight forward emails
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08:36 CIA-44 bioclipse: jonalv * r5463 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Added BeanPostProcessor that solves problem with path to xml file. (Now the test fails due to data integrity trouble so not done yet)
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09:58 CIA-44 bioclipse: jonalv * r5464 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Now creates an admin for each database after created the databases
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11:38 CIA-44 bioclipse: jonalv * r5465 /bioclipse2/trunk/plugins/net.bioclipse.stru​cturedb/src/net/bioclipse/structuredb/intern​albusiness/SQLMapPathBeanPostProcessor.java: Added a few comments to the class javadoc
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11:53 mateusz Hi
11:53 mateusz is it possible to plan gene cloning in bioeclipse?
11:53 jonalv hi
11:53 mateusz for example restriction enzymes analysis
11:53 mateusz primers design
11:54 mateusz plasmid visualisation
11:54 mateusz with used cuting sites in mcs
11:54 mateusz There are a some comercial applications like Clone, Vector for that
11:54 mateusz but they're windows only
11:55 jonalv Hm I would have to say: Not yet. But we are very interested in use cases of this sort
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11:58 jonalv There are work going on for a multiple alignment editor which I assume would be useful in at least primers design?
12:15 mateusz jonalv, not really
12:15 jonalv okey
12:15 mateusz jonalv, perlprimer is quite good
12:16 mateusz it shows melting temp
12:16 mateusz which should be the same for two primers
12:16 mateusz or similar
12:16 mateusz % of GC
12:16 jonalv aha
12:16 * jonalv was just wondering what it might be... :)
12:17 mateusz GC pair bases :)
12:17 mateusz AT are less stable than GC... so the more GC, the higher temp is requited to melt
12:18 jonalv yea I realised that. But are you telling that there is an easy way to actually get a real temperature from just the sequences?
12:19 * jonalv isn't exactly an expert on the PCR field... :)
12:19 mateusz hmm aproximated
12:19 mateusz sure
12:20 mateusz also drawing circle like image of vector with MCS awould be good idea
12:20 jonalv biojava might have such calculations perhaps? Or maybe there is some webservice? In that case it would be easy to do that from Bioclipse I guess
12:20 mateusz I often use Clone win32 program or vector to prepare visualisation of cloning vector..
12:21 jonalv You should really talk to masak...
12:21 * jonalv summons masak
12:21 masak joined #bioclipse
12:21 masak ahem.
12:21 mateusz masak, HI
12:21 masak mateusz: hello there
12:21 jonalv mateusz, has lots of interesting bioinformatics ideas
12:21 jonalv or questions
12:21 masak interesting.
12:22 mateusz masak, I wonder if there is a place in bioclipse for tool that allows primers design
12:22 * jonalv will brb
12:22 masak mateusz: absolutely
12:22 mateusz restriction enzymes analise of given sequence
12:22 masak mateusz: do you have access to the bioclipse mailing list?
12:22 mateusz for example fetching nucleotide sequences of plazmids
12:23 masak would you care to write a few use cases there?
12:23 mateusz and then selecting enzymes from Rebase
12:23 masak sounds cool.
12:23 mateusz and showing it on circle visualisation of this vector
12:23 masak circle visualisations are something I'm working on
12:23 mateusz yes I am subscribed to bioclipse ml
12:23 mateusz really ?
12:23 mateusz thats great
12:24 masak yes
12:24 masak a combination of SVG and SWT, I think
12:24 mateusz in Batik ?
12:24 masak mateusz: but we'd still need to work in the rest of your request in there
12:24 masak mateusz: maybe Batik, yes
12:24 masak don't know yet
12:25 mateusz would be cool to scale pictures for publiaction
12:25 masak depends on whether I need to actually render the SVG in Bioclipse
12:25 mateusz so svg is the right chose
12:25 masak SWT is pretty powerful, too
12:25 masak but don't let me stop you from putting your bioinformatics requests in an email :)
12:26 mateusz Hmm:P does bioeclipse have R plugin ?
12:26 masak yes
12:26 mateusz for statistical analysis
12:26 masak it's in its early stages
12:26 mateusz hmm cool
12:27 mateusz brb
12:27 * jonalv is back
12:27 * mateusz doing pcr gel..
12:27 jonalv aha :)
12:34 CIA-44 bioclipse: jonalv * r5466 /bioclipse2/trunk/plugins/net.bioclipse.hsql​db/src/net/bioclipse/hsqldb/HsqldbUtil.java: Added an ugly Thread.sleep hack to circumvent a deadlock like situation with HSQLDB. I hope this is not the final solution.
12:34 masak jonalv: yeech!
12:34 * jonalv is seriously considering switching to Derby instead
12:35 jonalv I quickly ran into yet another java.io.EOFException
12:35 jonalv I don't think that's an exception I should ever see...
12:36 masak no...
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13:47 olas hi all
13:47 * olas is back in Sweden again
13:50 jonalv wb :)
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16:12 CIA-44 bioclipse: ospjuth * r5468 /bioclipse2/trunk/plugins/net.bioclipse.b​iomart/src/net/bioclipse/biomart/editors/ (AttributesPage.java MartAttributesFilter.java): Added a filter for unwanted attributes.
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16:26 CIA-44 bioclipse: ospjuth * r5469 /bioclipse2/trunk/plugins/net.bioclip​se.biomart/src/net/bioclipse/biomart/ (4 files in 2 dirs): Structured filters in treeview according to biomart group and collection.
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