Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-06

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All times shown according to UTC.

Time Nick Message
04:09 egonw joined #bioclipse
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08:32 edrin joined #bioclipse
08:32 edrin hi
08:33 edrin i submitted the proposal to the stpeter
08:33 edrin -
08:33 edrin do you know what a bootstrap (bioinformatics/phylogenetic tree) is? can you explain this in simple words to me?
08:35 egonw yes
08:35 egonw bootstrap, from bootstrapping
08:35 egonw is the process where you pull yourself up using your bootstraps
08:36 egonw thus, refers to a process which depends that the end situation already exists...
08:36 egonw it's like compiling a compiler both written in the same language
08:36 egonw ... with itself
08:36 edrin ok
08:37 edrin when i calculate a phylogenetic tree, what do the bootstrap values tell me?
08:37 egonw applied to statistics, it's a method to estimate the standard error on some distribution, without actually having a distribution
08:37 edrin ok
08:37 egonw the bootstrap will typically tell you something about the robustness of your model, tree in this case
08:38 egonw this is done by repeatedly sample (with replacement!) from your input data...
08:38 egonw this will get you 999+ trees
08:38 egonw which gets you your distribution you did not have earlier
08:38 egonw allowing you to calculate means (often biased) and a standard error (typically *not* biased)
08:38 egonw the latter can be shown mathematically IIRC
08:39 edrin ok
08:41 edrin how is the program doing this? it just takes some partial sequence of each protein and aligns it to the rest. this it does several times with taking yet another subsequence of some proteinsequence... and then it just accumulates the results and gives me some values?
08:41 egonw possibly...
08:41 edrin ok
08:41 egonw simplest would be to just sample whole sequences
08:42 egonw one sequence, one object
08:42 egonw then sample from the objects
08:42 egonw that's what normally is done...
08:42 egonw but subsequence sampling sounds interesting too
08:43 * egonw will be afk
08:43 egonw bbl
08:48 edrin thank you :)
10:06 egonw joined #bioclipse
13:51 CIA-46 bioclipse: miguelrojasch * r5808 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.jchempaint/src/net/bioclipse/cdk10/business/ (CDK10Manager.java CDK10Reaction.java RDFWriter.java): added method to handle reactions into CDK10Manager
13:56 rojasm where can I add a file in this rdf format into the repository?
14:18 egonw rojasm: net.bioclipse.data.sampledata/ I think
14:32 edrin stupid. i designed my sequencing primer in the wrong direction and now I got the sequence of plasmids resistance cassette!
16:12 rojasm joined #bioclipse
16:19 CIA-46 bioclipse: miguelrojasch * r5809 /bioclipse2/trunk/plugins/ (67 files in 17 dirs): added new plugin to visualize reaction in a table
16:23 rojasm kake
16:23 rojasm I missed the name of the file
16:25 CIA-46 bioclipse: miguelrojasch * r5810 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.rdfeditor/: added name file. I missed completely
16:31 CIA-46 bioclipse: miguelrojasch * r5811 /bioclipse2/trunk/plugins/src/: missed the correct path
16:32 CIA-46 bioclipse: miguelrojasch * r5812 /bioclipse2/trunk/plugins/icons/: missed the correct path
16:32 CIA-46 bioclipse: miguelrojasch * r5813 /bioclipse2/trunk/plugins/META-INF/: missed the correct path
16:34 CIA-46 bioclipse: miguelrojasch * r5814 /bioclipse2/trunk/plugins/bin/: missed the correct path
16:51 CIA-46 bioclipse: miguelrojasch * r5815 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.rdfeditor/ (33 files in 11 dirs): New plugin showing rdf fields into a table together with their properties
16:54 CIA-46 bioclipse: miguelrojasch * r5816 /bioclipse2/trunk/plugins/net.bioclipse.data.sa​mpledata/data/reactions/qsar-reaction-test.rdf: added a rdf file containing a list of rxn reactions
17:26 edrin left #bioclipse
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