Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-15

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All times shown according to UTC.

Time Nick Message
00:02 CIA-1 jmol: hansonr * r8081 /trunk/Jmol/src/org/opensci​ence/jmol/app/GuiMap.java: 11.3.10 preliminary webExport for application
00:03 CIA-1 jmol: hansonr * r8082 /trunk/Jmol/src/org/openscience/jmol/​Properties/Jmol-resources.properties: 11.3.10 preliminary webExport for application
02:26 CIA-1 jmol: hansonr * r8083 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (7 files): 11.3.10 preliminary webExport for application
05:40 CIA-1 cdk: egonw * r8690 /branches/cdk-1.0.x/patches.txt: Added more recent candidate patches
05:45 jbrefort joined #cdk
06:33 CIA-1 jmol: hansonr * r8084 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (7 files): 11.3.10 preliminary webExport for application
06:40 CIA-1 jmol: hansonr * r8085 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java: 11.3.10 version -- adds export web page
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09:05 mashuuk Hi
09:05 mashuuk anyone here familiar with mass spectrometry ?
09:07 neksa_ changed the nick to neksa
09:10 mashuuk Is software used for protein identification using MS or MSMS finger print ?
09:12 mashuuk I have peptids from enzyme digestion and molecular weight should be specyfic for each peptide.. MS gives that information, why MSMS is commonly used instead ?
09:12 mashuuk And what kind of software uses MSMS data ?
09:13 mashuuk Does it identifiy peptides by its MSMS only.. and then i have to use another software to identify proteins ?
09:17 CIA-1 jmol: nicove * r8086 /trunk/Jmol-FAH/projects/p3623.xyz.gz: Folding@Home
09:20 jpansanel moin
09:22 jpansanel mashuuk : my wife is working in a proteomics lab
09:22 jpansanel She can help
09:24 jbrefort peptide mass is not enough to identify a peptide IMHO
09:24 jbrefort isomers are possible
09:25 jbrefort hence the use of MSMS
09:25 jpansanel It don't give the sequence of the peptide
09:25 mashuuk jpansanel, does your wife use jabber or irc?
09:25 mashuuk jbrefort, hm.. isomers of peptides ?
09:26 jpansanel mashuuk : no, she isn't
09:26 mashuuk jbrefort, you mean becuase of ionisation ?
09:26 jpansanel She uses Mascot for Peptide identification
09:26 jpansanel http://www.matrixscience.c​om/search_form_select.html
09:26 lambdabot2 Title: Matrix Science - Mascot
09:27 jpansanel hum lambdabot2
09:27 mashuuk jpansanel, What Mascot takes on input ?
09:27 mashuuk jpansanel, Raw MSMS ?
09:27 mashuuk jpansanel, and what it gives back ?
09:27 jbrefort mashuuk, two peptides might have the same mass, but not the same formula
09:27 jpansanel raw msms
09:28 mashuuk jbrefort, ok..
09:28 mashuuk jpansanel, and it outputs only a peptide list right ?
09:28 jpansanel gives possible proteins
09:28 jpansanel here is more information:
09:28 jpansanel http://www.matrixscience.com/search_intro.html
09:28 lambdabot2 Title: Matrix Science - Help - Mascot Search Overview
09:28 mashuuk thx
09:32 jpansanel mashuuk : if you are interesting with MS, here are two interesting software :
09:33 jpansanel - massXpert (previously polyXmass) from F. Rusconi (a friend)
09:33 mashuuk jpansanel, only identyfing proteins with MSMS
09:33 jpansanel - IPC http://isotopatcalc.sourceforge.net
09:33 lambdabot2 Title: Isotopic Pattern Calculator
09:34 mashuuk jpansanel, do You know any other software like MascotScan ?
09:34 jpansanel wait, I ask my wife
09:35 mashuuk thanks a lot
09:36 jpansanel she tells me something about Sequest
09:37 jpansanel http://fields.scripps.edu/sequest/
09:37 lambdabot2 Title: SEQUEST Home Page
09:38 jpansanel none of the both software are Free Software
09:41 mashuuk ok thx
09:42 mashuuk So Mascot fits MSMS to single peptide. Then searchs database with peptides and find proteins that contains those peptides.
09:43 mashuuk The more peptides matches protein the more it is probable that its in solution
09:43 mashuuk right ?
09:43 jpansanel right
09:43 jpansanel the scoring function is very important
09:44 mashuuk say thanks to Your wife, and also thanks to You as well :)
09:44 jpansanel thk :)
09:54 jpansanel carsten : kopenbabel works fine
09:54 jpansanel I need only to fixe some stuff with icon addressing
09:56 carsten good good good
10:13 mashuuk jpansanel, one more thing, when Mascot does protein identification. What does it use database for ? for example NBCI. Does database contain information about what type of sequence have what mass ? or only sequences and program is calcualting theoretical masses ?
10:13 mashuuk jpansanel, sorry.. does database contain information what kind of peptides can protein be digested on?
10:37 jpansanel mashuuk : I don't know
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10:39 jpansanel I think you can choose your database
10:39 jpansanel (for example, you can use a local databse)
10:40 jpansanel a little bit of laugh :
10:40 jpansanel http://imgs.xkcd.com/comics/compiling.png
10:44 edrin joined #cdk
10:53 CIA-1 cdk: archvile18 * r8691 /trunk/cdk/src/org/openscience/cdk/test/l​ayout/StructureDiagramGeneratorTest.java: Added test case for bug #1772609 "NPE with bridged rings in SDG/RingPlacer".
10:54 jpansanel he he
10:54 mashuuk :D
10:55 jpansanel new application-science icons of KDE is an erlenmeyer flask
10:55 mashuuk What kind of hardware they use, or what king of project they're working on? :)
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11:58 CIA-1 bioclipse: laszlofischer * r3696 /trunk/plugins/net.bioclipse.jmol/src/net/biocl​ipse/plugins/actions/AbstractScriptAction.java: Enabled to use script action from jmol toolbar, same changes as in AbstractToggleScriptAction.
11:59 CIA-1 bioclipse: laszlofischer * r3697 /trunk/plugins/net.bioclipse.jmol/​src/net/bioclipse/plugins/actions/ (3 files): Some new actions for easier animation in jmol.
12:08 CIA-1 bioclipse: laszlofischer * r3698 /trunk/plugins/net.bioclipse/src/n​et/bioclipse/util/ImageUtils.java: Method to access icons for jmol toolbar.
12:08 CIA-1 bioclipse: laszlofischer * r3699 /trunk/plugins/net.bioclipse/icons/view/ (next.gif play.gif previous.gif): New icons for toolbar.
12:41 CIA-1 bioclipse: laszlofischer * r3700 /trunk/plugins/net.bioclipse.jmol/src/ne​t/bioclipse/plugins/views/JmolView.java: Added buttons.
12:49 CIA-1 jmol: hansonr * r8087 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (PopInJmol.java ScriptButtons.java WebExport.java): 11.3.10 version -- adds export web page
13:09 CIA-1 jmol: hansonr * r8088 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java: 11.3.10 version -- adds export web page
13:45 CIA-1 jmol: hansonr * r8089 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (4 files): 11.3.10 version -- adds export web page
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14:11 CIA-1 jmol: hansonr * r8090 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java: 11.3.10 version -- adds export web page
14:11 laszlof joined #cdk
14:39 CIA-1 cdk: fichte01 * r479 /trunk/protonprediction/Data/output2/ (16 files):
15:05 CIA-1 jmol: hansonr * r8091 /trunk/Jmol/src/org/ (3 files in 2 dirs): 11.3.10 version -- adds export web page
15:10 CIA-1 jmol: hansonr * r8092 /trunk/Jmol/build.xml: 11.3.10 version -- adds export web page
16:29 carsten joined #cdk
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17:24 egonw moin
19:00 CIA-1 cdk: egonw * r8692 /trunk/cdk/src/org/openscience/cdk/ (4 files in 4 dirs): Having a go at sulphur atom typing
19:09 CIA-1 cdk: egonw * r8693 /trunk/cdk/src/org/openscience/cdk/ (4 files in 4 dirs): Added H atom type perception
19:09 CIA-1 cdk: egonw * r8694 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Better error reporting for atom type perception and its testing
19:12 mashuuk joined #cdk
19:12 mashuuk Hi
19:13 egonw hi mashuuk
19:14 mashuuk BLOSUM matrix is calculated from log of observed probabilyty of substitution divided by expected. I dont understand how to calculat expected
19:14 mashuuk I am trying to read somewhere about it..
19:14 egonw sorry... outside my knowledge base
19:16 mashuuk Ok I found it..
19:16 mashuuk http://helix.mcmaster.ca/721/distance/node10.html
19:16 lambdabot2 Title: BLOSUM Matrices
19:19 * egonw is leaving... cu tomorrow
21:14 mashuuk joined #cdk
21:14 mashuuk Hi
21:14 mashuuk anyone here familiar with R /

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