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HIV Study Tutorial
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"build out msg.txt" attached to message "Why build Labkey but the ./build/deploy/modules is empty?"

egatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68) at net.sf.antcontrib.logic.IfTask.execute(IfTask.java:217) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

25 Jan 2007 08:37:45,274 INFO : Mascot search for CAexample_mini.mzXML 25 Jan 2007 08:37:45,274 INFO : ======================================= 25 Jan 2007 08:37:45,326 INFO : MzXML2Search output 25 Jan 2007 08:37:45,326 INFO : ======================================= 25 Jan 2007 08:37:45,330 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 25 Jan 2007 08:37:45,385 INFO : 25 Jan 2007 08:37:45,386...

Error - A failure occurred during LabKey Server startup.

I have been compiling TPP 5.0 on our Linux cluster (running also Labkey Server 16.3) having lot of problem. But an unexpected problem occurred when I found out that the Labkey Server stopped working - Below is the error I receive in web browser. Permissions on logs folder are for tomcat:tomcat drwxr-xr-x. 2 tomcat tomcat 36864 Jun 14 06:12 logs Thanks for any advice. Tomas 500: Unexpected...

"PhysicalExam.xls" attached to page "R Report Builder"

data ParticipantID Date Height Weight Temperature Systolic Diastolic Pulse Respirations ARV? ARVRegimenType 101 2008-05-17 184.4000 86 36.0 129 76 64 17 101 2008-08-04 184.7000 84 37.0 133 79 67 18 101 2008-09-02 183.4000 83 37.0 133 85 68 15 101 2008-11-23 185.3000 80 36.7 135 85 70 14 101 2009-01-18 184.8000 79 36.8 142 90 75 17 101 2009-02-17 185.2000 79 37.3 129 87 79 13 101 2009-03-16...

"FindPeptides mass accuracy.eml" attached to message "An unexpected error occurred"

Return-path: <support@labkey.org> Envelope-to: rune@philosof.dk Delivery-date: Wed, 04 Jun 2008 23:12:08 +0200 Received: from jarcon.fhcrc.org ([140.107.42.30]:60634 helo=smtp.fhcrc.org) by hosting.kollegienet.dk (envelope-from <support@labkey.org>) with esmtp (Exim 4.69) id 1K40H8-0001Gv-Ag for rune@philosof.dk; Wed, 04 Jun 2008 23:12:08 +0200 Received: from bushmaster (BUSHMASTER.FHCRC.ORG...

"build message.txt" attached to message "Build failed"

PS C:\Labkey\LABKEY_HOME\server-23.12.RC0> .\gradlew deployApp -PdeployMode=prod --stacktrace Starting a Gradle Daemon, 1 incompatible and 2 stopped Daemons could not be reused, use --status for details > Task :server:modules:platform-23.12.RC0:assay:compileGwtAssayApplication Loading inherited module 'gwt.AssayApplication' Loading inherited module 'org.labkey.api.gwt.Internal' ...

"QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf.log" attached to message "Mascot searching"

20 maj 2008 13:26:15,186 INFO : Mascot search for QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf 20 maj 2008 13:26:15,187 INFO : ======================================= 20 maj 2008 13:26:15,740 INFO : Check FASTA validity 20 maj 2008 13:26:15,775 INFO : ======================================= 20 maj 2008 13:26:15,848 INFO : 20 maj 2008 13:26:16,108 INFO : MzXML2Search output 20 maj 2008 13:26:16,108...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

01 Feb 2007 11:30:50,922 INFO : Mascot search for CAexample_mini.mzXML 01 Feb 2007 11:30:50,923 INFO : ======================================= 01 Feb 2007 11:30:50,996 INFO : MzXML2Search output 01 Feb 2007 11:30:50,996 INFO : ======================================= 01 Feb 2007 11:30:51,039 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 01 Feb 2007 11:30:51,259 INFO : 01 Feb 2007 11:30:51,259...

"labkey23_cc_clean_build.txt" attached to message "Startup issues with Labkey 2.3 branch"

C:\Suns\SDK\jdk\bin\java -Xmx128m "-Dant.home=C:\Program Files\JetBrains2\IntelliJ IDEA 7.0.1\lib\ant" -Dfile.encoding=windows-1252 -classpath "C:\Program Files\JetBrains2\IntelliJ IDEA 7.0.1\lib\ant\lib\ant-antlr.jar;C:\Program Files\JetBrains2\IntelliJ IDEA 7.0.1\lib\ant\lib\ant-apache-bcel.jar;C:\Program Files\JetBrains2\IntelliJ IDEA 7.0.1\lib\ant\lib\ant-apache-bsf.jar;C:\Program Files\JetBrains2\IntelliJ...

Tutorial: Inferring Datasets from Excel and TSV Files

Use the following step-by-step instructions to quickly create and import study datasets from Excel and/or TSV files. This method of creating datasets via study folder import is especially useful for any of the following scenarios: You want to avoid manually defining all the fields in all your study datasets. You want to define and import study datasets as an initial, one-time job, and then develop...

"cpas.log" attached to message "Example1.xar.xml"

20 Jan 2006 09:25:45,234 DEBUG ModuleLoader : ModuleLoader init 20 Jan 2006 09:25:45,590 DEBUG CoreModule : Ensuring databases are present 20 Jan 2006 09:25:45,686 DEBUG CoreModule : Attempting to create database cpas 20 Jan 2006 09:25:47,631 DEBUG CoreModule : Just created "cpasDataSource" database; attempting to run bootstrap script. 20 Jan 2006 09:25:47,679 INFO DbSchema :...

Can't access web server after installing on Windows machine: HTTP Status 404 - Requested Resource Not Available

Hello all, I just installed LabKey using the Windows stand-alone installer, however, upon trying to open the webpage - http://localhost:8080/labkey/, I receive the following error: HTTP Status 404 - Requested Resource Not Available. I've attached a screenshot. I am running Windows 7 on a virtual machine (VMWare) from my Macbook Pro. I should note that I also have SAS 9.4 installed, and when I try...

10-13A12-IgA-Biotin.xls

ENV1 (31) File Name: 10-13A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 15-Jul-2011, 01:37 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 10-13A12 Signed By: Elizabeth Van Nostrand Document ID: 9997 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100...

10-13A12-IgA-Biotin.xls

ENV1 (31) File Name: 10-13A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 15-Jul-2011, 01:37 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 10-13A12 Signed By: Elizabeth Van Nostrand Document ID: 9997 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100...

10-13A12-IgA-Biotin.xls

ENV1 (31) File Name: 10-13A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 15-Jul-2011, 01:37 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 10-13A12 Signed By: Elizabeth Van Nostrand Document ID: 9997 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100...

10-13A12-IgA-Biotin.xls

ENV1 (31) File Name: 10-13A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 15-Jul-2011, 01:37 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 10-13A12 Signed By: Elizabeth Van Nostrand Document ID: 9997 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100...

Running test data set

Hi, I have been assigned a project which involves analysis and evaluation of CPAS in proteomics lab. I installed CPAS successfully and even ran the test dataset that came along with it. Today i tried to ran some different datasets, however, when i assign proper path to data file and to database file, and i return to pipeline module to upload and run, folders are shown, but when i click on the datafile...

01-11A12b-IgA-Biotin.xls

ENV1 (31) File Name: 01-11A12b-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 21-Jun-2011, 01:47 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 01-11A12b Signed By: Elizabeth Nelson Document ID: 9994 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group...

01-11A12b-IgA-Biotin.xls

ENV1 (31) File Name: 01-11A12b-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 21-Jun-2011, 01:47 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 01-11A12b Signed By: Elizabeth Nelson Document ID: 9994 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group...

01-11A12b-IgA-Biotin.xls

ENV1 (31) File Name: 01-11A12b-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 21-Jun-2011, 01:47 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 01-11A12b Signed By: Elizabeth Nelson Document ID: 9994 RP1 PMT (Volts): 738.95 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group...