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HIV Study Tutorial
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"labkey.log" attached to message "FastaAdmin already exists"

INFO ModuleLoader 2015-09-15 13:33:36,894 localhost-startStop-1 : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2015-09-15 13:33:39,144 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

"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...

dataset5007.tsv

ParticipantId date QCStateLabel CD4 Lymphocytes Hemoglobin ViralLoad 101344 2008-04-30 00:00:00.0 811 1491 14.0 101344 2008-05-28 00:00:00.0 794 1446 13.0 101344 2008-06-25 00:00:00.0 653 1560 12.0 101344 2008-07-23 00:00:00.0 1176 1486 11.0 101344 2008-08-20 00:00:00.0 1292 1343 11.0 101344 2008-09-17 00:00:00.0 1210 1186 12.0 101344 2008-10-15 00:00:00.0 1158 1320 13.0 101344 2008-11-12...

"labkey.log" attached to message "MS SQL Server setup"

INFO ModuleLoader 2015-09-24 07:53:54,391 localhost-startStop-1 : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2015-09-24 07:53:57,657 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

"CompareRuns_QueryBeta_2007-11-16 12_40_25.034.xls" attached to message "IPI repeated in Search Engine Comparison"

data Best Name Seq Id Description First IPI interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) Group interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) Prob interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) Peptides interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml) Group interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml) Prob interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml)...

HIV Disease Progression - Demo Study-Lab Results-2019-04-11-0948.tsv

ParticipantId sourcelsid date Day DataSets/Demographics/Gender oldcd4 Lymphocytes Hemoglobin DataSets/Demographics/Group DataSets/Demographics/TreatmentGroup CD4 119180 4/20/2008 0 f 239 1802 17 Group 1: Acute HIV-1 No ARV 119.5 119180 5/18/2008 28 f 266 1787 18 Group 1: Acute HIV-1 No ARV 133 119180 6/15/2008 56 f 224 1843 19 Group 1: Acute HIV-1 No ARV 112 119180 7/13/2008 84 f 163 1780 17 Group...

Lab Results.xls

data ParticipantID Source_Lsid Date Day CD4+ Lymphs Hemoglobin Cohort Viral_Load 101344 2009-03-04 311 1570 1455 15.0 101344 2008-04-30 3 811 1491 14.0 101344 2008-07-23 87 1176 1486 11.0 101344 2008-08-20 115 1292 1343 11.0 101344 2008-09-17 143 1210 1186 12.0 101344 2008-10-15 171 1158 1320 13.0 101344 2008-11-12 199 1059 1442 14.0 101344 2008-12-10 227 772 1591 15.0 101344 2009-01-07...

Lab Results.xls

data Participant ID Source Lsid Date Day CD4+ (cells/mm3) Lymphs (cells/mm3) Hemoglobin Cohort Viral Load 101344 2009-03-04 311 1570 1455 15.0 101344 2008-04-30 3 811 1491 14.0 101344 2008-07-23 87 1176 1486 11.0 101344 2008-08-20 115 1292 1343 11.0 101344 2008-09-17 143 1210 1186 12.0 101344 2008-10-15 171 1158 1320 13.0 101344 2008-11-12 199 1059 1442 14.0 101344 2008-12-10 227...

"catalina.out" attached to message "Upgrade to 19.1 and Java upgrade on Linux"

Jul 15, 2015 2:34:02 PM org.apache.catalina.startup.SetAllPropertiesRule begin WARNING: [SetAllPropertiesRule]{Server/Service/Connector} Setting property 'maxSpareThreads' to '75' did not find a matching property. Jul 15, 2015 2:34:02 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server version: Apache Tomcat/7.0.63 Jul 15, 2015 2:34:02 PM org.apache.catalina.startup.VersionLoggerListener...

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

01 Feb 2007 12:39:41,243 INFO : Mascot search for CAexample_mini.mzXML 01 Feb 2007 12:39:41,243 INFO : ======================================= 01 Feb 2007 12:39:41,338 INFO : MzXML2Search output 01 Feb 2007 12:39:41,338 INFO : ======================================= 01 Feb 2007 12:39:41,342 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 01 Feb 2007 12:39:41,419 INFO : 01 Feb 2007 12:39:41,420...

HIV Disease Progression - Demo Study-Lab Results-2019-04-11-0952.tsv

ParticipantId date QCStateLabel CD4 Lymphocytes Hemoglobin ViralLoad 101344 2008-04-30 00:00:00.0 811 1491 14.0 101344 2008-05-28 00:00:00.0 794 1446 13.0 101344 2008-06-25 00:00:00.0 653 1560 12.0 101344 2008-07-23 00:00:00.0 1176 1486 11.0 101344 2008-08-20 00:00:00.0 Not Yet Reviewed 1292 1343 11.0 10000 101344 2008-09-17 00:00:00.0 1210 1186 12.0 101344 2008-10-15 00:00:00.0 1158 1320...

"cpas[1].log.1" attached to message "CPAS MS2 problem"

24 Feb 2006 21:08:31,570 DEBUG FastaDbLoader : Fri Feb 24 21:08:31 PST 2006 Entering insertIdentifiers, before collecting unparsed identifiers from temp table 24 Feb 2006 21:09:20,804 DEBUG FastaDbLoader : Fri Feb 24 21:09:20 PST 2006 In insertIdentifiers, before inserting parsed identifier batch into temp table 24 Feb 2006 21:09:24,773 DEBUG FastaDbLoader : Fri Feb 24 21:09:24 PST 2006 In insertIdentifiers,...

"ms2.module" attached to message "Sequest Fractions XAR import failed"

META-INF/MANIFEST.MF Manifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_04-b05 (Sun Microsystems Inc.) ModuleClass: org.labkey.ms2.MS2Module SVNRevision: 9275 SVNURL: https://hedgehog.fhcrc.org/tor/stedi/branches/release8.2/server BuildUser: jeckels BuildTime: August 7 2008, 10:25 AM BuildOS: Windows 2003 BuildPath: D:\\release8.2\\server\\modules\\ms2 (הלא�ט+ו�¦���_��¬¦���¦...

Luminex_Assay_200-2015-06-09-1237.tsv

container date wellRole fiBackgroundNegative stdCurve fiOORIndicator specimenID type singlePointControl excluded samplingErrors protocol regressionType outlier resVar fiBackground fiBackgroundString dilution name extraSpecimenInfo stdDevOORIndicator expConc stdDev maxStandardRecovery obsConc fi obsConcOORIndicator minStandardRecovery obsConcString beadCount description lsid dataId fiString obsOverExp...

Luminex_Assay_200-2015-06-09-1221.tsv

container date wellRole fiBackgroundNegative stdCurve fiOORIndicator specimenID type singlePointControl excluded samplingErrors protocol regressionType outlier resVar fiBackground fiBackgroundString dilution name extraSpecimenInfo stdDevOORIndicator expConc stdDev maxStandardRecovery obsConc fi obsConcOORIndicator minStandardRecovery obsConcString beadCount description lsid dataId fiString obsOverExp...

"09FEB02_OT_57.log" attached to message "Java Heap Memory Errors"

03 Nov 2010 17:25:47,334 INFO : Starting to run task 'org.labkey.ms2.pipeline.mascot.MascotSearchTask' at location 'webserver' 03 Nov 2010 17:25:47,334 INFO : Copying E:\Sandy\Dhaval\Controls\@files\Control\09FEB02_OT_57.mzXML to E:\Sandy\Dhaval\Controls\@files\Control\mascot\PSD_protocol_Copy9\09FEB02_OT_57.work\09FEB02_OT_57.mzXML 03 Nov 2010 17:25:47,397 INFO : MzXML2Search output 03 Nov 2010...

HIV Disease Progression - Demo Study-ViralLoad (NASBA Method)-2019-04-11-0936.tsv

Participant ID Date Day ViralLoad (NASBA Method) Treatment Group ARVRegime Type 101344 39568 3 100 ARV ETR 101344 39596 31 193324 ARV ETR 101344 39624 59 59582 ARV ETR 101344 39652 87 702 ARV ETR 101344 39680 115 309 ARV ETR 101344 39708 143 720 ARV ETR 101344 39736 171 287 ARV ETR 101344 39764 199 183 ARV ETR 101344 39792 227 149 ARV ETR 101344 39820 255 99 ARV ETR 101344 39848 283 1980 ARV ETR 101344...

dataset5006.tsv

ParticipantId date QCStateLabel HIVWestern HIVStdAntibody HIVLoadIneq HIVLoadQuant HIVLoadQual HIVRapidTest HIVSourceLab 103866 2008-04-30 00:00:00.0 0 103866 2008-05-28 00:00:00.0 183255 103866 2008-06-25 00:00:00.0 38618 103866 2008-07-23 00:00:00.0 7774 103866 2008-08-20 00:00:00.0 3125 103866 2008-09-17 00:00:00.0 2489 103866 2008-11-12 00:00:00.0 ...

HIV Test Results.xls

data Participant ID Group Assignment Country Gender Start Date Height Source Lsid Date Day HIV Western Blot Standard HIV Antibody Viral Load > = < Viral Load Quantified (copies/ml) Viral Load Qualitative Result HIV Rapid Blood Test Source of HIV Tests 103866 Group 1: Acute HIV-1 USA m 2008-04-21 69 2009-05-27 401 3 103866 Group 1: Acute HIV-1 USA m 2008-04-21 69 2009-06-24 429 15 103866...

"mixture.txt" attached to message "msInspect"

# algorithm=org.fhcrc.cpas.tools.FeatureStrategyCombined # date=Wed Jan 25 18:23:44 EST 2006 # java.vendor=Sun Microsystems Inc. # java.version=1.5.0_06 # revision=2395 # user.name=piecheng scan time mz accurateMZ mass intensity charge chargeStates kl background median peaks scanFirst scanLast scanCount totalIntensity description 56 55.014 521.0833 false 0.0 7.0122375 0 1 -1.0 5.063446 0.0...