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HIV Study Tutorial
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"Physical Exam works.xlsx" attached to message "Unable to import dates"

data ParticipantID Date SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Height Weight ARVRegimenType Pregnancy Language Signature 133428 2008-08-15 131 91 72 15 165 81.5 NVP-XR FALSE English TRUE 133428 2008-10-10 145 104 67 17 165 78.5 NVP-XR FALSE English TRUE 133428 2009-09-11 132 114 66 20 165 82.5 NVP-XR FALSE English TRUE 133428 2009-11-06 163 90 76 20 165 82.5 NVP-XR FALSE...

"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...

"comet_error_log_file.txt" attached to message "Error: Failed to locate comet/tandem."

10 Oct 2018 23:37:05,289 INFO : Comet search for AG_MAP_Plasma_Bound_F1 10 Oct 2018 23:37:05,289 INFO : ======================================= 10 Oct 2018 23:37:05,305 INFO : AG_MAP_Plasma_Bound_F1.mzXML 10 Oct 2018 23:37:05,336 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check' 10 Oct 2018 23:37:05,336 INFO : Check FASTA validity 10 Oct...

"CPAS for Proteomics ASMS 2007.ppt" attached to message "ASMS Presentations"

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CPAS Comparative Proteomics Analysis System Adam Rauch LabKey Software adam@labkey.com How many from different institution? How many expect to run analysis against raw data v. use proteomics lab? What Is CPAS? A proteomics analysis system that handles all data processing & management for high-throughput labs and core facilities Designed from the start to manage all data processing in high-through...

"labkey-different-hang.txt" attached to message "Server not starting"

/Library/Java/JavaVirtualMachines/jdk1.8.0_92.jdk/Contents/Home/bin/java -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:62664,suspend=y,server=n -Dcatalina.base=./ -Dcatalina.home=./ -Djava.io.tmpdir=./temp -Ddevmode=false -Dsun.io.useCanonCaches=false -Xmx1G -XX:MaxPermSize=512M -classpath "./bin/bootstrap.jar:./bin/tomcat-juli.jar:/Applications/IntelliJ IDEA.app/Contents/lib/idea_rt.jar" -javaagent:...

"data_run2.xls" attached to page "Exploring Laboratory Data"

data ParticipantID VisitID Date WBC MCV HGB 101 7/10/08 4540 159 14.2 202 10/4/08 5442 224 11.4 303 7/20/08 4145 205 15.2 404 10/4/08 3202 187 14.1 505 7/10/08 5141 141 19.2 606 10/4/08 4220 152 15.3 101 11/18/08 10562 173 13.5 202 7/25/08 5210 146 17 303 3/10/09 7369 143 17.9 404 7/18/08 9156 95 18.1 505 3/31/09 10674 106 17.9 606 1/20/09 5233 107 16.1 101 1/20/09 8931...

"Advanced CPAS ASMS 2007.ppt" attached to message "ASMS Presentations"

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Advanced CPAS Adam Rauch LabKey Software adam@labkey.com How many from different institution? How many expect to run analysis against raw data v. use proteomics lab? Agenda Demo of recent & advanced features Pipeline architecture & configuration Production installations What Is CPAS? A proteomics analysis system that handles all data processing & management for high-throughput labs...

MASCOT on a remote server, Database error

We were trying to use MASCOT on CPAS, all the required information, i.e. Mascot server, user name and password were entered correctly, and then we tested using the given test option in CPAS. CPAS did not gave any error. I went to pipeline and setup a directory of data. I clicked on Process and Upload Data. That gave me a button to do "Mascot Peptide Search." I clicked on that. That took me to a "Search...

"CPAS for Proteomics ASMS 2006.ppt" attached to message "ASMS Presentations"

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CPAS for Proteomics Research Adam Rauch LabKey Software adam@labkey.com CPAS Computational Proteomics Analysis System Free web-based system for processing, storing, and analyzing results of MS/MS experiments Key goals: Handle high-throughput processing and analysis of results Automate & control data pipeline from instrument to analysis Provide universal access to results and support collaboration...

"labkey-20171024.log" attached to message "Trouble loading assay"

INFO DbScope 2017-10-23 17:13:39,149 p-apr-0.0.0.0-80-exec-23 : no schema metadata xml file found for schema "assayresult" INFO DbScope 2017-10-23 17:13:39,149 p-apr-0.0.0.0-80-exec-23 : Shouldn't be loading metadata for Provisioned schema "assayresult" WARN Table 2017-10-24 02:00:00,251 QuartzScheduler_Worker-3 : SQL Exception org.postgresql.util.PSQLException:...

Configuration error deteced at LabKey Server Startup

Hello,   I am trying to install a local LabKey server on a machine running CentOS 6. I went through the installation steps, but am receiving this error when I go to open labkey in my browser. Also, I am only able to start up postgres when I am logged in as root; does this have something to do with the error? I am relatively new to Linux so please bear with me.   org.labkey.api.util.ConfigurationException:...

Creating New Modules

Hi guys, Wondering if I can get any guidance on coding my own module. I've compiled 1.4 from source code, tinkered with the demo module, and taken a look at the build scripts. As a first step, I copied the demo module into another directory in the modules folder and modified the build script: added <antcall target="myModule"/> to "build_module_classes" target 2. added   <target name="myModule"...

lin_384_well_metadata.xls

data SampleWellGroup PlateLocation SpecimenID ParticipantID VisitID Date SampleDescription Lot Number InitialDilution Factor Method Specimen 1 A3-A4 4E10 Antibody Lot 1 10 3 Concentration Specimen 2 B3-B4 2F5 Antibody Lot 1 10 3 Concentration Specimen 3 C3-C4 2G12 Antibody Lot 1 10 3 Concentration Specimen 4 D3-D4 sCD4 Antibody Lot 1 10 3 Concentration Specimen 5 E3-E4 HIVIG Antibody...

"getContainers-atlas-test.txt" attached to message "Strange behavior with LABKEY.Security.getContainers() function"

https://atlas-test.scharp.org/cpas/project/HVTN/Specimen%20Management/Lab%20Program/begin.view? https://atlas-test.scharp.org/cpas/project/HVTN/getContainers.view?_dc=1348616911600&container=%2FHVTN%2FSpecimen%20Management%2FLab%20Program%2F&includeSubfolders=false _dc=1348616911600 container=/HVTN/Specimen Management/Lab Program/ includeSubfolders=false { "sortOrder": 0, "children": [...

Fail to run labkey. Failed to start component [SOLVED]

Dear All, I have tried to install Labkey server but without any success. When i enter the adress localhost:8080/labkey i have this error in the tomcat manager. I use java 8, tomcat 8.5 on a debian stretch. If anyone can help i would be very grateful. I found the installation very complicated. THanks a lot, Bests, Thierry Hi Theirry, Can you send us the full catalina and labkey log...

"labkey20180611.log" attached to message "Assay run imports are successful, but no data rows are visible"

INFO ModuleLoader 2018-03-30 16:38:25,393 main : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR DbScope 2018-03-30 16:38:27,675 main : Connection to "labkeyDataSource" at jdbc:postgresql://localhost/labkey failed...

Luminex_Assay_200-2015-06-09-1230.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_200-2015-06-09-1237.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_200-2015-06-09-1229.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_200-2015-06-09-1233.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...