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HIV Study Tutorial
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Biologics: Chain and Structure Formats

Premium Feature — Available with LabKey Biologics LIMS. Learn more or contact LabKey. This topic covers the process of assigning chain and structure formats in Biologics LIMS. Overview Chain Formats Chain Format Syntax Structure Formats Overview After the classification engine has determined the pattern of regions within the sequence, the chain and structure format information that...

"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...

"labkey-errors.log" attached to message "Compare view?"

ERROR ManagerBase 2007-12-20 15:24:09,279 Thread-1 : IOException while loading persisted sessions: java.io.InvalidClassException: org.labkey.api.data.Container; local class incompatible: stream classdesc serialVersionUID = -4897634681326991901, local class serialVersionUID = 2752793104866219513 java.io.InvalidClassException: org.labkey.api.data.Container; local class incompatible: stream...

"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 :...

Error When Setting Up Developer Machine

I've been following the documentation for setting up a developer machine (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine) but I ran into issues in the "Build LabKey" section. When running the command "gradlew deployApp" the build fails immediately after the "Task :server:stageModules" starts. (stacktrace pasted below) The only other inconsistency I found in the guide was in...

HIV Disease Progression - Demo Study-Lab Results-2019-04-11-09492.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 120 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...

06-15A12-IgA-Biotin.xls

ENV1 (31) File Name: 06-15A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 24-Jun-2011, 02:10 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 06-15A12 Signed By: Cory Nathe Document ID: 9999 RP1 PMT (Volts): 738.22 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

06-15A12-IgA-Biotin.xls

ENV1 (31) File Name: 06-15A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 24-Jun-2011, 02:10 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 06-15A12 Signed By: Cory Nathe Document ID: 9999 RP1 PMT (Volts): 738.22 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

06-15A12-IgA-Biotin.xls

ENV1 (31) File Name: 06-15A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 24-Jun-2011, 02:10 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 06-15A12 Signed By: Cory Nathe Document ID: 9999 RP1 PMT (Volts): 738.22 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

06-15A12-IgA-Biotin.xls

ENV1 (31) File Name: 06-15A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 24-Jun-2011, 02:10 PM Reader Serial Number: LX10007031402 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 06-15A12 Signed By: Cory Nathe Document ID: 9999 RP1 PMT (Volts): 738.22 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

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:...

HIV Disease Progression - Demo Study-Lab Results-2019-04-11-0949.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 120 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...

Troubleshoot: Error Messages

If you have encountered errors or other problems when installing and starting LabKey Server, first review this topic: troubleshootingAdmin The list below includes some possible errors, example messages, and common problems with suggested solutions. Database Startup Unsupported JDK Version Postgres Join Collapse Limit Font-related Errors WebSocket Errors Pipeline Serialization Errors...

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...

"Compare_Search_Engine_Proteins_2007-11-16 12_12_32.706.xls" attached to message "IPI repeated in Search Engine Comparison"

Compare Search Engine Proteins Numbers below represent total peptides and unique peptides mapping to each protein in each run. Peptide Filter: (PeptideProphet >= 0.9) AND (Trypic Ends >= 1) Protein Filter: interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml) interact-GLHDLT5B.pep.xml (interact-GLHDLT5B.prot.xml) interact-GLHDLT5A.pep.xml...

"running threads.txt" attached to message "NCBI database - annotatins problem?"

Currently Running Threads ajp-8009-Acceptor-0 (RUNNABLE) ajp-8009-Poller-0 (WAITING) ajp-8009-Poller-1 (WAITING) ajp-8009-Poller-2 (WAITING) ajp-8009-Poller-3 (WAITING) ajp-8009-Poller-4 (WAITING) ajp-8009-Poller-5 (WAITING) ajp-8009-Poller-6 (WAITING) ajp-8009-Poller-7 (WAITING) AnnotLoader7 (WAITING) AnnotLoader8 (WAITING) AWT-Windows (RUNNABLE) BreakpointThread (TIMED_WAITING) ContainerBackgroundProcessor[StandardEngine[Catalina]]...

"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": [...

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...

"labkey.log" attached to message "Error while running trigger script"

INFO ScriptService$Console 2020-04-07 17:59:07,547 io-127.0.0.1-8080-exec-4 : ** evaluating: queries/study/BasicsCase.js INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Getting entries in BasicsCase, success: 33 rows returned. INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Selected rows BasicsCase: INFO ScriptService$Console...