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HIV Study Tutorial
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08-12A12-IgA-Biotin.xls

ENV1 (31) File Name: 08-12A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 25-Jun-2011, 04:16 PM Reader Serial Number: LX10011084403 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 08-12A12 Signed By: Steve Hanson Document ID: 9995 RP1 PMT (Volts): 684.74 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

08-12A12-IgA-Biotin.xls

ENV1 (31) File Name: 08-12A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 25-Jun-2011, 04:16 PM Reader Serial Number: LX10011084403 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 08-12A12 Signed By: Steve Hanson Document ID: 9995 RP1 PMT (Volts): 684.74 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

08-12A12-IgA-Biotin.xls

ENV1 (31) File Name: 08-12A12-IgA-Biotin.srbx Analyte: ENV1 (31) Acquisition Date: 25-Jun-2011, 04:16 PM Reader Serial Number: LX10011084403 Standard Lot: Standard1 Expiration Date: <none> Plate ID: 08-12A12 Signed By: Steve Hanson Document ID: 9995 RP1 PMT (Volts): 684.74 RP1 Target: 16357 Analyte Type Well Description FI FI - Bkgd Std Dev %CV Obs Conc Exp Conc (Obs/Exp) * 100 Group Ratio...

Reagents.tsv

Key Reagent 1 AD-mix 2 Acetyl chloride 3 Aluminium chloride 4 Armstrong's acid 5 Azobisisobutyronitrile 6 9-Borabicyclononane 7 Benzyl chloroformate 8 Benzyltrimethylammonium fluoride 9 1,8-Bis(dimethylamino)naphthalene 10 (Bis(trifluoroacetoxy)iodo)benzene 11 Bis(trimethylsilyl)acetamide 12 Bis(trimethylsilyl)amine 13 N-Bromosuccinimide 14 Burgess reagent 15 Tert-Butyl hydroperoxide 16 N-Butyllithium...

"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...

org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist Position: 681

org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist   Position: 681        at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231)        at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)...

Dataset Properties

The properties of a dataset include how it is keyed, categorized, and shown or shared. Dataset Properties Page Action Buttons Edit Dataset Properties Data Row Uniqueness Additional Key Fields Using Time as an Additional Key Advanced Settings Edit Dataset Fields Dataset Properties Page Administrators can view and edit dataset properties either by clicking the name of a dataset...

List - Index out of Range Error

hi, I am running 17.2 on our development server, and though I can create lists I can't populate them with data. Whenever I try, I get an index out of range error. I am not sure what's causing this. Any suggestions would be welcome. Thanks, bront -- from labkey.log INFO ScriptService$Console 2017-08-10 16:19:35,306 ajp-nio-8009-exec-5 : RhinoEngine.createTopLevel: initialize...

Minimum permissions for Tomcat's conf directory

On Linux, is it possible to run LabKey with Tomcat's conf directory as read-only? It is usually recommended to make this directory read-only (The user running Tomcat is the owner of this directory and its contents, with permissions 0400)? I've tried it out and was unable to reach LabKey's homepage and had to revert back to 0740, but I would still like to restrict how the configuration files are able...

dataset5004.tsv

ParticipantId date QCStateLabel Weight_kg Temp_C SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Signature Pregnancy Language ARV ARVtype height_cm 101344 2008-04-27 00:00:00.0 68 37.0 117 83 61 173.0 101344 2008-05-25 00:00:00.0 69 36.8 145 103 71 175.0 101344 2008-06-22 00:00:00.0 71 38.2 166 101 68 175.0 101344 2008-08-17 00:00:00.0 73 36.5 125 95 74 ...

"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...

Sample Finder

This topic describes how to find samples in bulk using sample properties, attributes of their deriveSamples or associateSources, or in the Professional Edition, based on related assays. The Sample Finder helps you build a set of criteria to find samples of interest across all the Sample Types in your system. For example, you might want to find all samples of different types from a specific source...

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...

Step 5: Link Luminex Data to Study

Premium Feature — Available upon request with all Premium Editions of LabKey Server. Learn more or contact LabKey. Linking assay data into a study allows you to integrate it with other types of data from other sources. If you wish, you can skip this step and proceed to the next Luminex tutorial: advancedLuminexTutorial. In the steps below, we move selected, quality-controlled Luminex assay data...

FASTA parsing and Gene name

Dear Labkey, I'm using the mouse Complete Proteome Set as my FASTA, which contains a mixture of SwissProt and TrEMBL entries. It would be a massive help if the FASTA file is parsed to reconise GN= as the text that specifies the gene name which can then be viewed in MS dashboard. As the system is currently set up very few entries appear under the Heading 'Best gene name' Can this be achieved? ...

"Physical Exam doesnt work.xls" 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 16 165 67.5 NVP-XR English 133428 2008-10-10 145 104 67 19 165 83.5 NVP-XR English 133428 2009-09-11 132 114 66 12 165 89.5 NVP-XR English 133428 2009-11-06 163 90 76 14 165 71.5 NVP-XR English 133428 2009-12-04 164...

"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...

Filter Data

You can filter data displayed in a grid to reduce the amount of data shown, or to exclude data that you do not wish to see. By default, these filters only apply for the current viewer and session, but filters may be saved as part of a grid view if desired. Filter Column Values Filter by Value Filtering Expressions Filter Value Variables Persistent Filters Faceted Filtering Understand...

"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...

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

ERROR LuceneSearchServiceImpl 2017-10-23 16:54:11,638 Module Upgrade : Error: Unable to initialize search index. Search will be disabled and new documents will not be indexed for searching until this is corrected and the server is restarted. java.nio.channels.OverlappingFileLockException at sun.nio.ch.SharedFileLockTable.checkList(FileLockTable.java:255) at sun.nio.ch.SharedFileLockTable.add(FileLockTable.java:152)...