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HIV Study Tutorial
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HIV Disease Progression - Demo Study-ViralLoad (NASBA Method)-2019-04-11-0937.tsv

Participant ID Date Day ViralLoad (NASBA Method) Treatment Group ARVRegime Type 101344 4/30/2008 3 100 ARV ETR 101344 5/28/2008 31 193324 ARV ETR 101344 6/25/2008 59 59582 ARV ETR 101344 7/23/2008 87 702 ARV ETR 101344 8/20/2008 115 309 ARV ETR 101344 9/17/2008 143 720 ARV ETR 101344 10/15/2008 171 287 ARV ETR 101344 11/12/2008 199 183 ARV ETR 101344 12/10/2008 227 149 ARV ETR 101344 1/7/2009 255...

"labkey.log" attached to message "HTTP 500 Bad SQL Grammar by SqlScriptRunner during module update on LabKey startup RHEL 7.3"

INFO ModuleLoader 2017-04-05 23:20:53,578 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2017-04-05 23:20:58,263 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

Sample ID Naming

Each Sample and Source in the system must have a unique name/id within its type. The unique names can be provided by the user, or can be generated by the system. When you ask the system to generate names, you specify a Naming Pattern to use. For each type, you will choose one of these two options. If you already use a unique naming structure outside the system, you will want to ensure those names...

"labkey_log.txt" attached to message "500 error trying to export a large query"

INFO DataSetDefinition 2011-09-27 09:46:44,914 TP-Processor11 : imported InfImmRec : 0.004s INFO DataSetDefinition 2011-09-27 09:46:55,738 TP-Processor1 : imported InfImmRec : 0.005s INFO DataSetDefinition 2011-09-27 09:48:00,614 TP-Processor1 : imported InfImmRec : 0.004s INFO DataSetDefinition 2011-09-27 09:48:21,426 TP-Processor5...

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...

Troubleshoot Installation and Configuration

In case of errors or other problems when installing and running LabKey Server, first review installation basics and options linked in the topic: config. This topic provides additional troubleshooting suggestions if the instructions in that topic do not resolve the issue. LabKey Logs Log Rotation and Storage Service Startup Must Create labkey-tmp Location Linux Service Troubleshooting...

youtil.R

## # Copyright (c) 2011 Fred Hutchinson Cancer Research Center # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License...

youtil.R

## # Copyright (c) 2011 Fred Hutchinson Cancer Research Center # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License...

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...

"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...

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...

"error.log" attached to message "Error comparing MS2 runs"

ERROR Table 2008-04-22 12:20:05,726 t: http-8080-Processor17 : internalExecuteQuery org.postgresql.util.PSQLException: ERROR: integer out of range at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192)...

"labkey.log" attached to message "Error during configuration"

INFO ModuleLoader 2016-04-04 15:02:46,253 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 15:02:47,552 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

"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...

"labkey.log" attached to message "Remote DataSource Access Error"

INFO ModuleLoader 2016-12-19 17:59:44,325 localhost-startStop-1 : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-12-19 17:59:48,171 localhost-startStop-1 : Attempting to create database "labkey" INFO DbScope 2016-12-19...

"Test.csv" attached to message "List with timestamps unsorted"

Date Time SpO2-O2(%) HR-HR(bpm) RR-RR(rpm) Pulse-Pulse(bpm) 2020-05-13 12:00:04.054 ? 61 2020-05-13 12:00:05.078 154 42 2020-05-13 12:00:06.103 152 40 2020-05-13 12:00:07.127 152 42 2020-05-13 12:00:08.152 150 44 2020-05-13 12:00:09.176 151 45 2020-05-13 12:00:10.201 151 46 2020-05-13 12:00:11.225 151 45 2020-05-13 12:00:12.250 152 47 2020-05-13 12:00:13.274 154 47 ...

"labkey.log" attached to message "Remote DataSource Access Error"

INFO ModuleLoader 2016-12-19 17:59:44,325 localhost-startStop-1 : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-12-19 17:59:48,171 localhost-startStop-1 : Attempting to create database "labkey" INFO DbScope 2016-12-19...

What is the new way to build and include custom modules on a dev machine?

Good morning! I am running the following version of the Labkey server at the moment: [09:26:28]:~/Labkey/release/server svn info Path: . URL: https://hedgehog.fhcrc.org/tor/stedi/branches/modules13.2/server Repository Root: https://hedgehog.fhcrc.org/tor/stedi Repository UUID: a4ab64de-fbdc-0310-83ae-be1847ca59a0 Revision: 27966 Node Kind: directory Schedule: normal Last Changed Author:...

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...