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HIV Study Tutorial
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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...

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:...

Interactive Example - Study-MedicalHistory-2019-04-09-1616.tsv

Participant ID Date city state zip DOB PrimaryCarePhysician LastMedicalExam LastEyeDoctor LastEyeExam ContactByEmail Phone Occupation DrugAllergy CurrentMedication Married 101344 2008-04-27 Sparks NV 89436 3/15/1963 Upton Hundall 7/4/1969 3/16/1969 2/8/1972 FALSE 775-643-7120 Senior Developer Miconazole Nitrate Willow Fern TRUE 103505 2008-04-24 Lakeland FL 33811 11/19/1959 Alicia Grunson 5/11/1989...

Interactive Example - Study-Medical History-2019-04-09-1614.tsv

Participant ID Date city state zip DOB PrimaryCarePhysician LastMedicalExam LastEyeDoctor LastEyeExam ContactByEmail Phone Occupation DrugAllergy CurrentMedication Married 101344 2008-04-27 Sparks NV 89436 3/15/1963 Upton Hundall 7/4/1969 3/16/1969 2/8/1972 FALSE 775-643-7120 Senior Developer Miconazole Nitrate Willow Fern TRUE 103505 2008-04-24 Lakeland FL 33811 11/19/1959 Alicia Grunson 5/11/1989...

"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 ...

"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...

"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�¦���_��¬¦���¦...

"rebuild.txt" attached to message "gradle build: intellij hot swapping not working anymore?"

Information:java: Errors occurred while compiling module 'api_main' Information:javac 1.8.0_131 was used to compile java sources Information:12/11/2017 1:50 PM - Compilation completed with 41 errors and 1,085 warnings in 24m 15s 511ms C:\discvr17.2\externalModules\snprcEHRModules\snprc_r24\resources\transform\src\MicrobiomeTransform.java Warning:Warning:line (46)java: getCellType() in org.apache.poi.ss.usermodel.Cell...

"cleavableICAT_ms2x2_2.log" attached to message "MASCOT on a remote server, Database error"

30 Mar 2007 11:56:15,545 INFO : Mascot search for cleavableICAT_ms2x2_2.mzXML 30 Mar 2007 11:56:15,546 INFO : ======================================= 30 Mar 2007 11:56:48,260 INFO : MzXML2Search output 30 Mar 2007 11:56:48,260 INFO : ======================================= 30 Mar 2007 11:56:50,128 INFO : running: MzXML2Search -mgf cleavableICAT_ms2x2_2.mzXML 30 Mar 2007 11:56:50,151 INFO : 30 Mar...

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

25 Jan 2007 08:40:34,716 INFO : Mascot search for SmallICAT.mzXML 25 Jan 2007 08:40:34,716 INFO : ======================================= 25 Jan 2007 08:40:34,781 INFO : MzXML2Search output 25 Jan 2007 08:40:34,781 INFO : ======================================= 25 Jan 2007 08:40:34,885 INFO : running: MzXML2Search -mgf SmallICAT.mzXML 25 Jan 2007 08:40:34,909 INFO : 25 Jan 2007 08:40:34,909 INFO...

"050727-Brachypodium-SDS-spot_418.xtan.xml" attached to message "FATAL: Upload FAILED"

Rs_BP|59353pri:N|_4 3e-19 UniRef90_Q948Y7 VMP3 protein related cluster QQTPTKTPRT GHSAIVQRWW RCSIQCHGRQ AGFCRTGDVR RQGSVNGSRE **DRRRRRGK WRGRAWRRGR AGGARGMAAW IGGARREGCR RGGATAESSR GGGGGGARER RPGGM*ARRG MRRAGSLWRG TVGGRGAAGR AAAGSGRGGG CRRRGRPRRS *RAPRGAPPG RSPPRWPQP* WRTPRP*RRP SRRAGGWPRP *GGRRRGVLS VALCPDEG 050727-Brachypodium-SDS-spot_418.mzXML scan 415 (charge 2) 1315.6...

"log_0207.txt" attached to message "Mascot upload"

07 Feb 2007 11:59:07,159 INFO : Mascot search for u937_1.mzXML 07 Feb 2007 11:59:07,159 INFO : ======================================= 07 Feb 2007 11:59:07,222 INFO : MzXML2Search output 07 Feb 2007 11:59:07,222 INFO : ======================================= 07 Feb 2007 11:59:07,470 INFO : running: MzXML2Search -mgf u937_1.mzXML 07 Feb 2007 11:59:07,515 INFO : 07 Feb 2007 11:59:07,515 INFO...

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

MIME-Version: 1.0 (Generated by Mascot version 1.0) Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p --gc0p4Jq0M2Yt08jU534c0p Content-Type: application/x-Mascot; name="parameters" LICENSE=Licensed to: NIH Central Mascot Server (263-MD-216066), (6 processors). MP= NM= COM=Conversion of E:\Sandy\Dhaval\Controls\@files\Control\mascot\PSD_protocol_Copy9\09FEB02_OT_57.work\09FEB02_OT_57.mzXML...

2020.12.03.408500v1.full.pdf

See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/346632754 An Integrated Clinical, Omic, and Image Atlas of an Evolving Metastatic Breast Cancer Preprint · December 2020 DOI: 10.1101/2020.12.03.408500 CITATIONS 0 READS 5 38 authors, including: Some of the authors of this publication are also working on these related projects: ...

"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)...

Luminex_Assay_200-2015-06-09-12292.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_200-2015-06-09-1228.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...

"logfile.txt" attached to message "Failed to remove work directory"

29 дек 2008 13:07:14,338 INFO : Check FASTA validity 29 дек 2008 13:07:14,338 INFO : ======================================= 29 дек 2008 13:07:14,338 INFO : 29 дек 2008 13:07:15,260 INFO : MzXML2Search output 29 дек 2008 13:07:15,260 INFO : ======================================= 29 дек 2008 13:07:15,260 INFO : running: MzXML2Search -mgf 9_1-F,8_01_3855.mzXML 29 дек 2008 13:07:15,307 INFO :...

"MarkeyLog09Mar16_OT_03.txt" attached to message "Processsing Errors preclude access to valid search results"

21 Dec 2010 16:06:19,457 INFO : Starting to run task 'org.labkey.ms2.pipeline.mascot.MascotSearchTask' at location 'webserver' 21 Dec 2010 16:06:19,488 INFO : Copying E:\Sandy\Dhaval\Controls\@files\Control\09MAR16_OT_03.mzXML to E:\Sandy\Dhaval\Controls\@files\Control\mascot\remainingS2_filesDec21_Copy6\09MAR16_OT_03.work\09MAR16_OT_03.mzXML 21 Dec 2010 16:06:21,739 INFO : MzXML2Search output 21...