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HIV Study Tutorial
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"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...

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...

"search2.log" attached to message "Xar XML file import problems after peptide database search"

29 Mar 2006 19:27:04,666 INFO : MS2 analysis for 7MIX_STD_110802_1.mzXML 29 Mar 2006 19:27:04,666 INFO : ======================================= 29 Mar 2006 19:27:06,976 INFO : tandem.exe output 29 Mar 2006 19:27:06,976 INFO : ======================================= 29 Mar 2006 19:27:07,005 INFO : 29 Mar 2006 19:27:07,005 INFO : X! TANDEM 2 (2005.02.01) 29 Mar 2006 19:27:07,005 INFO : 29 Mar 2006...

"labkey-errors.log" attached to message "java.lang.VerifyError"

ERROR ExceptionUtil 2013-11-20 09:38:48,131 http-8080-1 : Exception detected and logged to mothership: java.lang.NoClassDefFoundError: org/labkey/api/study/assay/AbstractAssayView at java.lang.Class.getDeclaredConstructors0(Native Method) at java.lang.Class.privateGetDeclaredConstructors(Class.java:2493) at java.lang.Class.getConstructors(Class.java:1517) at org.labkey....

"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...

REDCap Survey Data Integration problem

Hi, Trying to follow the documentation on REDCap Survey Data Integration ( https://www.labkey.org/wiki/home/Documentation/page.view?name=redCap ) without any success so far. Confusion follows after steps creating netrc file. - "Download the distribution file. Unzip the file." 1. Does this mean the "Binaries for Manual Linux/Unix/Mac Installation (tar.gz)", or the source? - Execute the...

Example1.xar.xml

I have installed CPAS 1.1 on Fedora Core 4. Using MS Internet Explorer, I am trying to load Example1.xar.xml on my project by clicking "Upload Experiment" under the Experiment tab. I have an error when doing that, so I click on the link "upload.xar.log" only to see this: 13 Jan 2006 15:56:29,211 INFO : Experiment Import for Uploaded file: 1/13/2006 15:56:29 13 Jan 2006 15:56:29,211 INFO : =======================================...

"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...

Building for production, gradle error: could not determine dependencies

Following this guide: https://www.labkey.org/Documentation/wiki-page.view?name=productionBuilds If I run a simple ./gradlew deployApp (optionally cleanBuild), then everything goes smoothly. Naturally I run into the following error on the web server:     Configuration Error Detected at LabKey Server Startup     This server does not appear to be compiled for production mode        org.labkey.api.util.ConfigurationException:...

"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...

Sequest cluster problem

We are trying to use SEQUEST Cluster on CPAS. I installed labkey server using binary installer. Also I downloaded and installed SequestQueue on the master node of my Sequest Cluster. I tested Sequest search on CPAS for a mzXML file, and got such error message in log file. As you know, the master node of Sequest Cluster is based on Windows, and other nodes are based on Linux. So, I think this...

"AID_fluoro2.xlsx" attached to page "FluoroSpot Assay"

PlateData Plate:JVL 10 IFN IL17 plate 4, Date:Monday, January 19, 2015, User: enzymatic, Path: R:\Users\MNPH\ELISpot register 3 JVL 10\Fluorospot IFN and IL17\Plate 4\JVL 10 IFN IL17 plate 4\JVL 10 IFN IL17 plate 4.plt Plate Data - Spots Number(in first image: FITC) 1 2 3 4 5 6 7 8 9 10 11 12 A 4 2 3 2 7 2 1 0 3 2 1 3 B 1246 1221 1187 1478 1462 1495 1462 1256 1651 1421 1377 1330 C 10 23...

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:...

Module Upgrade : Error: Unable to initialize search index.

ALL SITE ERRORS returns me this log file. Can you help me? ERROR LuceneSearchServiceImpl 2021-03-03 09:24:27,258 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.file.NoSuchFileException: C:\Program Files\Apache Software Foundation\Tomcat...

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"...

Upgrade to 19.1 and Java upgrade on Linux

Hi, I am trying to upgrade our Labkey Server to 19.1 and have to upgrade Java in the process (from Java 8). Per this page, https://www.labkey.com/the-java-shake-up-what-it-means-to-labkey-and-you/, downloaded OpenJDK12 with HotSpot VM from https://adoptopenjdk.net/. Installed and added the PATHs as references in the Labkey Server manual installation instructions. However, although it appears that...

study_load_2017-03-01_22-51-53.log

01 Mar 2017 22:51:54,728 INFO : Study reload was initiated by a configured automatic reload timer 01 Mar 2017 22:51:54,730 INFO : User "Bernard" is configured as the reload user for this study. This can be changed by visiting the "Manage Reloading" page. 01 Mar 2017 22:51:54,788 INFO : Starting to run task 'org.labkey.study.importer.StudyImportInitialTask' at location 'webserver' 01 Mar 2017 22:51:54,791...

"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...

Sample Naming Patterns

Each sample in a Sample Type must have a unique name/id. If your data does not already contain unique identifiers for each row, the system can generate them upon import using a Naming Pattern (previously referred to as a name expression) as part of the Sample Type definition. Overview and Basic Examples Naming Pattern Elements/Tokens Format Number Values Include Default Values Use String...