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HIV Study Tutorial
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"CellCulture_baddata.xls" attached to page "Tutorial: Assay Data Validation"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-011 PT-101 05/17/19 -2 93 Media B S-012 PT-101 05/18/19 2 198 Media B S-013 PT-101 05/19/19 3 332 Media B S-014 PT-101 05/20/19 4 484 Media B S-015 PT-101 05/21/19 5 693 Media B S-016 PT-101 05/22/19 6 904 Media B S-017 PT-101 05/23/19 7 1527 Media B S-018 PT-101 05/24/19 8 2330 Media B S-019 PT-101 05/25/19 9 2815 Media...

"CellCulture_006.xls" attached to page "Step 5: Collect Experimental Metadata"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-011 PT-101 05/17/19 1 93 Media B S-012 PT-101 05/18/19 2 198 Media B S-013 PT-101 05/19/19 3 332 Media B S-014 PT-101 05/20/19 4 484 Media B S-015 PT-101 05/21/19 5 693 Media B S-016 PT-101 05/22/19 6 904 Media B S-017 PT-101 05/23/19 7 1527 Media B S-018 PT-101 05/24/19 8 2330 Media B S-019 PT-101 05/25/19 9 2815 Media...

"CellCulture_002.xls" attached to page "Step 1: Assay Tutorial Setup"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-011 PT-101 05/17/19 1 93 Media B S-012 PT-101 05/18/19 2 198 Media B S-013 PT-101 05/19/19 3 332 Media B S-014 PT-101 05/20/19 4 484 Media B S-015 PT-101 05/21/19 5 693 Media B S-016 PT-101 05/22/19 6 904 Media B S-017 PT-101 05/23/19 7 1527 Media B S-018 PT-101 05/24/19 8 2330 Media B S-019 PT-101 05/25/19 9 2815 Media...

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...

"config_test.log" attached to message "First-time Setup redirects me to home, unable to complete administration set up, cannot log in"

INFO: Initializing ProtocolHandler ["http-nio-8080"] Nov 24, 2016 3:52:18 PM org.apache.coyote.AbstractProtocol init SEVERE: Failed to initialize end point associated with ProtocolHandler ["http-nio-8080"] java.net.BindException: Address already in use at sun.nio.ch.Net.bind0(Native Method) at sun.nio.ch.Net.bind(Net.java:433) at sun.nio.ch.Net.bind(Net.java:425) ...

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...

Step 2: Import Lab Data

In this step we import two different, but related, data tables to the buildLW1 you just created: Plasma sample inventory: a spreadsheet that describes different vials of plasma. Assay result data: a spreadsheet that holds the experimental results of assaying the plasma. These tables are connected by the fact that the assay data describes properties of the plasma in the vials. We will capture...

"11.1 API changes.pptx" attached to message "labkey PIVOT syntax?"

LabKey Server 11.1 What’s New for Developers Josh Eckels March 17, 2011 11.1 Feature List Improved look and feel GPAT data persistence in hard tables Server-side validation script enhancements JavaScript reports AJAX report designer Copy-to-study by reference Study data visualization File management UI enhancements Easier initial data import for GPAT Additional LabKey SQL syntax Agilent feature...

Example Workflow: Develop a Transformation Script

This topic describes the process for developing a transformation script to transform assay data. You can use transformation scripts to change both run data and run properties as needed. In this example, we use perl, but using any scripting language will follow these general steps. Script Engine Setup Add Script to Assay Design Download Template Files Define the Desired Transformation Write...

Import Visit Names / Aliases

When data is collected by different sites and organizations, it can be difficult to keep visit naming standards consistent. The datasets generated might use many different ways of referring to the same visit. For example, the following list of values might all refer to the same visit: "Month 1" "M1" "Day 30" "First Month" Instead of editing your datasets to force them to be consistent, you...

"F004268-tt.log" attached to message "Mascot2XML"

12 Jun 2006 09:49:27,637 INFO : Clearing out existing MS2 data for F004268-tt.pep.xml 12 Jun 2006 09:49:28,163 INFO : Finished clearing out existing MS2 data for F004268-tt.pep.xml 12 Jun 2006 09:49:28,229 INFO : Loading FASTA file 12 Jun 2006 09:49:30,285 INFO : Fasta file "/opt/fasta/MSDB_20050929.fasta" has already been loaded. 12 Jun 2006 09:49:30,384 INFO : Loading MS/MS results is 0% complete...

"F004658.log" attached to message "Mascot pepXML upload"

12 Jul 2006 14:18:34,090 INFO : Clearing out existing MS2 data for F004658.pep.xml 12 Jul 2006 14:18:34,137 INFO : Finished clearing out existing MS2 data for F004658.pep.xml 12 Jul 2006 14:18:34,153 INFO : Loading FASTA file 12 Jul 2006 14:18:34,574 INFO : Fasta file "c:/INETPUB/MASCOT/sequence/BrachypodiumRS/current/Brachypodium_Emboss_Rs_060613.fasta" has already been loaded. 12 Jul 2006 14:18:34,590...

"vector_import.tsv" attached to page "Bulk Registration of Entities"

name description nucSeqId selectionMethods tstV-101 pACYC177 Vector Sequence NS-25 ["kanamycin", "ampicillin"] tstV-102 pET-24(+) Vector Sequence NS-26 ["kanamycin"] tstV-103 pLysS sequence NS-27 ["chloramphenicol"] tstV-104 pPCR-Script NS-28 ["ampicillin"] tstV-105 thoroughly made up NS-24 ["blasticidin", "bleomycin"]

"labkey-errors.log" attached to message "Upgrade to 19.1 and Java upgrade on Linux"

ERROR DbScope 2019-03-27 15:33:04,691 main : Connection to "labkeyDataSource" at jdbc:postgresql://localhost/labkey failed with the following error: ERROR DbScope 2019-03-27 15:33:04,698 main : Message: FATAL: role "labkey" does not exist SQLState: 28000 ErrorCode: 0 org.postgresql.util.PSQLException: FATAL: role "labkey" does...

"use1point0asxpresstolerance_sec20_feb21_interact_edit.log" attached to message "Error importing protein prophet file"

21 Feb 2011 14:30:41,505 INFO : Starting to clear out any previously imported data for use1point0asxpresstolerance_sec20_feb21_interact_edit.pep.xml 21 Feb 2011 14:30:41,536 INFO : 0.03 seconds to clear out any previously imported data for use1point0asxpresstolerance_sec20_feb21_interact_edit.pep.xml 21 Feb 2011 14:30:41,536 INFO : Starting to import FASTA file D:\LabKey Server\files\Kolla MS2\@files\databases\IPI_human_20100820.fasta...

First-time Setup redirects me to home, unable to complete administration set up, cannot log in

Hello all, I set up LabKey for the first time on a new server. Everything seemed fine at first, I could go to http://<server-name>:8080/labkey and start setting up an e-mail and password for the administrator. Then, when I continued to the next step I was immediately brought to the homepage ((http://<server-name>:8080/labkey/home/project-begin.view?). When I try to sign in from the Sign-In link in...

conversion over network drive

Seem to be have some trouble with converting files over a network share (Works fine on local files). I pasted the tomcat log below. I have also attached the conversion configuration file. Any ideas have is muchly appreciated, have run out of ideas. Thanks -Rich 27 Feb 2008 07:19:39,923 ERROR ConvertSpectrum: Could not setup job to process M:\Richard_Green\raw\152066.RAW 27 Feb 2008 07:27:20,688...

"SQL_Latin1_General_CP1_CI_AS.docx" attached to message "unexpected server error specimen import"

500: Unexpected server error SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [S1000]; error code [468]; Cannot resolve the collation conflict between "SQL_Latin1_General_CP1_CI_AS" and "Latin1_General_CI_AS" in the equal to operation.; nested exception is java.sql.SQLException: Cannot resolve the collation conflict between "SQL_Latin1_General_CP1_CI_AS" and "Latin1_General_CI_AS"...

Physical Exam.xls

data Participant ID Date Height (cm) Weight (kg) Temperature (C) Systolic Blood Pressure xxx/ Diastolic Blood Pressure /xxx Pulse Respirations Clinician Signature/Date Pregnancy Form Language ARV? ARV Regimen Type 101344 2008-04-27 173.0000 68 37.0 117 83 61 101344 2008-05-25 175.0000 69 36.8 145 103 71 101344 2008-06-22 175.0000 71 38.2 166 101 68 101344 2008-08-17 173.0000 73 36.5 125 95 74...

Trouble with Visit Days

If I specify a visit day that has a range of values, ie 100.0-110.0, it works fine with datasets and the Study Navigator view. However, the specimen inventory tables do not seem able to resolve the right visit day. So, when looking at vials, for visit day, I see <103.0> instead of "Season 1" (which is the label for the visit day). Not too big a deal, but the real problem is in the vial reports,...