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HIV Study Tutorial
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"CellCulture_003.xls" attached to page "Step 1: Assay Tutorial Setup"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-021 PT-102 05/17/19 1 99 Media B S-022 PT-102 05/18/19 2 198 Media B S-023 PT-102 05/19/19 3 345 Media B S-024 PT-102 05/20/19 4 485 Media B S-025 PT-102 05/21/19 5 664 Media B S-026 PT-102 05/22/19 6 982 Media B S-027 PT-102 05/23/19 7 1548 Media B S-028 PT-102 05/24/19 8 2393 Media B S-029 PT-102 05/25/19 9 2821 Media...

Participant Aliases

A single study participant can be known by different names in different research contexts. One lab might refer to the subject using the name "LK002-234001", whereas another lab might use the name "Primate 44". It is often necessary (and even desirable) to let the different providers of data use their own names, rather than try to standardize them at the various sources. LabKey Server can align all...

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...

NAb_highthroughput_testdata.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata-1.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata-1.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

NAb_highthroughput_testdata.xlsx

384 Well HIV Neut Mab Assay QC Well-ID : : unique ID used by automation software for data tracking purposes. Run-ID : : Unique ID used by automation software for data tracking Labware Family : : Used by automation method Run Assay ID : : Run ID PlateNumber : : Plate number 1-13 VirusName : : Virus ID Well VirusLot : : Virus lot number Well VirusDilution : : virus dilution factor...

JOIN Queries

This topic covers using JOIN in LabKey SQL to bring data together. All data is represented in tables, or queries. A list or dataset or user defined query are all examples of queries. Queries are always defined in a specific folder (container) and schema, but can access information from other queries, schema, and folders using JOINs. JOIN Columns from Different Tables Handle Query/Table Names...

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...

"labkey-errors.log" attached to message "Help with manual installation"

ERROR ModuleLoader 2015-02-16 09:12:08,996 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException: This server does not appear to be compiled for production mode at org.labkey.api.module.ModuleLoader.verifyProductionModeResources(ModuleLoader.java:438) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:311) at...

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...

"localhost.2006-08-19.log" attached to message "Error Run 551:Not found on MS2 page"

Aug 19, 2006 8:03:07 PM org.apache.catalina.core.StandardHostValve custom SEVERE: Exception Processing ErrorPage[errorCode=500, location=/error.gm] java.lang.IllegalStateException: getOutputStream() has already been called for this response at org.apache.catalina.connector.Response.getWriter(Response.java:599) at org.apache.catalina.connector.ResponseFacade.getWriter(ResponseFacade.java:195)...

"localhost.2015-02-16.log" attached to message "Help with manual installation"

Feb 16, 2015 9:12:08 AM org.apache.catalina.core.ApplicationContext log INFO: Initializing Spring root WebApplicationContext Feb 16, 2015 9:12:08 AM org.apache.catalina.core.StandardContext filterStart SEVERE: Exception starting filter Set Character Encoding java.lang.ClassNotFoundException: org.labkey.core.filters.SetCharacterEncodingFilter at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1720)...

"labkey.log" attached to message "DB related problem"

ERROR ModuleLoader 2008-04-10 13:55:24,745 main : Failure ocurred during ModuleLoader init. javax.servlet.ServletException: /opt/labkeyhome/labkeywebapp/WEB-INF/server-config.wsdd (Permission denied) at org.labkey.api.module.ModuleLoader.extractModules(ModuleLoader.java:350) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:209) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:168)...

"labkey-errors.log" attached to message "DB related problem"

ERROR ModuleLoader 2008-04-10 14:25:04,469 main : Failure ocurred during ModuleLoader init. javax.servlet.ServletException: /opt/labkeyhome/labkeywebapp/WEB-INF/server-config.wsdd (Permission denied) at org.labkey.api.module.ModuleLoader.extractModules(ModuleLoader.java:350) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:209) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:168)...

Linking Data Records to Image Files

This topic explains how to link data grids to image files which reside either on the same LabKey Server, or somewhere else on the web. This feature can be used with any LabKey data table as an alternative to propertyFields. For assay designs, see the following topic: assayImage. Scenario biopsies5.png Suppose you have a dataset where each of row of data refers to some image or file. For example,...