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HIV Study Tutorial
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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...

dataset001.tsv

patient_document date participant_id study_id testfield2 testfield1 participantId meds given_birth eat first_name email specify_mood height aerobics address comments telephone_1 sex last_name weight drink date_enrolled dob gym age bmi Consent.docx Wed Jun 16 02:02:01 PDT 2021 PT-101 Malcolm Malcolm SpaceCowboy@gmail.com 53 187 Thursday,Tuesday 101 Serenity Ship, Out-of-sight, NoWhere, 18533...

Uploading of files with mutiple tabs within the same folder/project

I have 3 Tabs in one project area. In each Tab I added in the web part "Files". When I upload a file in Tab1 it is also shown in Tab2 and Tab3. How do I restrict this so that any file that get uploaded in a specific tab is only shown in that tab. Can someone show me or point me to an example of how this can be done. Thanks in advance Hi Mark, The Files Web Part is only specific to the...

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...

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...

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,...

How is Study Data Stored in LabKey Server?

This topic answers a few questions about how study data is stored inside the server: When you create a study dataset and import data to it, how is that data stored and managed in the system? How is data from different studies related? Is the data from different studies physically or logically separated? Topics Data Tables within Schema Import Process System Tables Visit Labels ...

"labkey-errors.log" attached to message "500: Unexpected server error A failure occurred during LabKey Server startup."

ERROR Table 2013-11-13 09:02:38,423 main : SQL Exception org.postgresql.util.PSQLException: ERROR: column reference "resourceid" is ambiguous Position: 224 at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2157) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1886) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)...

"Physical Exam doesnt work.xls" attached to message "Unable to import dates"

data ParticipantID Date SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Height Weight ARVRegimenType Pregnancy Language Signature 133428 2008-08-15 131 91 72 16 165 67.5 NVP-XR English 133428 2008-10-10 145 104 67 19 165 83.5 NVP-XR English 133428 2009-09-11 132 114 66 12 165 89.5 NVP-XR English 133428 2009-11-06 163 90 76 14 165 71.5 NVP-XR English 133428 2009-12-04 164...

08-12A12-IgA-Biotin.labkey_luminex_transform.Rout

Processing start time: 2015-06-09 12:32:15 [1] "/loc1/labkey/tomcat-tmp/ExternalScript/AssayId_1487/44548/Standard1_QC_Curves_4PL" [1] "Calculating the 4pl curve fit params for Standard1 ENV1 (31)" [1] "Calculating the 4pl curve fit params for Standard1 ENV2 (41)" [1] "Calculating the 4pl curve fit params for Standard1 ENV3 (59)" [1] "Calculating the 4pl curve fit params for Standard1 ENV4 (26)"...

07-12A81-IgA-Biotin.labkey_luminex_transform.Rout

Processing start time: 2015-06-09 12:31:05 [1] "/loc1/labkey/tomcat-tmp/ExternalScript/AssayId_1487/44914/Standard1_QC_Curves_4PL" [1] "Calculating the 4pl curve fit params for Standard1 ENV1 (31)" [1] "Calculating the 4pl curve fit params for Standard1 ENV2 (41)" [1] "Calculating the 4pl curve fit params for Standard1 ENV3 (59)" [1] "Calculating the 4pl curve fit params for Standard1 ENV4 (26)"...

"labkey.log" attached to message "500: Unexpected server error A failure occurred during LabKey Server startup."

INFO DbScope 2013-11-13 09:02:07,073 main : Attempting to create database "labkey" INFO DbScope 2013-11-13 09:02:27,178 main : Database "labkey" created INFO DbScope 2013-11-13 09:02:27,336 main : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource...

LuminexAssay-2018-03-21-1343.thawList

Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124...

LuminexAssay-2018-03-21-13433.thawList

Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124...

LuminexAssay-2018-03-21-13432.thawList

Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124...

Luminex_Assay_100-2015-05-27-1249.thawList

Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124...

IndexMap.xls

Sheet1 Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124 526455140.2404.452 125 249328597.2604.561...

IndexMap.xls

Sheet1 Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124 526455140.2404.452 125 249328597.2604.561...

IndexMap.xls

Sheet1 Index SpecimenID ParticipantID VisitID Date 111 87443202.2604.480 112 526455139.2404.476 113 526515796.3704.408 114 249320897.2404.514 115 526522193.4304.464 116 526515802.3704.402 117 526515315.6304.370 118 106443199.2404.501 119 526455350.4404.456 120 526517827.2604.384 121 249320938.2604.672 122 249325717.2404.493 123 526515651.3704.358 124 526455140.2404.452 125 249328597.2604.561...