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HIV Study Tutorial
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ImmuneScore - Assay.xlsx

data ParticipantID Date VisitId SpecimenId M1 M2 M3 InstrumentSetting OperatorEmail Comment PT-101 1/1/08 1 vl-100 28.0 31.0 90.5 3.0 john@labkey.com PT-101 2/2/08 2 vl-100 29.0 42.0 87.0 4.0 john@labkey.com PT-101 3/3/08 3 vl-100 13.5 66.0 90.0 2.0 john@labkey.com PT-101 4/4/08 4 vl-100 13.0 53.5 89.0 4.0 john@labkey.com PT-101 5/5/08 5 vl-100 35.5 69.0 80.0 2.0 john@labkey.com PT-101 6/6...

"LabResults.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

data ParticipantId VisitId Date CD4 Lymphocytes Hemoglobin PT-101 18 2021-06-20 843 2374 13.0 PT-101 3 2020-04-26 210 553 11.0 PT-101 4 2020-05-24 223 805 13.0 PT-101 5 2020-06-21 351 941 11.0 PT-101 6 2020-07-19 298 847 14.0 PT-101 24 2021-12-05 768 2060 11.0 PT-101 23 2021-11-07 744 2334 12.0 PT-101 7 2020-08-16 404 2549 12.0 PT-101 8 2020-09-13 536 1425 15.0 PT-101 9 2020-10-11 475 1654...

"LabResults.xls" attached to page "Step 2: Import Datasets"

data ParticipantId SequenceNum Date CD4 Lymphocytes Hemoglobin PT-101 18 2021-06-20 843 2374 13.0 PT-101 3 2020-04-26 210 553 11.0 PT-101 4 2020-05-24 223 805 13.0 PT-101 5 2020-06-21 351 941 11.0 PT-101 6 2020-07-19 298 847 14.0 PT-101 24 2021-12-05 768 2060 11.0 PT-101 23 2021-11-07 744 2334 12.0 PT-101 7 2020-08-16 404 2549 12.0 PT-101 8 2020-09-13 536 1425 15.0 PT-101 9 2020-10-11 475...

"testFile.csv" attached to message "Date error msg: "couldn’t convert date field, should be of type timestamp""

ParticipantId SequenceNum Date CD4 Lymphocytes Hemoglobin PT-101 18 2021-06-20 843 2374 13.0 PT-101 3 2020-04-26 210 553 11.0 PT-101 4 2020-05-24 223 805 13.0 PT-101 5 2020-06-21 351 941 11.0 PT-101 6 2020-07-19 298 847 14.0 PT-101 24 2021-12-05 768 2060 11.0 PT-101 23 2021-11-07 744 2334 12.0 PT-101 7 2020-08-16 404 2549 12.0 PT-101 8 2020-09-13 536 1425 15.0 PT-101 9 2020-10-11 475 1654...

"PhysicalExam.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

data ParticipantId VisitId Date Weight_lb Temperature_F SystolicBloodPressure DiastolicBloodPressure Pulse Clinician_Signature_Date PT-101 23 2021-11-07 145 99.4 122 91 68 FALSE PT-101 24 2021-12-05 148 97.2 113 90 65 FALSE PT-101 22 2021-10-10 197 97.9 109 95 72 FALSE PT-101 21 2021-09-12 146 94.4 124 86 64 FALSE PT-101 20 2021-08-15 187 98.7 128 88 80 FALSE PT-101 19 2021-07-18 170 101.1...

"PhysicalExam.xls" attached to page "Step 2: Import Datasets"

data ParticipantId SequenceNum Date Weight_lb Temperature_F SystolicBloodPressure DiastolicBloodPressure Pulse Clinician_Signature_Date PT-101 23 2021-11-07 145 99.4 122 91 68 FALSE PT-101 24 2021-12-05 148 97.2 113 90 65 FALSE PT-101 22 2021-10-10 197 97.9 109 95 72 FALSE PT-101 21 2021-09-12 146 94.4 124 86 64 FALSE PT-101 20 2021-08-15 187 98.7 128 88 80 FALSE PT-101 19 2021-07-18 170 101.1...

"LabResults.xls" attached to message "Date error msg: "couldn’t convert date field, should be of type timestamp""

data ParticipantId VisitId Date CD4 Lymphocytes Hemoglobin PT-101 18 6/20/21 0:00 843 2374 13 PT-101 3 4/26/20 0:00 210 553 11 PT-101 4 5/24/20 0:00 223 805 13 PT-101 5 6/21/20 0:00 351 941 11 PT-101 6 7/19/20 0:00 298 847 14 PT-101 24 12/5/21 0:00 768 2060 11 PT-101 23 11/7/21 0:00 744 2334 12 PT-101 7 8/16/20 0:00 404 2549 12 PT-101 8 9/13/20 0:00 536 1425 15 PT-101 9 10/11/20 0:00 475...

"Demographics.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

Sheet1 ParticipantId VisitId Date StartDate Country PrimaryLanguage Sex TreatmentGroup StatusOfInfection PT-101 0 2020-02-02 2020-02-02 Germany German f ETR HIV Positive PT-102 0 2020-02-02 2020-02-02 USA English f DRV HIV Positive PT-103 0 2020-02-02 2020-02-02 USA English m No Treatment HIV Positive PT-104 0 2020-02-02 2020-02-02 USA French m HIV Negative HIV Negative PT-105 0 2020-02-02 2020-02-02...

"Demographics.xls" attached to page "Step 2: Import Datasets"

Sheet1 ParticipantId SequenceNum Date StartDate Country PrimaryLanguage Sex TreatmentGroup StatusOfInfection PT-101 0 2020-02-02 2020-02-02 Germany German f ETR HIV Positive PT-102 0 2020-02-02 2020-02-02 USA English f DRV HIV Positive PT-103 0 2020-02-02 2020-02-02 USA English m No Treatment HIV Positive PT-104 0 2020-02-02 2020-02-02 USA French m HIV Negative HIV Negative PT-105 0 2020-02-02...

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...

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...

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...

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 ...

"immune-score.xlsx" attached to page "Step 2: Import Lab Data"

Sheet1 ParticipantId SpecimenId Date M1 M2 M3 pt-1 vl-100 4/4/20 1 0.8 0.12 pt-1 vl-200 6/4/20 0.9 0.6 0.22 pt-1 vl-300 8/4/20 0.8 0.7 0.32 pt-2 vl-400 4/4/20 0.77 0.4 0.33 pt-2 vl-500 6/4/20 0.99 0.5 0.44 pt-2 vl-600 8/4/20 0.98 0.55 0.41 pt-3 vl-700 4/4/20 0.94 0.3 0.32 pt-3 vl-800 6/4/20 0.8 0.77 0.21 pt-3 vl-900 8/4/20 0.88 0.88 0.22 pt-3 vl-1000 10/4/20 0.87 0.66 0.11

immune-score.xlsx

Sheet1 ParticipantId SpecimenId Date M1 M2 M3 pt-1 vl-100 4/4/20 1 0.8 0.12 pt-1 vl-200 6/4/20 0.9 0.6 0.22 pt-1 vl-300 8/4/20 0.8 0.7 0.32 pt-2 vl-400 4/4/20 0.77 0.4 0.33 pt-2 vl-500 6/4/20 0.99 0.5 0.44 pt-2 vl-600 8/4/20 0.98 0.55 0.41 pt-3 vl-700 4/4/20 0.94 0.3 0.32 pt-3 vl-800 6/4/20 0.8 0.77 0.21 pt-3 vl-900 8/4/20 0.88 0.88 0.22 pt-3 vl-1000 10/4/20 0.87 0.66 0.11

"CellCulture_005.xls" attached to page "Step 5: Collect Experimental Metadata"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-001 PT-101 05/17/19 1 127 Media A S-002 PT-101 05/18/19 2 258 Media A S-003 PT-101 05/19/19 3 428 Media A S-004 PT-101 05/20/19 4 638 Media A S-005 PT-101 05/21/19 5 885 Media A S-006 PT-101 05/22/19 6 1279 Media A S-007 PT-101 05/23/19 7 2004 Media A S-008 PT-101 05/24/19 8 3158 Media A S-009 PT-101 05/25/19 9 4202 Media...

"CellCulture_001.xls" attached to page "Step 1: Assay Tutorial Setup"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-001 PT-101 05/17/19 1 127 Media A S-002 PT-101 05/18/19 2 258 Media A S-003 PT-101 05/19/19 3 428 Media A S-004 PT-101 05/20/19 4 638 Media A S-005 PT-101 05/21/19 5 885 Media A S-006 PT-101 05/22/19 6 1279 Media A S-007 PT-101 05/23/19 7 2004 Media A S-008 PT-101 05/24/19 8 3158 Media A S-009 PT-101 05/25/19 9 4202 Media...

"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...