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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...

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...

Step 2: Study Reports

In this step we will look at the variety of reports available in the online example. We will look at both built-in reports (automatically available in all study folders) and custom reports (created by the study researchers or data analysts). As you progress with the walkthrough, notice two things: First, all of these reports are 'live', that is, they represent the current state of the underlying...

Ontology Lookup

Premium Feature — Available in the Enterprise Edition of LabKey Server. Learn more or contact LabKey. Ontology Lookup Data Type Lookup Rules Usage Example Concept Picker for Insert/Update with Type-ahead Initialize Expected Vocabulary Ontology Lookup Data Type Once an ontology has been loaded and the module enabled in your folder, the fieldEditor will include an Ontology Lookup data...

"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...

"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...

"CellCulture_004.xls" attached to page "Step 1: Assay Tutorial Setup"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-031 PT-102 05/17/19 1 99 Media B S-032 PT-102 05/18/19 2 198 Media B S-033 PT-102 05/19/19 3 345 Media B S-034 PT-102 05/20/19 4 485 Media B S-035 PT-102 05/21/19 5 664 Media B S-036 PT-102 05/22/19 6 982 Media B S-037 PT-102 05/23/19 7 1548 Media B S-038 PT-102 05/24/19 8 2393 Media B S-039 PT-102 05/25/19 9 2821 Media...