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HIV Study Tutorial
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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...

"PhysicalExam.xls" attached to page "R Report Builder"

data ParticipantID Date Height Weight Temperature Systolic Diastolic Pulse Respirations ARV? ARVRegimenType 101 2008-05-17 184.4000 86 36.0 129 76 64 17 101 2008-08-04 184.7000 84 37.0 133 79 67 18 101 2008-09-02 183.4000 83 37.0 133 85 68 15 101 2008-11-23 185.3000 80 36.7 135 85 70 14 101 2009-01-18 184.8000 79 36.8 142 90 75 17 101 2009-02-17 185.2000 79 37.3 129 87 79 13 101 2009-03-16...

Limits on HTML in WIKI pages?

What are the limits on HTML in WIKI (and I assume, MESSAGE) pages? I tried to place an excel-converted spreadsheet on a wiki page. Initially it crashed the page display service and made the page very hard to delete. After removing external namespace references it displays properly on normal browsers (firefox, ie, safari) but loses all its formatting, color and fonts on the WIKI page. Well there...

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...

Query Metadata: Examples

This topic provides examples of metadataSql used to change the display and behavior of fields in tables and queries. Auditing Level Conditional Formatting Include Row Selection Checkboxes Hide a Field from Users Show/Hide Columns on Insert and/or Update Use a Format String for Display Use a Text Expression for Display Set a Display Width for a Column Display Columns in Specific Order...

"unix-ms2admin-exception.txt" attached to message "Error getting "Protein Annotations Loaded" status in showMS2Admin.view"

03 Feb 2006 17:22:38,295 ERROR GroovyView : error executing /_views/HomeTemplate.gm java.io.IOException: java.lang.ClassCastException: java.lang.Thread at MS2.MS2Controller$DisplayThreadStatusColumn.renderGridCellContents(MS2Controller.java:1286) at org.fhcrc.cpas.data.DisplayColumn.renderGridDataCell(DisplayColumn.java:261) at org.fhcrc.cpas.data.DataRegion.renderTableRow(DataRegion.java:663)...

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...

job stuck waiting status

Hi,    a user submit a job but it is stuck in waiting status in the activemq log after it finish the first FAASTA check. 01 Dec 2017 11:40:26,278 INFO : X! Tandem search for all 01 Dec 2017 11:40:26,281 INFO : ======================================= 01 Dec 2017 11:40:26,283 INFO : abac.mzXML 01 Dec 2017 11:40:26,285 INFO : casfdsa.mzXML 01 Dec 2017 11:40:26,287 INFO : cafdsa.mzXML 01 Dec...

Tutorial: Inferring Datasets from Excel and TSV Files

Use the following step-by-step instructions to quickly create and import study datasets from Excel and/or TSV files. This method of creating datasets via study folder import is especially useful for any of the following scenarios: You want to avoid manually defining all the fields in all your study datasets. You want to define and import study datasets as an initial, one-time job, and then develop...

can a group_concat column have a URL?

we have a SQL statement that includes a column generated using group_concat(). in general, labkey allows you to assign a URL for a given column. when i tried to do this for the group_concat column, i got this error: An unexpected error occurred java.lang.AssertionError        at org.labkey.api.data.MultiValuedRenderContext.next(MultiValuedRenderContext.java:76)        at org.labkey.api.data.MultiValuedDisplayColumn.renderGridCellContents(MultiValuedDisplayColumn.java:51)...

Reagents.tsv

Key Reagent 1 AD-mix 2 Acetyl chloride 3 Aluminium chloride 4 Armstrong's acid 5 Azobisisobutyronitrile 6 9-Borabicyclononane 7 Benzyl chloroformate 8 Benzyltrimethylammonium fluoride 9 1,8-Bis(dimethylamino)naphthalene 10 (Bis(trifluoroacetoxy)iodo)benzene 11 Bis(trimethylsilyl)acetamide 12 Bis(trimethylsilyl)amine 13 N-Bromosuccinimide 14 Burgess reagent 15 Tert-Butyl hydroperoxide 16 N-Butyllithium...

Dataset Properties

The properties of a dataset include how it is keyed, categorized, and shown or shared. Dataset Properties Page Action Buttons Edit Dataset Properties Data Row Uniqueness Additional Key Fields Using Time as an Additional Key Advanced Settings Edit Dataset Fields Dataset Properties Page Administrators can view and edit dataset properties either by clicking the name of a dataset...

dataset5004.tsv

ParticipantId date QCStateLabel Weight_kg Temp_C SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Signature Pregnancy Language ARV ARVtype height_cm 101344 2008-04-27 00:00:00.0 68 37.0 117 83 61 173.0 101344 2008-05-25 00:00:00.0 69 36.8 145 103 71 175.0 101344 2008-06-22 00:00:00.0 71 38.2 166 101 68 175.0 101344 2008-08-17 00:00:00.0 73 36.5 125 95 74 ...

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...

Preparing Data for Import

This topic explains how to best prepare your data for import so you can meet any requirements set up by the target data structure. LabKey Server provides a variety of different data structures for different uses: Assay Designs for capturing instrument data, Datasets for integrating heterogeneous clinical data, Lists for general tabular data, etc. Some of these data structures place strong constraints...

CPAS Linux install failure after custom build

Hi, It seems I bumped into another problem. :-( Altough the debian build succeeded, I couldn't find a directory or file that resembled the cpas binary package that is distributed on the cpas website. As I wanted to follow the install instruction found from the cpas website. Therefore I looked through the ant targets and found dist_standard, dist_cpas and two others. Trying to run these resulted...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

25 Jan 2007 08:37:45,274 INFO : Mascot search for CAexample_mini.mzXML 25 Jan 2007 08:37:45,274 INFO : ======================================= 25 Jan 2007 08:37:45,326 INFO : MzXML2Search output 25 Jan 2007 08:37:45,326 INFO : ======================================= 25 Jan 2007 08:37:45,330 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 25 Jan 2007 08:37:45,385 INFO : 25 Jan 2007 08:37:45,386...

TPP v3.4.2

Is TPP v3.4.2 the only compatible version for CPAS. spctools-discuss said they thought that some CPAS users were using more recent versions. Thanks, Bill Hi Bill, Although CPAS is shipping with the older version of the TPP, some of our users have been using version 4.x. I made several changes in version 9.1 to fix compatibility issues with newer TPP releases. Thanks, Josh I'm trying to...

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...

Mascot Parameters

We are having trouble with Mascot searches and setting the parameters using CPAS. First, the setting for the peptide charge seems to be ignored, whether the setting is:     <note type="input" label="mascot, peptide_charge">1+, 2+ and 3+</note> or:     <note type="input" label="mascot, peptide_charge">3+</note> The setting returned in the .dat file is always:     CHARGE=2+ and 3+...