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HIV Study Tutorial
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"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...

"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...

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...

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...

XTamden error

Hi, I got the following error when hitting the "X!Tandem peptide search" button. This is on Labkey/CPAS 8.1 and the xtandem (/tandem_2007-07-01_2) downloaded from the labkey website, and on a Debian Linux box. Any clues? -Aschwin --------- An unexpected error occurred [Show more details] java.lang.NullPointerException        at org.labkey.jsp.compiled.org.labkey.ms2.pipeline.search_jsp._jspService(search_jsp.java:187)...

"labkey.log" attached to message "HTTP Status 500 - Internal Server Error"

INFO ModuleLoader 2016-01-13 16:18:47,610 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR DbScope 2016-01-13 16:18:48,567 localhost-startStop-1 : Connection to "labkeyDataSource" at jdbc:postgresql://localhost/labkey failed...

"ListsErrors.log" attached to message "Upgrade version 15.2 to 16.1 (16.2)"

An unexpected error occurred 05_Darce_Serotonin_assay.ID (primary key) has not been provisioned properly. Ensure the domain is established before constructing. java.lang.IllegalStateException: 05_Darce_Serotonin_assay.ID (primary key) has not been provisioned properly. Ensure the domain is established before constructing. at org.labkey.list.model.ListTable.<init>(ListTable.java:105) ...

"labkey.log" attached to message "Corrupted datasets view"

WARN AuditLogImpl 2013-06-19 09:47:07,858 FifteenMinuteDigest : user was not specified, defaulting to guest user. WARN AuditLogImpl 2013-06-19 10:02:07,940 FifteenMinuteDigest : user was not specified, defaulting to guest user. WARN AuditLogImpl 2013-06-19 10:17:07,877 FifteenMinuteDigest : user was not specified, defaulting to guest user. WARN...

"vector_import.tsv" attached to page "Bulk Registration of Entities"

name description nucSeqId selectionMethods tstV-101 pACYC177 Vector Sequence NS-25 ["kanamycin", "ampicillin"] tstV-102 pET-24(+) Vector Sequence NS-26 ["kanamycin"] tstV-103 pLysS sequence NS-27 ["chloramphenicol"] tstV-104 pPCR-Script NS-28 ["ampicillin"] tstV-105 thoroughly made up NS-24 ["blasticidin", "bleomycin"]

First-time Setup redirects me to home, unable to complete administration set up, cannot log in

Hello all, I set up LabKey for the first time on a new server. Everything seemed fine at first, I could go to http://<server-name>:8080/labkey and start setting up an e-mail and password for the administrator. Then, when I continued to the next step I was immediately brought to the homepage ((http://<server-name>:8080/labkey/home/project-begin.view?). When I try to sign in from the Sign-In link in...

"catalina.out" attached to message "Caused by: java.lang.IllegalStateException: Why am I in a transaction?"

Jul 17, 2015 11:49:07 AM org.apache.coyote.AbstractProtocol init INFO: Initializing ProtocolHandler ["http-bio-8080"] Jul 17, 2015 11:49:07 AM org.apache.catalina.startup.Catalina load INFO: Initialization processed in 832 ms Jul 17, 2015 11:49:07 AM org.apache.catalina.core.StandardService startInternal INFO: Starting service Catalina Jul 17, 2015 11:49:07 AM org.apache.catalina.core.StandardEngine...

"2023.04.06_labkey_bad_SQL_grammar_error.txt" attached to message "Getting duplicate key error after upgrade"

HTTP Status 500 – Internal Server Error Type Exception Report Message compliance-0.000-22.000.sql : SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "ownerentityid" of relation "signedsnapshot" already exists Description The server encountered an unexpected condition that prevented it from fulfilling the request. Exception ...

prophet parameter

Hi. It looks like the pipeline can't handle pepxml results where there are spectrum queries without search hits (sequest search). We wanted to keep all original search info through out the pipeline so the pipeline prophet min probability was set to 0. It errors at 'ERROR: MS2 import failed' and 'FATAL: XAR import FAILED' The peptide and protein prophet reports are generated but the job...

import Mascot pep.xml error

The attached file will not import. There are N-term protein modifications in this search. Are these supported? Thanks, Bill 26 Sep 2008 11:19:54,468 INFO : Trying to load data file file:/Z:/projects/UKPCF/cytoA_B/mascot/QTOF_PARAMS5/JJ-090606cytoAplusB-s1.mgf into the system 26 Sep 2008 11:19:54,484 INFO : No ExperimentDataHandler registered for data file file:/Z:/projects/UKPCF/cytoA_B/mascot...

Upgrade version 15.2 to 16.1 (16.2)

Hi. I have tested Labkey server 16.1 and several tables (about 10 from 23 module lists) gives the message   500: Unexpected server error   Biostanice1.Index (primary key) has not been provisioned properly. Ensure the domain is established before constructing.   java.lang.IllegalStateException: Biostanice1.Index (primary key) has not been provisioned properly. Ensure the domain is established...

Error at startup after upgrading to the trunk version: 27583

500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoSuchMethodError: org.labkey.api.ehr.EHRService.registerSimpleFormType(Lorg/labkey/api/ehr/EHRService$FORM_TYPE;Lorg/labkey/api/module/Module;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V        at org.labkey.onprc_ehr.ONPRC_EHRModule.registerEHRResources(ONPRC_EHRModule.java:184)        at...

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...

Is it Possible to Add a Specimen through JS?

I'm thinking the answer is No, but thought id post here just in case :-) code:         LABKEY.Query.insertRows({                     'schemaName' : 'study',                     'queryName' : 'SpecimenDetail',                     'rows' : [                             {                                 'VialId' : '6002',                                 'SampleId' : '6002',                                 'DrawDate'...