© 2008 LabKey Software www.labkey.com

Simplifying Scientific Data Management with LabKey Server

January 29, 2009Presenter: Peter Hussey, peter@labkey.com

Agenda

The Problem The LabKey Server Solution Working with Assay Datasets (demo) Benefits Questions and Next Steps

If you think of questions during the presentation, use the chat feature of GoToMeeting. You can also ask questions over the phone at the end of the presentation.

Instrument data lives in many small files File per chip/plate/run On researcher’s PCs Separated from clinical

data

The Problem: Scattered Research Data

Lab Scientists

Clinicians

Principal Investigators and Statisticians

Research Subjects

Making it difficult to answer questions like Where are the results from the

Luminex tests we did last May? What is the average immune

response 6 weeks after an event? How do participant X’s physical

exams correlate with his gene expression results over time?

The LabKey Solution

Lab Scientists

Clinicians

Principal Investigators and Statisticians

Research Subjects

A lab data repository and portal Based on a robust SQL database Accessible via secure web pages Easy and powerful

LabKey Server

LabKey Study Framework

Assay data comes in many shapes Instrument-specific formats

A LabKey study links assay data to Specimens Participants (subjects) Time

Metadata is vital for consolidation Who, what, where, when,

how an assay was run Custom categories Often neglected

Participant

Specimen

Time point

Vial (sample)

Assay X data

Assay Y data

Run

Run

Cohort

Demographics

Demonstration Scenario

Research project: identify the measurable changes that occur around the incidence of a specific viral infection.

Subjects: human participants from at-risk populations who agree to monthly clinic visits and blood draws.

There is no fixed schedule of visits. We are interested in the changes that occur on a monthly basis.

Participants start on different dates.

Choosing Timepoints in a LabKey Study

My research does not measure changes over time. Use the date a test was run as your timepoint. Useful

for:–finding or grouping results–assessing instrument calibration

Example: Comparative studies on samples from a tissue bank

– “How do the results we’re getting now compare to thosewe were seeing back in March?”

OR My research follows subjects over time.OR My research has a detailed schedule of visits.

Calendar

Jan Feb Mar Apr

Date-based Study, Single Start Date

Study Timeline

Month 1 Month 2 Month 3

Affy

A

rray

NA

b

ELI

Spo

t ru

n Lum

inex

Sample S1

Month 4

Sample S2A

ffy

Arr

ay NA

b

ELI

Spo

t run ELI

Spo

t rer

un

Study Start Date

Choosing Timepoints (2)

My research does not measure changes over time.OR My research follows subjects over time.

Time intervals are the interesting data Example: cancer study in mice, with mouse exposed to

a carcinogen and then tested weekly– “On average, how long does it take for the tumor to reach a

given size?”

OR My research has a detailed schedule of visits.

Calendar

Jan Feb Mar Apr

Date-based Study, Separate Start Dates

Study Timeline

Exp

ose

Jan

5

Blo

od

Dra

w

Jan

19 Blo

od

Dra

w

Feb

24

Bio

psy

Apr

il 5

Subject M

Subject N

Exp

ose

Feb

4

Blo

od

Dra

wFe

b 18 Blo

od

Dra

wM

ar 1

8

Day 1 Day 14 Day 42 Day 90

M’s

Sta

rt D

ate

N’s

Sta

rt D

ate

Choosing Timepoints (3)

My research does not measure changes over time.OR My research follows subjects over time.OR My research has a detailed schedule of visits.

Visits: planned dates with protocols for clinical tests and specimen draws

Example: study of volunteers at risk of contracting malaria

– “What changes do we see in the blood assays in the 6 months after first exposure ?”

Calendar

Jan Feb Mar Apr

Visit-based Study

Study Timeline

IntakeVisit

Week 2Visit

Week 6Visit

3 MonthVisit

Inta

ke

Jan

5

Vis

itJa

n 17

Vis

it

Feb

25

Vis

itA

pr 3

Participant A

Participant B

Inta

ke

Feb

4

Vis

itFe

b 18

Vis

it

Mar

18

Agenda

Describing the Problem The LabKey Server Solution Working with Assay Datasets (demo)

Create a study, define timepoints, load specimens Define and load demographic and clinical data Define an assay and customize metadata

– General type– Built-in specialized types: ELISpot, NAb, Luminex,…

Load assay datasets Navigate and analyze the consolidated data

Benefits Questions and Next Steps

Assay Architecture

Assay Design Types Built for specific data formats (instrument output) Know how to parse the assay data and where to store it Specify default metadata and custom design page(s) Written in Java

–Can be installed on the server as an external module–Can derive from existing functionality (e.g. plate layout editor)–Coming in next release: configurable

Named Assay Design Named customization of metadata for a design type Metadata fields describe

–Data type, valid ranges, pattern checks–Upload form UI: labels, select lists, help text

Assay Architecture (2)

Import Data Upload a group of data files at one time Specify metadata for entire group and for individual

runs Definition of a run determined by Assay design type

Copy to Study Separation of upload step from data integration step Matches data based on choice of keys

–Specimen ID–Participant ID and timepoint / visit– ID Mapping file / spreadsheet

Lets users curate data prior to “publishing” in study

LabKey Assay Forms

Example barcodes for specimen identifiers shown at right

Barcode reader acts as keyboard in assay upload forms

Benefits of Assay Data Management

Improved Data Quality Limit data entry errors

–Select lists, smart defaults –Range and pattern checks

Stage data before making public Broader Uses of Data

LabKey tools: Navigator, charting, reports External languages: R, JavaScript, SAS

Standardization Lexicon Best practices

Rapid Adaptation Define new formats and metadata as needs change

Agenda

Describing the Problem The LabKey Server Solution Working with Assay Datasets Benefits Questions and Next Steps

Next Steps

Explore LabKey Server at www.labkey.org –Documentation–Videos–Demo data–Support boards–Windows-based evaluation server

Contact LabKey Software (www.labkey.com)–Email sales@labkey.com–Ask us to send our whitepaper on LabKey in HIV/AIDS

research (Feb ’09)–Interested in trying LabKey as a hosted web service?

We are looking for some beta customers–Give feedback on this and future webinars

Thank you!

--The Management