WikiLIMS

BioTeam.net

Dilbert 1

1st Next Gen Sequencer

• Centerpiece of a lab

• Generates new workflows– These cannot be known in advance

• When they order 2 more sequencers– Still want a single repository for all runs

Tasks/Workflows

• Production – Few tasks, all repeated many times– Rigorous standards– Ideal for software

• Research– Many one-off tasks– Ad hoc standards– Difficult for software

Sequencer’s Input

• Infinite variety of – Samples, handling and lab prep

• All details might matter– Usually only a few do

The 454 Solution

• A single strict [A-Z0-9]+ field

• Intended as an external primary key

• Makes sample tracking an upstream problem

• Part of the results directory nameR_TIMESTAMP_MACHINEID_USER_YOURFIELD

• Clean technical solution

These are Researchers

• Apparently they wanted a LIMS

• Found a way to cram it in

• PROJIDxxSPECIESxxSAMPLExxDESCxxNOTES

• More or less consistent

Additional Details

• 3 machines

• Signs of strain by the 50th run– Difficult to look across machines

– Too many DESCRIPTION variants– Desire to rename old data

Dilbert 2

Key Terms

• Wiki – Fast in Hawaiian

• LIMS– Laboratory Information Management System

• Mediawiki– Software that runs Wikipedia

Wikipedia/ UC Berkeley

flexible --- database 1/3

flexible database

flexible --- database 2/3

‘ ’ . N o need to abuse a com m ents field E verything is a com m entuntilyou m ake it.structured

flexible --- database 3/3

‘ ’ . N o need to abuse a com m ents field E verything is .a com m entuntilyou m ake itstructured

Full History

• A uditTrail• FullH istory• 2 D ifferences betw een any versions

Version Differences

File data

raid

Meta data

wiki

Next Gen Data Store

File data

raid

Meta data

wiki

Next Gen Data Analysis

People

Programs

File data

raid

Meta data

wiki

Next Gen Data Analysis

People

Programs

Automatic data capture - Raw

M oststructured contentcan be captured and recorded by program s as itis

generated

Automatic data capture - Pretty 1/3

, A llcaptured autom atically atthe454 m achine

Automatic data capture - Pretty 2/3

, A llcaptured autom atically atthe454 m achine

Automatic data capture - Pretty 3/3

, A llcaptured autom atically atthe454 m achine

File Browser

A ccess raw files

CGI

File data

raid

Meta data

wiki

Next Gen Data Analysis

People

Programs

Custom HTML ’ Tricks you ve never

. seen w ikipedia do

A dding a record via a.form

/ R un custom perlphp.code

* * G enerate any htm lon . the fly A JA X

Project Dashboard

S teerthe ongoing analysis

User Interface

Traditionally LIMS UI• Must be done up-front• Can be hardest part to get right

Wiki provides a minimal UI• Instantaneous and consistent• Focus on data first• Improve it when and where needed

As Details Emerge

Users can edit data with only a browser• Won’t make 5000 changes by hand

– But 50 is faster and cheaper than calling in a coder

• Write software only for the heavy lifting– Cost effective only if we will do something many

times – Deferred until patterns emerge

• and become tedious

Reading Wiki From Perl

use Perlwikipedia;

$bot = Perlwikipedia->new;

$bot->set_wiki($hostname, $directory);

$bot->login($username, $password);

$pagetext = $bot->get_text("Main Page");

Edit Wiki Pages

@pages = $bot->get_all_pages_in_category(

"Category:Is_a_454_Run");

foreach $page (@pages) {

$oldtext = $bot->get_text($page);

$newtext ="$oldtext changed by bot";

$bot->edit($page, $newtext, $comment);

}

Dilbert 3

SPARQLPREFIX abc:

<http://mynamespace.com/exampleOntologie#>

SELECT ?capital ?country

WHERE {

?x abc:cityname ?capital.

?y abc:countryname ?country.

?x abc:isCapitalOf ?y.

?y abc:isInContinent abc:africa.

}

Select all African capitol cities from wikipedia

DBpedia.org

• Use SPARQL to query directly against wikipedia

• Make a local relational cache • Query with SQL• You hide your SQL behind a layer

anyway…..right?

Concerns

It can’t scalesee http://en.wikipedia.org

No theoretical basisThis is a semantic web

Conclusion

• Extremely flexible database• Unifies next gen, microarrays, inventory, …• History of all changes

• Initiate/steer tasks • Perl for deep customization• The human intelligence of a wiki