WikiLIMS: DEVELOPING A LABORATORY INFORMATION MANAGEMENT SYSTEM FOR NEXT GENERATION SEQUENCING DATA

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WikiLIMS DEVELOPING A LABORATORY
INFORMATION MANAGEMENT SYSTEM FOR

NEXT GENERATION SEQUENCING DATA
Melissa Kramer 1, Michael Cariaso 2,
Stan Gloss 2, and W. Richard McCombie1. 1. Cold
Spring Harbor Laboratory, 1 Bungtown Road, Cold
Spring Harbor NY 11724 2. BioTeam Inc., 7
Derosier Drive, Middleton MA 01949
Abstract
PCR worksheets can be created quickly using
standard primer sets
Custom forms with pull down menus simplify data
entry and reduce errors while free text areas
allow an electronic lab notebook to be created.
Buttons make it easy to create new pages. Users
can edit with ease but a full audit history
provides a safety net.
Next generation sequencers provide a vast amount
of sequence data, and provide the opportunity to
explore a wide variety of scientific questions.
However, this large volume of information can
present new challenges for data management. CSHL
is working with BioTeam Inc. to create a
laboratory information management system (LIMS)
to track data in our current Illumina sequencing
pipeline. The system uses mediawiki software to
provide a flexible web-based user interface with
an underlying mySQL relational database. Perl
scripts will be used for custom queries and to
automate data capture and curation. The basic
functionalities to be implemented in the wikiLIMS
fall into 3 main categories 1) data organization
and storage 2) interactivity with various
software tools from the wiki (such as the
Illumina data analysis software or custom tools
used in the lab) 3) custom scripts to access and
process stored quality control information for
display on the wiki (i.e. graphing the weekly
success rate for each 1G machine). The LIMS
system will allow us to standardize and automate
many elements of the sequencing process, thereby
increasing quality control and decreasing error.
In addition, the flexible format of the wiki
will allow us to easily modify and extend the
LIMS as our projects evolve. Creating a
centralized management system will be imperative
to achieving maximal sequencing efficiency,
process control and project coordination.
Graphical displays allow large data sets to be
more easily studied and trends to be identified.
Signal graphs generated by the Illumina analysis
pipeline are read from the RAID and displayed in
the wikiLIMS.
A text file read from the Illumina software is
converted to a graphical display in the wiki to
allow differences in signal intensity to be
viewed at the start of the run
Centralized access to analyzed data and statistics
Quality Control
Interactivity with Illumina Instruments
Remote access to the Illumina sequencers with VNC
allows users to view run status and data transfer
progress from the WikiLIMS
Acknowledgements
Quality Control A perl script calculates the
percentage of high quality bases generated for
weekly runs and results are displayed in a
histogram
Dick McCombie Maureen Bell Danea Rebolini Laura
Cardone Michael Regulski Lori Spiegel Stephanie
Muller Jennifer Parla BioTeam Michael
Cariaso Stan Gloss Wiliam Van Etten
Greg Hannon Emily Hodges Yaniv Erlich Michelle
Rooks Zhenyu Xuan Illumina/Solexa Stanley
Family and Foundation National Institutes of
Health National Science Foundation