mik black bioinformatics symposium
DESCRIPTION
Mik Black bioinformatics symposiumTRANSCRIPT
![Page 1: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/1.jpg)
How to make bioinformatics accessible to normal people! ���
Mik Black���Department of Biochemistry���
University of Otago���
![Page 2: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/2.jpg)
Some musings…
• Accessibility - two aspects: 1. Methodology development & distribution
(can you get it?) 2. Methodology uptake (can you use it?)
• “Normal people”: 1. Who are they? 2. What do they want? What do they
need? Is there a happy medium?
![Page 3: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/3.jpg)
My background
• Statistical design and analysis of microarray experiments: – Methodology development – Applying existing bioinformatics techniques – Adapting “standard” statistical methods
– “Forensic” analysis
• Technologies: – Microarrays (mRNA, SNPs, CNV/CGH) – Second generation sequencing (SNP/CNV)
![Page 4: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/4.jpg)
http://www.r-project.org/
![Page 5: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/5.jpg)
![Page 6: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/6.jpg)
The joys of the command line…
• Large amounts of statistical genomics methodology available via R – Accessible? – Uptake? – Who are the end users?
• Can’t we just teach EVERYONE to use R?
![Page 7: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/7.jpg)
• GenePattern provides a web-based method for analysing microarray (and other) data.
• Provides a simple interface to tools developed in Java, R, Matlab and other languages.
• Analysis performed on server: – no compute resources required by users. – Facilitates sharing of results.
http://www.broad.mit.edu/cancer/software/genepattern/
Reich et al. (2006) GenePattern 2.0., Nature Genetics, 38, 500-501.
![Page 8: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/8.jpg)
Using GenePattern
• User friendly – Third year bioinformatics course at Otago.
– Workshop for lab personnel at TGen.
• Guided analysis – Facilitates use of standard analysis methods. – Pipeline creation and “versioned” analysis.
• End users? – At Otago: 3rd & 4th year Biochemistry students – At TGen: lab techs, iterns, bench scientists, PIs
![Page 9: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/9.jpg)
Common analysis tasks
• Basic data analysis/exploration: – Heatmap creation
– Hierarchical clustering – Identifying differentially expressed genes – Gene set analysis
– Survival analysis
• GenePattern provides these tools in a modular format.
![Page 10: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/10.jpg)
GenePattern interface
![Page 11: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/11.jpg)
Simple analysis pipeline
![Page 12: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/12.jpg)
![Page 13: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/13.jpg)
![Page 14: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/14.jpg)
![Page 15: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/15.jpg)
Δ
Power calculations P
![Page 16: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/16.jpg)
Network analysis
![Page 17: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/17.jpg)
BeSTGRID: Broadband-enabled Science and Technology GRID ���
http://www.bestgrid.org
![Page 18: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/18.jpg)
GenePattern on BeSTGRID
• Services: – GenePattern server
– Development environment (server and SVN)
• GenePattern training (coming soon): – Basic usage – Module development (uptake path for
bioinformatics tool developers)
![Page 19: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/19.jpg)
Next steps…
• Full GenePattern deployment: – Transfer of development modules to public server – Documentation and training
– Use of ROCKS cluster for job submission
• Modules for Second Gen Sequencing data: – DNAseq, RNAseq, ChIPseq – R/Bioconductor (e.g., ShortRead, Biostrings,
RSamTools, GenomeGraphs…)
– Analysis, visualization and quality assurance
![Page 20: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/20.jpg)
Community effort
• Some current examples: – VISG/MapNet: statisticians & geneticists
– BeSTGRID: middleware development & deployment through to end users
– CTCR: cancer researchers & clinicians
• Each group has the goal of placing powerful (and useful, and usable) tools into the hands of end users.
![Page 21: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/21.jpg)
Bioinformatics community
• NZGL provides opportunity for community-based effort. – National infrastructure for genomics research – Includes strong bioinformatics component
• Key issue: engagement with end users – Methodology development and distribution – Uptake, interaction and training
![Page 22: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/22.jpg)
Bioinformatics community
• NZGL provides opportunity for community-based effort. – National infrastructure for genomics research – Includes strong bioinformatics component
• Key issue: engagement with end users – Methodology development and distribution – Uptake and interaction
LETS GO FIND US SOME “NORMAL” PEOPLE!
![Page 23: Mik Black bioinformatics symposium](https://reader033.vdocuments.mx/reader033/viewer/2022052505/55617426d8b42a171a8b4a07/html5/thumbnails/23.jpg)
Acknowledgements University of Otago Marcus Davy Tim Molteno Thomas Allen Sarah Song Chris Brown Anthony Reeve Tony Merriman
University of Canterbury Vladimir Mencl
The University of Auckland Nick Jones Mark Gahegan Yuriy Halytskyy Cristin Print Daniel Hurley Christoff Knapp