The iPlant Collaborative Community Cyberinfrastructure for Life Science

Network for Integrating Bioinformatics into Life Sciences EducationApril, 2014 – Omaha, Nebraska

Jason Williams Cold Spring Harbor Laboratory / iPlant Collaborative

Cyberinfrastructure is a key enabler for bioinformatics education

What is Cyberinfrastructure?

iPlant Data Store100 GB allocation per user – up to ~10TB

Discovery Environment

100’s Bioinformatics Apps in WYSIWYG interface

AtmosphereOne-click access to configurable

virtual machines

DNA SubwayClassroom-friendly workflows

for Annotation, DNA Barcoding, RNA-Seq

Training and SupportOnline and onsite training, user forums, support

HPC ResourcesUA Condor Cluster + XSEDE resources at TACC

Science APIsLow-level system APIs + Public Science APIs

Faculty identified guiding requirements that shape the development of iPlant’s educational platforms:

• Mix lecture and lab – have a wet bench “hook”

• Student-scientist partnerships – someone has to care about the data

• Co-investigation – projects should potentially lead to publications

• Scale – platforms should support projects multiple classrooms can join.

Guiding Principles

DNA SubwayEducational workflows for Genomes, DNA Barcoding, RNA-Seq

Commonly used bioinformatics tools in streamlined workflows

Teach important concepts in biology and bioinformatics

Inquiry-based experiments for novel discovery and publication of data

Sequencing

Towards an egalitarian biologyNA purification

Towards an egalitarian bioinformatics

$ tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq$ tophat -p 8 -G genes.gtf -o C1_R2_thout genome C1_R2_1.fq C1_R2_2.fq$ tophat -p 8 -G genes.gtf -o C1_R3_thout genome C1_R3_1.fq C1_R3_2.fq$ tophat -p 8 -G genes.gtf -o C2_R1_thout genome C2_R1_1.fq C1_R1_2.fq$ tophat -p 8 -G genes.gtf -o C2_R2_thout genome C2_R2_1.fq C1_R2_2.fq$ tophat -p 8 -G genes.gtf -o C2_R3_thout genome C2_R3_1.fq C1_R3_2.fq

$ cufflinks -p 8 -o C1_R1_clout C1_R1_thout/accepted_hits.bam$ cufflinks -p 8 -o C1_R2_clout C1_R2_thout/accepted_hits.bam$ cufflinks -p 8 -o C1_R3_clout C1_R3_thout/accepted_hits.bam$ cufflinks -p 8 -o C2_R1_clout C2_R1_thout/accepted_hits.bam$ cufflinks -p 8 -o C2_R2_clout C2_R2_thout/accepted_hits.bam$ cufflinks -p 8 -o C2_R3_clout C2_R3_thout/accepted_hits.bam

$ cuffmerge -g genes.gtf -s genome.fa -p 8 assemblies.txt

$ cuffdiff -o diff_out -b genome.fa -p 8 –L C1,C2 -u merged_asm/merged.gtf \./C1_R1_thout/accepted_hits.bam,./C1_R2_thout/accepted_hits.bam,\./C1_R3_thout/accepted_hits.bam \./C2_R1_thout/accepted_hits.bam,\./C2_R3_thout/accepted_hits.bam,./C2_R2_thout/accepted_hits.bam

CI enables bioinformatics education

www.urbanbarcodeproject.org