The iPlant Collaborative Community Cyberinfrastructure for Life Science Network for Integrating Bioinformatics into Life Sciences Education April, 2014.

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