Post on 01-Jan-2016
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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