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The iPlant Collaborative Community Cyberinfrastructure for Life Science

The iPlant Collaborative Community Cyberinfrastructure for Life Science. Network for Integrating Bioinformatics into Life Sciences Education April, 2014 – Omaha, Nebraska Jason Williams Cold Spring Harbor Laboratory / iPlant Collaborative.

deanna-levine
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The iPlant Collaborative Community Cyberinfrastructure for Life Science

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  1. The iPlant Collaborative Community Cyberinfrastructure for Life Science Network for Integrating Bioinformatics into Life Sciences Education April, 2014 – Omaha, Nebraska Jason Williams Cold Spring Harbor Laboratory / iPlant Collaborative

  2. Cyberinfrastructure is a key enabler for bioinformatics education

  3. What is Cyberinfrastructure? Training and Support Online and onsite training, user forums, support Discovery Environment 100’s Bioinformatics Apps in WYSIWYG interface Atmosphere One-click access to configurable virtual machines DNA Subway Classroom-friendly workflows for Annotation, DNA Barcoding, RNA-Seq Science APIs Low-level system APIs + Public Science APIs iPlant Data Store 100 GB allocation per user – up to ~10TB HPC Resources UA Condor Cluster + XSEDE resources at TACC

  4. Guiding Principles 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.

  5. DNA Subway Educational 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

  6. Towards an egalitarian biology NA purification Sequencing

  7. 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

  8. CI enables bioinformatics education www.urbanbarcodeproject.org

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