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The iPlant Collaborative Cyberinfrastructure supports bioinformatics education by offering comprehensive resources for educators and students. This initiative provides online and onsite training, user support forums, and an extensive library of bioinformatics applications accessible through a user-friendly interface. With tools for DNA barcoding, RNA-Seq, and innovative educational workflows, the iPlant platform encourages student-scientist partnerships and inquiry-based experiments, fostering a collaborative environment for research and discovery within life sciences curricula.
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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
Cyberinfrastructure is a key enabler for bioinformatics education
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
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.
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
Towards an egalitarian biology NA purification Sequencing
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
