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Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
Big Data and Tangibles - TEI 13
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Big Data and Tangibles - TEI 13

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Slides created for the Tangible Embedded & Embodied Interaction conference 2013

Slides created for the Tangible Embedded & Embodied Interaction conference 2013

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  • 1. From Big Data to Insights: Opportunities and Challenges for TEI in Genomics Orit Shaer, Ali Mazalek, Brygg Ullmer, Miriam K. Konkel
  • 2. Outline Introduction to genomics/motivation Design challenges Case studies Opportunities for TEI Going forward
  • 3. Genomics “While the work is a challenge, making genetics interactive is potentially as transformative as the move from batch processing to time sharing” -Bafna V. et al. Communications of the ACM Jan 2013
  • 4. Project flow: Genome Sequencing Project Sequencing Centers High- throughput Sequencing Draft Sequence Finished Sequence Sequence Archiving Genome Annotation DNA Sequence Protein Prediction Pathways Comparative Analysis Target Selection
  • 5. Schkolne, Ishii, and Schroder 2004. TEI for Scientists Gillet et al. 2005Brooks et al. 1990 Project GROPE Tabard, A., et. al 2011. eLabBench.
  • 6. Challenges Scale Heterogeneous Data Diverse Audience
  • 7. Scale Filesystem @ Broad Inst.: 13+PB One run of an Illumina HiSeq 2500: 6 billion paired-end sequences (600 gigabases, or 120Gb/day) Thousand Genomes project: 692 collaborators 110 institutions >15 groups in (bi-)weekly conference calls Blue Waters cluster: >380K CPU cores + >3K GPUs
  • 8. Heterogeneous Data
  • 9. Diverse Audience Genomic Scientists Citizen Scientist General Public Future Scientists
  • 10. How can TEI systems be designed to • Empower citizens to make informed health decisions? • Communicate scientific data to communities? • Enhance learning of complex concepts? • Support experts interacting with big data?
  • 11. Challenges Scale Heterogeneous Data Diverse Audience
  • 12. Case Studies Tabletop Genome Browsing & Primer Design Tangible-targeted Computational Genomics Tangibles For Visualizing Systems Biology
  • 13. Locate Learn Retrieve Annotate Compare
  • 14. 48.4% 1.0%2.4% 46.6% 1.6% Human genome: understanding ca. 2012 Mobile elements Processed pseudogenes Tandem repeats & low complexity DNA Dark matter Protein & RNA coding regions Composition of other primate genomes is very similar Tangibles-targeted computational genomics
  • 15. Example projects: rhesus, orangutan, human, marmoset genomes • Often multi-institution, multi-person efforts – Above articles: ~250, 100 co-authors • Often long duration (e.g., 4-6 years before first publication) • Iterative fusion of computational and “wet bench” analyses • Some analyses “big CPU” (e.g., 200 cpu cores for weeks); others, “big RAM” (200+GB RAM)
  • 16. Tangible Visualization: persistent representations of people, projects, activities… Interactions 2012.07: Entangling space, form, light, time, computational STEAM, and cultural artifacts
  • 17. CS3: Systems Biology Modeling
  • 18. Lessons learned TEI can facilitate immediate, visible, and easily reversible manipulations • How to design TEI for open-ended creative inquiries? Tangible representations can facilitate multi-stage workflows • Important for execution and tracking of complex analyses • Need parametrized, annotatable representations of complex large datasets TEI could facilitate collaboration for distributed and co-located teams • Large interdisciplinary teams and distributed work are common in this area • Users can jointly manipulate assumptions and see consequences Tangible tools can support understanding and discovery • Provide access to different pieces of the problem (data, reactions) • Help users forms accurate mental models through tangible/embodied manipulation
  • 19. Opportunities for TEI Engagement Understanding Complex Problems Visualizing Biological Data Enabling Large Collaborations Supporting Diverse Audiences Managing Varied Timescales
  • 20. Understanding Complex Problems
  • 21. Enabling Large Collaborations
  • 22. Managing Varied Timescales Powers of 10,000: • Milliseconds • Minutes • Months • Millenia Entangling Space, Form, Light, Time, Computational STEAM, and Cultural Artifacts Examples • Many genome projects: 5+ years • Sequencing Lincoln’s DNA: under active discussion since 1991 • Most of us sequenced within decade? materially impacting all our descendants
  • 23. Going forward • Some aspects w/ broad TEI, computational science synergies • How to visualize and engage data, activity, progress spanning many systems, people, places, timescales? • What representational forms, device ecologies, most appropriate for large, abstract data? • Facilitating engagement with big data in ways that highlight connections between multiple forms of evidence • Some aspects specific to genomics • 2023: anticipate most of us in room + many thousands of species having genomes fully or partially sequenced • Commonalities, distinctions in engagements by scientists, students, street people, senators, senior citizens, solicitors, …
  • 24. THANKS! Orit Shaer: oshaer@wellesley.edu Ali Mazalek: mazalek@gatech.edu Brygg Ullmer: ullmer@lsu.edu Miriam Konkel: konkel@lsu.edu Consuelo Valdes (Wellesley College) and Andy Wu (Georgia Tech). This work has been partially funded by NSF IIS-1017693, DRL- 097394084, and CNS-1126739.

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