CI2Daggett Research Group

University of Washington - College of Engineering - School of Medicine - Department of Bioengineering

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Paper of the Month

DIVE: A data instensive visualization engine.
Paper of the Month
Bromley, D., Rysavy, S.J., Su, R., Toofanny, R.D., Schmidlin, T., Daggett V.
Bioinformatics 30:593, 2014

Modern scientific investigation is generating increasingly larger data sets, yet analyzing these data with current tools is challenging. DIVE is a software framework intended to facilitate big data analysis and reduce the time to scientific insight. Here we present features of the framework and demonstrate DIVE’s application to the Dynameomics project, looking specifically at two proteins. More...


Goals: Realistic simulation of protein dynamics, unfolding/folding, and conformational transitions linked to disease.

Protein Simulation and Analysis

Latest News

  • FINALLY, experimental results backing our 2004 hypothesis that alpha-sheet structure is associated with toxicity during amyloidosis has just gone live in eLife! Get the paper here.
  • Our recent IEEE Computer Graphics and Applications paper describing DIVE our new visual analytics framework was the 2nd most downloaded paper in CG&A in May and was the number 1 most downloaded paper in June. Get the paper here.
  • Congratulations to Dr. Sarah Nowakowski who very successfully defended her doctoral thesis on 6/12/14. Sarah gave a beautiful talk describing atomistic studies of myosin to investigate the mechanism of action of deoxy ATP and then moved to in vitro work, ex vivo beating heart experiments and finally various animal studies! Certainly multiscale. Congratulations Sarah!
  • Congratulations to Nishant Velagapudi who has just received a $1000 Scholarship through the I-School from the Bockman Endowed Fund for the 2014-15 academic year!
  • Congratulations to William Walker and Devin Gerboth who has just received two of four Bioengineering Scholarships for undergraduates through the College of Engineering for the 2014-15 academic year!
  • Congratulations to Devin Gerboth who received a 2014 NASA summer fellowship to support his research in the group!
  • Congratulations to Ivan Vulovic who will be joining the Molecular Engineering PhD Program Autumn 2014!
  • We have just released DIVE, our Data Intensive Visual Analytics software framework for accessing, streaming, interrogating, comparing, and visualizing big data. See our new papers in Bioinformatics and IEEE Computer Graphics and Applications (see Publications page). Get more information about downloading DIVE here.
  • Congratulations to Dr. Steve Rysavy who successfully defended his doctoral thesis entitled "Data-driven Methods and Models for Predicting Protein Structure using Dynamic Fragments and Rotamers" on 2/7/14. Steve did a fantastic job! He has also had two papers published recently, and he has several more submitted or nearly ready for submission, in addition to patent applications. Congratulations Steve!
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