This week’s tip isn’t about a specific tool–but a really interesting look at how a tool was used in the context of some general public outreach messaging. Recently I posted about Aquaria, a new tool available to let biologists explore protein structures, mutations, and domains in user-friendly ways. But an interesting example of how the information about protein structures can be used to drive understanding came from a video animation of protein accumulation in Alzheimer’s. Just have a look at the video first and enjoy it. How cool is that clathrin basket pulling the vesicle in?
Description from their brochure at the launch [PDF]:
Christopher Hammang’s “Alzheimer’s Enigma” which explores the neurons of the human brain, and reveals how normal protein breakdown processes become dysfunctional and result in plaque formation during Alzheimer’s disease.
I found out about it as I was looking at the upcoming VIZBI talks and exploring their site for other features. In the VizbiPlus section there are a number of excellent animations of molecular processes, and this video was one of them. Be sure to watch for other tweets with the #vizbi hashtag for the next few days. I bet you’ll see some amazing tools and visualizations, as always.
Recently I mentioned the longer, more comprehensive, video from the Aquaria team, but I didn’t use that for my tip–I just used the short version overview. But the longer version had this extra bonus piece of how their software had been used by this animator. Here is Christopher Hammang, creator of this video, describing how he used the Aquaria information to generate the structural model for his animation:
Often it helps people to see how someone else used a tool for a project to get a better grasp of it. And this seemed like such a compelling and unusual example, I wanted to highlight it.
So again I’ll point you to the Aquaria tool tip from earlier this month to explore more, now with an understanding of an example of its use. But I would also encourage you to have a look at the other animations coming out of VIZBI at the VizbiPlus page. I swear, the animated intestine is way cooler than you might expect. The diabetes + insulin receptor videos are really informative and helpful. A cancer video illustrates a misbehaving p53. Go look.
VizbiPlus videos: http://www.vizbi.org/Plus/
VizbiPlus Poster from Hammang and team: Alzheimer’s Enigma: Putting the Pieces Together http://www.vizbi.org/Posters/2015/B08
Vizbi Posters: http://www.vizbi.org/Posters/
O’Donoghue S.I., Kenneth S Sabir, Maria Kalemanov, Christian Stolte, Benjamin Wellmann, Vivian Ho, Manfred Roos, Nelson Perdigão, Fabian A Buske, Julian Heinrich & Burkhard Rost & (2015). Aquaria: simplifying discovery and insight from protein structures, Nature Methods, 12 (2) 98-99. DOI: http://dx.doi.org/10.1038/nmeth.3258