Top geek movie figures, part 1: Skull in Monster house

Chowder:

“Skull is in the game zone, right now. And you don’t want to mess with him when he is in the game zone. He once played for 4 days straight on 1 quarter, a gallon of chocolate milk and an adult diaper.”

 

 

Blogxperiment: mitochondrial division, the graphics way

In the blogxperiment series part 1 the question was: What is the best way to summarize peer-review articles for an open web readership and transmit scholarly knowledge and literature? Here is the cartoon way, figure 1. out of the context of The Machines that Divide and Fuse Mitochondria review, written by Suzanne Hoppins, Laura Lackner, and Jodi Nunnari of Section of Molecular and Cellular Biology, University of California, Davis.

You can read the legend in the rest of the post to check how much visual information you caught without textual context:

LabAction.com: new player on the science video niche market

Well, I am pleased to announce that we’ve just entered into an era of online scientific video sharing as there exists now a nascent niche market around. After the first mover JoVE (Journal of Visualized Expermients, covered many times here), LabAction.com was launched on 21st March 07 with as many as 3 biology-related videos. And I am more happy since one of my post had a little role as founder Ian Brown emailed me: “I read one of your blog on Science: video protocols can help to share the tacit dimension that appeared in October 06. It really inspired me to do a YouTube for LifeScientists. It took me quite some time to figure out what it takes to built a video sharing site but yes that was a good experience. I have recently launched a site www.labaction.com for sharing Biology videos.”

Ok, so LabAction is a definitely a YouTube-like video sharing surface, where everybody can upload their scientific related videos on protocols, products and so on. That means there won’t be any quality control here in contrast with JoVE’s editorial review process due to the novelty and required quality of video science publishing, but on the other hand LabAction could be popular because everybody can upload videos here. It could become a pop science site and for instance it may also be the place of high tech product adverstising, just like this cool microarray video ad, where at the turntable there is a guru made out of pipette tips scratching with a magnetic mixer, while eppendorf hiphop freaks are enjoying the perfomance of microarray built high tech break dancers.

From Ian’s writeup: LabAction.com presents a portal where researchers can share the much needed information on essential steps of new protocols and techniques. Videos and commentaries on every aspect of biology ranging from basic molecular biology to complex protein microarray experiments or trickiest surgery could be made accessible using video formats.

Nature Publishing Editor on the idea of a public scientific multimedia site

Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke (emphasis by me).

On the possibility of a community-approved public multimedia site (videos, audios, pictures) with open access supporting information from peer-review journals.

It would indeed be nice for authors and readers to have such a facility. If there were to be a multimedia database, accepted by the community, we’d be happy to consider making deposition mandatory. Our principle is that data described in our papers are freely available, so if there were a community-approved public multimedia site, which included annotatation and curation, we’d be happy to consider making it a condition of publication for movies etc to be deposited in it. It would need to be publisher-independent to work, so that authors could upload multimedia data wherever they’d published their paper.

The main point for us at Nature is that as a publisher we have to be confident that material published off our website is properly curated, archived and preserved. For example, when we introduced the microarray deposition policy we ensured that there was full community support for the two databases (in one of which, authors’ choice, we require deposition) before implementing the policy. So for this video idea to work, the “database” concerned would need to be publicly accessible (not commercial), curated, annotated etc.

On the status of online supporting information at Nature:

Supplementary Information on the Nature website is free, though you have to register. (Confirmed, see screenshot of a 3D supplementary animation showing that the gut-associated lymphoid tissue comprised of different subsets of haematopoietic cells, Veiga-Fernandes et al.)

On the problem and handling of online supporting information:

Terrific cell biology animation (decoded): a trailer now, and a video for all

One of the constant hits of Pimm is the Terrific Pixar-style Harvard animation on molecular biology. The early animation was full of riddles for the non-experts, since it lacked the informative narration, the act of naming, just like we were at the age of silent films. Not anymore! Thanks to alfredoalcalde the full video with narration was uploaded on January 13, 2007. Now all XVIVO (the makers of the animation) folks have to do is to write a whole script and sell it to Pixar-Disney in Hollywood, as they have a fantastic trailer now: The story of a single leukocyte hero who is preparing for a terrible inflammation through leukocyte extravasation, where at sites of inflammation and in normal immune surveillance, chemokines direct leukocyte migration across the endothelium….Success guaranteed, this trailer will be an all-time educational hit. Original link via Biosingularity.

Update: It turned out that Harvard considers the full length version of ‘Inner Life of the Cell’ a fully copyrighted work. So the video was removed.

You can view the whole movie here without legends and animation, so the riddle remains.

Terrific Pixar-style Harvard animation on molecular biology

In my biologically committed childhood I fantasized about a movie which presents all the main actors of the cell machinery: nucleic acids, enzymes, cytoskeleton (see left), ribosomes (mRNA translation into polypeptide chain, see right), hydrophob and hydrophil proteins, lipid membrane bilayers, kinesins and so on. Now BioVisions from Harvard made half my dreams (no intranuclear story just cytoplasmic) come true, although I am just not sure about the music. Conception and scientific content: Alain Viel, Robert A. Lue, animation by John Liebler. The company behind is XVIVO, a Connecticut based scientific animation company. The movie is extremely useful for educational purposes. Link via BoingBoing from astroshack.

Imagine this made out of Lego bricks. When will Lego produce MatterStorms for bioDIYers besides Mindstorms for infoDIYers? Bionicle is not about biology at all.