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Shiran Pasternak › Likes

Deepak Singh
Hadoop World video is out - http://mndoci.com/2009...
Only took, what, 2 months to post this... - Shiran Pasternak
Watching now. BTW, you've convinced me to try "hundreds of slides" approach some day - I wasn't sure it works in more scientific talks. - Pawel Szczesny
Pawel, I wasn't sure either, but I've had a chance to do deeper dives now (at Supercomputing) and it seems to work, especially as I get more comfortable talking science in this format. If I had to choose an alternate one it would be a pure storytelling/figure format, i.e. about some of your core results and work backwards if required. - Deepak Singh
that was a really great talk! - Jeremy Leipzig
Jeremy, thanks - Deepak Singh
Jonathan Eisen
Overselling genomics headline of day: Decoded Corn Genome Promises Higher Yields, Better Biofuels, New Plastics - http://www.popsci.com/node...
Let's not forget cure cancer, cut through metal, and pick up any stain. It's all there, in the Science paper. - Shiran Pasternak
Thank goodness. Been very worried about how to cut through metal these days - Jonathan Eisen
Michael Nielsen
Access denied? : Article : Nature - http://www.nature.com/nature...
"Every weekday, thousands of researchers around the world access the Arabidopsis Information Resource (TAIR), which contains the most reliable and up-to-date genomic information available on the most widely used model organism in the plant kingdom. But now, to those users' horror, TAIR faces collapse: the US National Science Foundation (NSF) is phasing out funding after 10 years as the data resource's sole supporter (see page 258). TAIR's plight is emblematic of a broader crisis facing many of the world's biological databases and repositories. Research funding agencies recognize that such infrastructures are crucial to the ongoing conduct of science, yet few are willing to finance them indefinitely. Such agencies tend to support these resources during the development phase, but then expect them to find sustainable funding elsewhere." - Michael Nielsen
Jan Aerts
Followed a presentation about Bio::DB::Sam. Impressive. Speaker mentioned only perl/java APIs to Ensembl. What about my ruby API?? :-(
Jonathan Eisen
The Human Genome in 3 Dimensions | Wired Science | Wired.com - http://www.wired.com/wiredsc...
Matt Wood
Todd Harris
I am my own model organism: getting genotyped (Part I) - http://toddharris.net/blog...
Cool - I used to read sequence on films as well :-) Genotyping will be on top of my wish list for Christmas. I need to decide on 23andme , DecodeMe or another supplier. I may go with DecodeMe just to support them....if they still exist... - Nils Reinton
@Nils: I'll detail why I went (initially) with 23andMe in a follow up post. But cost, data availability, and data sharing options where the main reasons. Navigenics charges $199 after the first year for updated analyses. And like you, I just wasn't sure about Decode being around for the long haul... - Todd Harris
Hmmm. Having myself genotyped vs having a lasik surgery to get rid of glasses. On a student budget, can't really afford either, but the latter would be more bang for the buck. Would be cool though. But not via the service my ex-employers back home in Iceland offer - financial situation pretty dire currently. - 'Mummi' Thorisson
Think I will put genotyping on my xmas wishlist as well. @Nils, @Todd: I too have read sequence on film; we are really dating ourselves by admitting to this! - Bill Hooker
It's going to be the nerdiest xmas ever! One of my most exciting moments at the bench was reading off a sequencing gel late in the night, finally coming across the first mutation in a gene I had been positionally cloning for years. It was at the limits of resolution but still clear enough to poke your eye out. Seems mundane now, huh? I still think the readouts from old school sequencing gels are amazing - such a tangible way of seeing the unseeable. - Todd Harris
I wish I'd kept a few of my old gel films -- I'd like to frame one to hang on a wall at home. Nerd art! - Bill Hooker
Me too! I had a boxes and boxes of autorads, lost somewhere along the way during the inevitable academic life-shuffle. - Todd Harris
@Bill, @Todd I'll dig out some of my old ones and send them to you for christmas...if you're lucky you'll get some of those with smiley bands in the corners and edges of the gel :-) - Nils Reinton
Steve Koch
60 minute video (real player): Dr. Collins' introductory presentation, first day on the job as NIH Director. - http://videocast.nih.gov/Summary...
derek
The Long And Short Of It « Nimble Code - http://nimblecode.com/2009...
Adriano
Neuroanatomy to Nirvana :: Stroke leads Jill Bolte Taylor to Insight - http://www.nytimes.com/2008...
Neuroanatomy to Nirvana :: Stroke leads Jill Bolte Taylor to Insight
Neuroanatomy to Nirvana :: Stroke leads Jill Bolte Taylor to Insight
"Jill Bolte Taylor was a neuroscientist working at Harvard's brain research center when she experienced nirvana. The incessant chatter that normally filled her mind disappeared. She could see that the atoms and molecules making up her body blended with the space around her; the whole world and the creatures in it were all part of the same magnificent field of shimmering energy. 'My perception of physical boundaries was no longer limited to where my skin met air,' she has written in her memoir, 'My Stroke of Insight.' Today, she says, she is a new person, one who 'can step into the consciousness of my right hemisphere' on command and be 'one with all that is.' To her it is not faith, but science. Her message, that people can choose to live a more peaceful, spiritual life by sidestepping their left brain, has resonated widely. She was chosen as one of Time magazine's 100 most influential people in the world for 2008." See also her video at TED http://www.ted.com/index... [thanks to @paul for posting the NYT article] #rsvp01 - Adriano from Bookmarklet
Todd Harris
Jan Aerts
Nice. While I like and appreicate good visualizations, there are too many cases (networks are my current bug bea), where it seems that the goal is just to make pretty pictures. In those cases, it has seemed to me that unless I know what I'm looking for, the visualization is worse than a summary (for practical purposes). Of course a combination of vis and summary is ideal. - Rajarshi Guha
Man, great thinking for a very often occuring problem ! - joergkurtwegner
I'm not sure how much Processing can help with ad hoc data visualization. There is still a learning and programmatic curve, albeit smaller. How can you easily load the data and provide a graphical UI to it? I played around with Spotfire a few years ago, which can readily transform any tabular data into particle plots and other agnostic yet intuitive visualizations. But Spotfire is super-expensive. Google and NYTimes are taking steps towards providing open visualization APIs. - Shiran Pasternak
I agree, I quickly looked into 'processing', and for my daily work I could not imagine to work without SpotFire, but I can ignore 'processing'. Beside, the interface in 'processing' seems not practical and flexible enough for scientific data ? - joergkurtwegner
@Shiran: "not sure how much Processing can help with ad hoc visualization". That's _exactly_ what I use it for. The scripts are often so small that they are merely "sketches" (in Processing-lingo). Even though a tool like Spotfire is very useful, it falls short when your data contains many types of information. For example: clone read pairs mapped on a genome: there are the actual mappings, whether or not they map where they should, quality values, inversions, ... Any visualization has to be custom. - Jan Aerts
In that case, do you have any example scripts you can share? I didn't mean to rag on Processing. It's a great tool (especially coming from a Java and OpenGL background), and the applications out there that use it are fascinating. - Shiran Pasternak
Jan I'd also be interested in some examples. The one and only processing sketch I've attempted is http://tinyurl.com/5r7543 to demonstrate a simple algorithm. When visualizing data I tend towards plots and molecular graphics. There's also ruby-processing http://github.com/jashken... which you might find easier as a ruby programmer. - Adam Kraut
@Shiran, Adam: As they're sketches of current work, am not allowed to put them online. But I will probably generalize one of my current visualizations and put it on github. Will let you know when that has happened. My very first hack was a proof-of-concept for comparative map viewer (http://tinyurl.com/5gkt85). - Jan Aerts
It is so cool to see Processing used to display scientific data! It can really lead to wider usage of advanced open source data vis libraries and APIs, that includes Google, NYT, and others. Check out the Javascript Processing.js which nicely expands the cross platform compatibility. If you get a chance to put more examples on github it would be appreciated, looking forward to seeing what else you are working on =) - Mike Chelen
Todd Harris
Hey! I got a wave from Maryanne Vollers on the Huffington Post! - http://is.gd/6m8s
Jan Aerts
Added Transcript#introns to the ruby ensembl API.
Todd Harris
finance.google.com needs to rotate their favicon.ico 90° clockwise. - http://finance.google.com/finance
Todd Harris
Designing potent posters: Process, Format, Presentation - http://thewildtype.com/2008...
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