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I'm following 18 peeps on FF and 5 were at #sbcPA
Mike Chelen, Cameron Neylon, Deepak Singh and 6 other people liked this
Brilliant people all - Ariel Waldman, Cameron Neylon, Duncan Hull, Martin Fenner, and Sirley Wu - first time to meet all of them in person. I also got to meet two SL friends in RL for the first time - Joanna Scott & Melanie Swan. It felt like a family reunion. :)
- Andrew Lang
Nice to meet you (for real) Andrew!
- Duncan Hull
like a kid in a candy store, right? :)
- Jean-Claude Bradley
Nice to meet you too Andrew, and all the others not mentioned. One and a half days is really short. So a little bit like the candy store 30 min before closing.
- Martin Fenner
Some interesting talks today but really it is the people that made the event. Many thanks to the organizers.
- Andrew Lang
Virtual conference quandary for researchers - http://www.rsc.org/chemist...
Egon Willighagen, Jean-Claude Bradley and Peter Miller liked this
I just wonder how much impact it can have if the materials are not freely accessible
- Jean-Claude Bradley
true - i did like the ability to go back and view any talk again.
- Andrew Lang
Hollywood Inserts Quarter For ‘Asteroids,’ Will Adapt Classic Atari Video Game - http://moviesblog.mtv.com/2009...
Solubility data uploaded to Google Fusion Tables - Displaying solid carboxylic acids in methanol.
Daniel Mietchen, Khalid Mirza, Konrad Förstner and 3 other people liked this
sweet - does it have an API?
- Jean-Claude Bradley
no API as of yet - today was the first day I could actually import the data. It has been very unGoogle-like in exhibiting bugs. For the future I can see this is the tool we'll use for the solubility data but just something fun to play with right now.
- Andrew Lang
Acetylcholinesterase in SL and Hex 5.1 - http://www.flickr.com/photos...
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Konrad Förstner, joergkurtwegner, Berci Mesko and 5 other people liked this
texturing to show the charges of the protein subunits would also be interesting
- Mike Chelen
I've used numbered grids to play around a little with texturing -- nice if it could be semi-automated. Some way beyond non-trivial for me, alas.You can use SculptyPaint as well, I guess.
- Peter Miller
manual texturing might be useful to highlight specific areas involved in a reaction
- Mike Chelen
Interesting. A custom texture web service should be possible. How are these things normally colour-coded, have any example images you can point me to?
- Andrew Lang
for atoms electrical charge is one way, http://personal.cscs.ch/~mvalle... (from http://personal.cscs.ch/~mvalle... ) and another is the electric fields http://www.chemcomp.com/journal... (from http://www.chemcomp.com/journal... ), similarly in proteins coloring can be based on the...
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- Mike Chelen
I looked at the pdb format and there is a column for atom charge in the specification but with a random selection of pdb files, that column was always blank, so I decided to color according to nearest amino acid residue, see: http://www.flickr.com/photos...
- Andrew Lang
that looks great! amino acids are indeed of primary consideration when viewing an entire protein. what is the coloring key, is it based on charge?
- Mike Chelen
Colors are as in jmol: http://jmol.sourceforge.net/jscolor...: amino acids, nucleotides
- Andrew Lang
Marvellous! Is the texture generated automagically alongside the sculpty?
- Peter Miller
@Peter - The texture is created and displayed next to the sculpt map. I just updated the original service.
- Andrew Lang
Many thanks!
- Peter Miller
These are looking great! Is the program source code available? The only other thing that would be useful is additional texture maps for polarity and charge: http://en.wikipedia.org/wiki...
- Mike Chelen
@Mike. IM me your email and I'll send you the code. asp.net
- Andrew Lang
Thanks for the link Mike - service now does polarity and charge colour textures - http://www.flickr.com/photos...
- Andrew Lang
Sending my email now, is the code under GPL or similar? Also, what do you think would be a good way to share the generated files on the web, and in world? The additional textures make these even better, think they are some of the best in-world learning tools for biology and chemistry!
- Mike Chelen
Uploading to flickr is good - we could tag them in some way - maybe 'slprotein'. I can release code - I'm thinking MIT licence right now, unless that's not good for you. I'm flexible. Didn't get your email. I'll zip up the code and put it on the website: http://slusage.com/sculpties/
- Andrew Lang
Flickr tags would be good, and could include the RCSB entry id. Would it be possible to output sculpty maps as lossless TIFF files? Maybe once there were a few collected, they could be put into a pack for SL. Any open-source license is fine by me, thanks for putting up the code! I imported it to github- http://github.com/mchelen... based on the file name, what would be the preferred title?
- Mike Chelen
Thanks for githubbing it for me.
- Andrew Lang
Andrew: sure thing, still learning git and need the practice :) tried switching the image format from Jpeg to Tiff- http://github.com/mchelen... don't have an asp/.net platform to test it on though
- Mike Chelen
Heard one feature request to allow direct upload of PDB (in addition to linking of file URL)
- Mike Chelen
WoW in education - http://wowinschool.pbworks.com/
Peter Miller liked this
see also: http://www.wow.com/2009...
- Andrew Lang
Game Theory - http://xkcd.com/601/
Love is like global thermonuclear war.
- Andrew Lang
Math and Society the 2009 Iranian Presidential Election - http://webapps.oru.edu/new_php...
Event: The Medea Hypothesis - http://network.nature.com/people...
Dr. Lang Headed to Science Foo Camp - June 16, 2009 - http://www.oru.edu/news...
Peter Miller liked this
Brilliant!
- Peter Miller
Plotting the Salary of Politicians versus their Effectiveness - http://infosthetics.com/archive...
The 7 Most Impressive Libraries From Throughout History - http://www.cartridgesave.co.uk/news...
Why we shouldn't get carried away with data visualization - http://www.hulu.com/watch...
Google Wave on GitHub - http://wave.thewe.net/2009...
Peter Miller liked this
Google Wave gadget emulator on GitHub.
- Andrew Lang
SkyLabs Launch: Hiro Sheridan demo - http://www.flickr.com/photos...
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Mike Chelen liked this
That was a great session -- just disappointed I had to leave so early and, given I was at work, only had low rez screen capture. I'm hoping this initiative could move things forward significantly, even if only by bringing some "old-timers" together on a more regular basis. :)
- Peter Miller
Dr Who fan has flashing blue light on Tardis coffin at his funeral. http://www.mirror.co.uk/news...
I like SF but not this much. ".... And instead of readings from the scriptures, the service used excerpts from Dr Who scripts."
- Andrew Lang
Been looking through the list of people going to sci-foo. My favourite so far - Bill Nye - what does that say about me?
Jean-Claude Bradley liked this
I haven't even got that far yet.....
- Cameron Neylon
now the planetary guy as well as the science guy :)
- Christina Pikas
Call to action - wikipedia editor questions the reliability of data from open science - please go to his talk page and add your support for the ONSchallenge: http://en.wikipedia.org/wiki...
Konrad Förstner, Arunn, Daniel Mietchen and 7 other people liked this
quote from editor: "Although I am sure that this school project was fun for the kids, Wikipedia needs to have data here from verifiable sources. Reference to a university site (Oral Roberts or Harvard) is not good enough. Otherwise your work risks being deleted. NIST, CRC etc, now they are authorities. I really encourage you to consult someone before launching on what looks like a well intentioned but naively planned project."
- Andrew Lang
Please help. Go to the talk page and make a comment. Thanks!
- Andrew Lang
There is probably a value in thinking carefully about the response here. I have heard some criticisms of the methodology being used and have suggested that people make those criticisms in the project notebooks but this hasn't happened as yet. Strictly the WP guidelines do require a traditionally published (non-web) verifiable source and one could make an argument that these results have...
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- Cameron Neylon
I think it has been peer reviewed - http://onschallenge.wikispaces.com/judges
- Andrew Lang
...but not in the traditional way...I agree with you but it's a subtle argument and it could get lost
- Cameron Neylon
I would also say that at the end of the day there is much more back up on our data than there is for a NIST or CRC value in many cases - at least you can tell what was measured. Just not sure whether that will be enough for the traditionalists. Just worth rehearsing the arguments I guess i what I am saying.
- Cameron Neylon
Can you link the actual page that's in dispute? Major flaw in WP talk imo, there are no auto links to the pages being discussed.
- Bill Hooker
@Bill Here's my edits - he's questioning them all: http://en.wikipedia.org/wiki...
- Andrew Lang
Lets keep in mind that none of the other properties even have references (see for example benzoic acid: http://en.wikipedia.org/wiki... )
- Jean-Claude Bradley
Just noticed in the urea talk page someone complaining in 2007 that all the solubility values were wrong and unreferenced :-)
- Cameron Neylon
Added my comment. It seems to me that, as a source to be quoted in WP, open notebooks are a new category (see http://en.wikipedia.org/wiki...). They are not "third-party published sources with a reputation for fact-checking and accuracy", but they are "produced by an established expert on the topic" in the sense that JC runs the project and we judges are all scientists. More to the point, WP has never been asked to consider this kind of source before.
- Bill Hooker
Thanks Bill.
- Andrew Lang
@Cameron Good find! I can see the ppt slide now. Here's the quote from 2007 about the solubility in water - it seems to have never been resolved - "The article provides some specific information about the solubility of urea without giving a source. The values were out by at least a factor of 10 (probably g/L rather than g/100mL), which I have corrected by knocking off the last zero, but...
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- Andrew Lang
I added my 2 cents: http://en.wikipedia.org/w... . Still do not get why none of you guys - so much engaged in doing open science - seem to have ever shown up at Citizendium, a place where expertise is actually valued. It is currently very small compared to Wikipedia, but so is Open Science compared to the rest. See also http://en.wikiversity.org/wiki... .
- Daniel Mietchen
Thanks for adding a post to the discussion on wikipedia Daniel. I will check out Citizendium.
- Andrew Lang
I believe the reason most of us stick to Wikipedia is that we believe that it is (a) the appropriate general resource and (b) since it is the source most people, and Google, go to, information will be found there.
- Deepak Singh
Certainly nothing wrong with reading or editing Wikipedia entries. But the sort of problem discussed in this thread would be much rarer over there at Citizendium (they have others), and since it tends to affect scientists quite often, I am wondering why they do not give this alternative a try. Andrew Su has done that, and he was disappointed (a feeling I share for his case, since I...
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- Daniel Mietchen
Daniel - thanks for the comments and for the link to Wikiversity and Citizendium - we'll certainly check it out. A first look does not show any entries for common chemicals like methanol. Additional portals are always of interest though. The reason Wikipedia is useful is that it turns out to be a significant way people looking for specific non-aqueous solubility find our results.
- Jean-Claude Bradley
Bing - "Solubility of benzoic acid" search results roll-over gives solubility values in THF, acetone, and acetonitile from ONSchallenge data.
Cameron Neylon and Jean-Claude Bradley liked this
Project Natal, Minority Report, and Holodecks - http://snsf.blogspot.com/2009...
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Just after reading about eHits on the PS3, this news comes out, and my kids want a Wii. What to do? I bet this won't be out for 18 months though.
- Andrew Lang
Yes, the more polished video is a "conceptualisation" rather than a product demo. As the SL peeps note, it's potentially a space hog too.
- Peter Miller
It probably won't live up to the promo but the concept is cool and potentially game-changing, pun intended. :)
- Andrew Lang
Project Natal Motion Sensing Controller for XBOX 360 - http://www.youtube.com/watch...
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ORU professors talk science fiction - http://www.journalrecord.com/article...
My newspaper co-interview about science and science fiction.
- Andrew Lang
Event: Evil Genes - http://network.nature.com/people...
Return To ‘Alien’ Becomes A Reality, Prequel Confirmed By Tony Scott - http://moviesblog.mtv.com/2009...
I can't wait.
- Andrew Lang
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