--- Log opened Sat May 28 00:00:07 2011
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04:07 < kanzure> this was announced on the openscad list:
04:07 < kanzure> http://jayesh3.github.com/cadmium/
04:07 < kanzure> * The modelling scripts are written in Python, you don't have to learn
04:07 < kanzure> any new syntax.
04:07 < kanzure> * Most of Cadmium code is written in Python itself. Only <200 lines of
04:07 < kanzure> C/C++ code is used to load CGAL
04:07 < kanzure> * It has no GUI. Therefore it's light weight. It generates output in
04:07 < kanzure> STL format, which can be viewed in STL viewer of your choice. By
04:07 < kanzure> dropping GUI requirements, Cadmium sports minimal dependencies. (only
04:07 < kanzure> one - CGAL)
04:07 < kanzure> i don't see any reason to be excited about it, though
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08:59 < kanzure> does anyone remember if cgal does anything other than polyhedral boolean operations?
09:00 < kanzure> like, does it do manifold surface boolean operations?
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10:09 < kanzure> human brain project http://www.spiegel.de/wissenschaft/mensch/0,1518,761995,00.html
10:09 < kanzure> "Und was den Kampf gegen Krankheiten angeht: Die Medikamentenentwicklung
10:09 < kanzure> komme auch deswegen nicht voran, weil Pharmakonzerne die Investitionen
10:09 < kanzure> nicht schultern könnten"
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10:15 < ybit> a local friend found transcendental man and became interested in transhumanism
10:16 < ybit> i've steered him away from kurzweil, and he's loving this stuff
10:16 < ybit> this makes me a little happy
10:26 < ybit> haven't gotten that far in the cgal docs to know
12:54 < bkero> kanzure: ping
13:00 < kanzure> pong bkero
13:00 < bkero> kanzure: you still know some folks who print reprap replicatable patrs?
13:00 < bkero> *parts
13:00 < kanzure> are you looking to buy reprap parts?
13:01 < bkero> yes
13:01 < kanzure> you should ask in #reprap and a legion of people will try to get your business
13:01 < bkero> haha ok
13:01 < bkero> thanks
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13:37 < ybit> bkero, strages. strages, bkero.
13:38 < bkero> ybit: strages?
13:38 < bkero> strages: hi
13:38 < ybit> or just #reprap :)
13:38 < bkero> indeed
13:38 < bkero> #reprap said gtf2ebay
13:38 < ybit> oh yeah
13:38 < ybit> i asked once, got the same response
13:39  * ybit fetches his old logs... uno momento
13:48 < ybit> bkero: http://pastie.org/1986298
13:49 < ybit> exert from the tlabs wiki page
13:49 < ybit> might be helpful
13:51 < bkero> tlabs?
13:52 < bkero> ybit: wonder if it translates to a prusa model
13:52 < ybit> i dunno unfortunately
13:53 < bkero> I'm also interested in finding out the maximum size of a printed object by each
13:55 < ybit> tlabs/tweak labs, a bunch of broke local people that were interested in forming a hackerspace, then they all realized they were broke
14:17 < bkero> lol
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15:51 < kanzure> Induction of human neuronal cells by defined transcription factors http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature10202.html
15:51 < kanzure> i'll have to grab that later.
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17:25 < delinquentme_> any idea on this statement ?  specifically the 35x coverage part?  The pipeline can analyze over 35x coverage of a human genome in one day on a 10-node local cluster,
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18:03 < kanzure> delinquentme_: think of it as how many times over the entire genome
18:04 < delinquentme_> kanzure, is that necessary for a high quality read? or is that kind of something just to say "weve got this much power/ speed"
18:04 < kanzure> well, it depends on the read length
18:04 < kanzure> if you read in short segments then you need to increase the coverage
18:05 < kanzure> if you read the entire genome in one pass you just need 1x coverage
18:06 < delinquentme_> hmmm
18:07 < delinquentme_> so the 1x makes sense
18:07 < kanzure> Coverage is the average number of reads representing a given nucleotide in the reconstructed sequence.
18:07 < delinquentme_> how does more coverage make for better alignment of short reads .. is it because you've got more data to compare it to .. to verify the sequence its about to assemble?
18:07 < kanzure> It can be calculated from the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L /
18:08 < kanzure> For example, a hypothetical genome with 2,000 base pairs reconstructed from 8 reads with an average length of 500 nucleotides will have 2x redundancy. This parameter also enables one to estimate other quantities, such as the percentage of the genome covered by reads (sometimes also called coverage).
18:08 < kanzure> A high coverage in shotgun sequencing is desired because it can overcome errors in base calling and assembly. The subject of DNA sequencing theory addresses the relationships of such quantities.
18:09 < kanzure> Sequence coverage is the average number of times a base is read (as described above). Physical coverage is the average number of times a base is read or spanned by mate paired reads.
18:10 < delinquentme_> hurm so some of this makes sense .. other parts not so much .. coverage = avg # reads, representing a given nucleotide in reconstructed seq
18:11 < delinquentme_> oh wait .. so within say a 500 base pair seq
18:11 < delinquentme_> any particular nucleotide will be "crossed" twice
18:12 < delinquentme_> giving us 2x coverage
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18:59 < kanzure> http://whyevolutionistrue.wordpress.com/2011/05/28/the-longest-cell-in-the-history-of-life/
18:59 < kanzure> since when have anatomists agreed that nerves are single cells?
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19:37 < delinquentme_> any idea if there would be a IRC channel w kids familiar with amazon web services?
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19:49 < kanzure> delinquentme_: sure, i'm familiar with aws
19:49 < kanzure> although i probably don't count as a kid any more
19:49 < kanzure> try also ##aws and #startups
19:50 < delinquentme_> kanzure, yeap im there :D
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22:48 < JayDugger> Good evening, er...morning, everyone.
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23:11 < delinquentme_>  howdy JayDugger
23:11 < delinquentme_> yeah haha 2 am ..
23:11 < delinquentme_> (here)
23:17 < JayDugger> Not too far from that here.
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--- Log closed Sun May 29 00:00:07 2011