--- Log opened Sat Mar 01 00:00:18 2014
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07:33 <@heath> hm, i'm not sure what to do with a montly meetup
07:33 <@heath> i'd rather just have a workspace dedicated to this stuff and people can join in whenever
07:36  * heath considers closing the diybio group here
07:41 < juri_> heath: where is 'here'?
07:42 <@heath> nashville tn
07:42 <@heath> usa
07:42  * juri_ nods.
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07:58 <@heath> well that felt better then I intended
08:00 < kanzure> gross
08:16 <@heath> s/then/than #make kanzure feel less icky
08:17 < curt1s> heh
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08:29 < kanzure> "To tell you the truth, irreproducible work doesn't come from mal intent the majority of time, it is just the way biology is. We had a chief scientist from NIST visit us once and he gave a presentation on an experiment they did where they gave out the same cell line and same exact reagents to 8 different random labs across the country to perform a very, very simple cell toxicity study all using the same exact procedure. The results were ...
08:29 < kanzure> ... shockingly different from almost every lab, with orders of magnitude differences in some cases. NIST developed the assay to be more reproducible by changing the way you plated the cells and added the reagents. Adding cells and reagents A1-A8 and then going down to F1-F8 produced stark differences compared to adding the same exact things but if you added it in a A1-F1 to A8-F8 manner on a 48 well plate. If you can explain why such a minor ...
08:29 < kanzure> ... difference as this could produce orders of magnitude differences that were observed between labs, NIST is all ears. To get the most reproducible results, NIST discovered you had to almost zig zag across the plate when adding everything. But I mean come on, how would anyone know this? No one seeds their assays like this."
08:29 < kanzure> http://www.reddit.com/r/science/comments/1z8w5k/scientists_propose_teaching_reproducibility_to/cfrqfo4
08:32 < kanzure> http://www.nist.gov/mml/bbd/cell_systems/ricin_assay.cfm
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08:39 < kanzure> fatal: '/data/repositories/5/nw/59/6e/02/100103306/15478853.wiki.git' does not appear to be a git repository
08:39 < kanzure> weird, github doesn't normally report their absolute paths in error messages
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09:32 < kanzure> i approve of this nick
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10:50 < Jarlemag> Hi.
10:50 < Jarlemag> Are there many people interested in DIYBio here?
10:51 < Jarlemag> Cathal Garvey's trying to fund an antibiotic-free bacterial transformation starter kit, and I kind of really want it to succeed, so I'm trying to spread the word a bit: http://www.indiegogo.com/projects/indiebb-your-first-gmo
10:58 < chris_99> i think that's been discussed a few times 'ere actually
11:01 < chris_99> does it use GFP?
11:02 < kanzure> Jarlemag: can you just check the logs for cathal's advice instead of asking us
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11:25 < Jarlemag> chris_99: That's cool. Yes, the wildtype.
11:26 < Jarlemag> Kanzure: What logs?
11:28 < kanzure> Jarlemag: http://gnusha.org/logs
11:28 < kanzure> see /topic
11:29 < Jarlemag> Thanks.
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19:22 < genehacker> Hey kanzure, you maintain nanoengineer right?
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19:43 < kanzure> genehacker: i certainly like to pretend to!
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19:47 < genehacker> anybody here?
19:49 < kanzure> yes
19:49 < kanzure> howdy
19:49 < genehacker> so you maintain nanoengineer right?
19:50 < genehacker> is there anyway I can add ligands+ions?
19:51 < genehacker> or metal ions like zinc?
20:00 < kanzure> hrm
20:00 < kanzure> yes i think so
20:00 < kanzure> there's a library of existing elements in lib/ somewhere
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20:06 < genehacker> any idea where?
20:11 < kanzure> https://github.com/kanzure/nanoengineer/tree/master/cad/partlib/biochemistry
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20:11 < kanzure> https://github.com/kanzure/nanoengineer/tree/master/cad/partlib/organic%20chemistry
20:11 < kanzure> https://github.com/kanzure/nanoengineer/tree/master/cad/partlib/others
20:12 < genehacker> I don't see zinc in there
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20:12 < kanzure> https://github.com/kanzure/nanoengineer/blob/master/cad/partlib/others/Lonsdaleite.mmp
20:12 < kanzure> i think you just use the atomic number
20:16 < genehacker> is there some good documentation for nanoengineer somewhere?
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20:25 < genehacker> I guess it is not possible to add an atom by atomic number in the gui?
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20:50 < kanzure> genehacker: there used to be a wiki but i think it's down now
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--- Log closed Sun Mar 02 00:00:19 2014