--- Log opened Wed Jul 20 00:00:02 2016
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02:48 < archels> http://66.media.tumblr.com/f22fe3161da0458db54827743950303b/tumblr_oa2j8f2YOa1rom810o1_500.jpg
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08:39 < kanzure> .tw https://twitter.com/jhewitt123/status/754035039491457026
08:39 < yoleaux> @AdamMarblestone why wouldn't George answer me when I emailed & tweeted him about his mirror world? as in here? http://phys.org/news/2016-06-deuterium-receptors.html (@jhewitt123, in reply to tw:754034346697293824)
08:41 < kanzure> .tw https://twitter.com/eboyden3/status/753980996329103360
08:41 < yoleaux> SynthNeuro grad student Jake Bernstein will defend his PhD thesis, "Scalable Neural Recording," 11A July 27, MIT Media Lab room E14-633. (@eboyden3)
08:42 < kanzure> http://reviverestore.org/ is the long now foundation's genetic rescue and storage thingy
08:48 < kanzure> http://biohackacademy.github.io/biofactory/participants/documentation/
08:48 < kanzure> http://biohackacademy.github.io/bha2/participants/documentation/
08:48 < kanzure> http://biohackacademy.github.io/bha3/participants/documentation/
08:48 < kanzure> http://biohackacademy.github.io/bha2/
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08:54 < chris_99> that looks very interesting
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10:00 < kanzure> "A movie of RNA Polymerase II transcription" https://www.youtube.com/watch?v=WlMV_l88Lus
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10:06 < kanzure> "Molecular dynamics of the catalytic and translocation cycle of RNA polymerase" https://www.youtube.com/watch?v=XUn0m-gbVvU
10:06 < kanzure> "A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation" https://www.youtube.com/watch?v=aGy9dKjpm_8
10:07 < kanzure> "Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue" https://www.youtube.com/watch?v=woplf2nlxlw
10:09 < kanzure> "Poliiovirus RNA-dependent RNA Polymerase" https://www.youtube.com/watch?v=TPjCjxxNlTU
10:09 < SloanOnLinux> What do you think of CRISPR?
10:09 < kanzure> "yeast RNA polymerase simulated with gromacs 4.04 (position of the protein restrained) 50 mmol NaCl" https://www.youtube.com/watch?v=yTdQ7Qwarr8
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10:12 < kanzure> "Ribosome Molecular Dynamics Simulation Animation Site" https://www.youtube.com/watch?v=KVFKk2d2lV0
10:12 < kanzure> seminar on molecular dynamics simulations https://www.youtube.com/watch?v=vN4RKPNOsEc
10:13 < kanzure> and one on gromacs https://www.youtube.com/watch?v=KEfMuHMTBQU
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10:23 < kanzure> SloanOnLinux: what would you like to know about crispr? not sure what you need.
10:27 < kanzure> "saudi human genome project" http://shgp.kacst.edu.sa/site/PDF/Phases.pdf
10:27 < nmz787_i> FWIW I heard they'd be harder to sell on synthesis (Saudis)
10:28 < nmz787_i> but there's supposed to be a pretty amazing startup/VC opportunity there
10:28 < nmz787_i> 'mecca valley'
10:28 < nmz787_i> or is it 'silicon mecca'
10:32 < nmz787_i> not sure what the exact program names are unfortunately...  but this seems related
10:32 < nmz787_i> http://www.arabnews.com/node/941821/saudi-arabia
10:32 < nmz787_i> .title
10:32 < yoleaux> Deputy Crown Prince Mohammed takes Vision 2030 to Silicon Valley | Arab News
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10:52 < kanzure> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
10:53 < kanzure> http://www.gromacs.org/GPU_acceleration
11:12 < kanzure> hm there's a pdb2gmx
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11:14 < kanzure> http://manual.gromacs.org/programs/gmx-pdb2gmx.html
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11:23 < kanzure> "Convergence and Reproducibility in Molecular Dynamics Simulations of Nucleic Acids" https://www.youtube.com/watch?v=JBYfQ9mUFo8
11:23 < nmz787_i> kanzure: be on the lookout for API/GUIs with ability to "delete all nodes/atoms further than 3 Amino-Acids from any  DNA atoms"
11:24 < kanzure> why's that?
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11:47 < nmz787_i> kanzure: mostly to reduce visual clutter... I might even want to peel off more aminos, to say "only show aminos touching the DNA" so I can see the touch-points, once these interactions are understood (how does a gecko stick to the wall, its fingerprints) then show more like the 'fingers' and complete 'hand'
11:48 < nmz787_i> I might also want to say something more complex like "show aminos touching DNA or that are adjacent with an unobstructed path between"
11:49 < nmz787_i> in other words, aminos whose charge/electronics wouldn't be shielded by other atoms
11:49 < nmz787_i> but aren't directly touching either
11:51 < kanzure> that's a visualization issue not a simulation issue
11:52 < kanzure> ther'es probably a plugin to VRD (or whatever it's called) or mayavi2
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12:01 < nmz787_i> I'm just saying keep an eye open, and FWIW mayavi2 was a ball of compile-headaches
12:02 < nmz787_i> I figure gromacs has an export/screenshot/render call/command somewhere... so if you also happen to see nice traversal/delete calls... just keep my idea in mind
12:02 < nmz787_i> (if your RAM is big enough)
12:03 < kanzure> i dunno about performance of this thing but spinning up a giant ec2 server for a few minutes is definitely doable
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12:12 < nmz787_i> I actually meant mental RAM, for you to keep a lookout for that kind of API/calls/features
12:15 < kanzure> okay i emailed zren@uic.edu he was very helpful
12:15 < kanzure> http://diyhpl.us/~bryan/papers2/polymerase/zhong-ren-molecular-events-during-200/
12:15 < nmz787_i> re:?
12:15 < kanzure> movies from his paper
12:15 < kanzure> he sent over those large gifs
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12:16 < nmz787_i> amaz-some
12:16 < nmz787_i> PDBs available somewhere?
12:16 < nmz787_i> (I will check the PDFs too)
12:17 < nmz787_i> g2g now
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13:13 < kanzure> wow researchgate is spammy. they email you to "follow" authors a few hours after you click their profile or read one of their publications. that's some nasty lifecycle email tactics...
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15:06 < kanzure> http://source.rcsb.org/jfatcatserver/
15:07 < kanzure> rsb pdb seems to show structure similarities between a polymerase enzyme and a dna ligase enzyme http://www.rcsb.org/pdb/workbench/showPrecalcAlignment.do?action=pw_ce&name1=d1bgxt1&name2=PDP%3A2OWOAe
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16:13 < kanzure> rev1 has a whole bunch of molecular pores and tunnels
16:14 < kanzure> "Rev1 is a Y family DNA polymerase; it is sometimes referred to as a deoxycytidyl transferase because it only inserts deoxycytidine (dC) across from lesions. Whether G, A, T, C, or an abasic site, Rev1 will always add a C. Rev1 has the ability to always add a C, because it uses an arginine as a template which complements well with C.[3] Yet it is believed[by whom?] that Rev1 rarely uses its polymerase activity, rather it is thought that ...
16:14 < kanzure> ... Rev1's primary role is as a protein landing pad, whereby it helps direct the recruitment of TLS proteins, especially Pol ζ (Rev3/Rev7)."
16:14 < kanzure> http://www.rcsb.org/pdb/explore/explore.do?structureId=3OSP
16:19 < kanzure> primase-helicase also looks pretty weird in pymol http://www.rcsb.org/pdb/explore/explore.do?structureId=1Q57
16:28 < kanzure> dna-directed rna polymerase http://www.rcsb.org/pdb/explore/explore.do?structureId=2WB1
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16:54 < kanzure> somewhat useful index of pdb files for dna polymerase things http://proteopedia.org/wiki/index.php/DNA_polymerase
17:03 < nmz787_i> kanzure: what is the 'same' color in that diff?
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17:21 < kanzure> http://proteopedia.org/wiki/index.php/RNA_polymerase
17:21 < kanzure> nmz787_i: hm?
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18:29 < nmz787_i> kanzure: is there no exact similarity between TAQ and ligase? I thought if there was common motif, there'd be 3 colors... same, TAQ's motif, ligase's motif
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18:41 < kanzure> apparently ligase has something called a "polymerase domain"
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19:03 < kanzure> "RNA recognition motif" http://pfam.xfam.org/family/PF00076
19:03 < kanzure> "DNA-binding domain" http://pfam.xfam.org/family?acc=PF13892
19:04 < kanzure> http://pfam.xfam.org/family?acc=PF00751
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19:41 < kanzure> this is nasty https://en.wikipedia.org/wiki/DNA_polymerase_III_holoenzyme
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19:51 < kanzure> i think pfu polymerase would be an interesting candidate, since it has proofreading
19:51 < kanzure> pfu dna polymerase http://www.rcsb.org/pdb/explore.do?structureId=2jgu
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20:05 < kanzure> "Synergistic template-free synthesis of dsDNA by Thermococcus nautili primase PolpTN2, DNA polymerase PolB, and pTN2 helicase" http://link.springer.com/article/10.1007/s00792-014-0706-1
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20:39 < kanzure> i think it just needs to be electrical resistance testing of dna polymerase, holding whatever nucleotide it finds, and then incorporation given by an external signal and no incorporation until that time.   and maybe another signal to release the currently captured nucleotide.
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20:39 < kanzure> alternatively the same could be accomplished with proofreading and exonuclease activity on the same enzyme, although i think it would be easier to just never make a mistake in the first place
20:42 < kanzure> multiple separate conformational shape changes can be achieved by using the same azobenzene amino acid in multiple different locations inside the polymerase, which could be helpful for stopping the incorporation of other nucleotides while you change the shape for one incorporation event
20:42 < kanzure> (such as to block the attachment of the next nucleotide while you are incorporating)
20:47 < juul> kanzure and others: What should happen to OpenWetWare.org ? Is it still relevant? Should it be restructured? Rebooted? Something else?
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20:59 < kanzure> juul: well the content should be preserved
20:59 < kanzure> also i might have rooted you guys, so i might have a backup already, not sure
20:59 < juul> alright
21:00 < kanzure> oh it was a mediawiki dump that i have
21:00 < kanzure> not root :(
21:00 < kanzure> Special:Dumpsomethingsomething
21:00 < kanzure> 144 MB openwetware.org/oww-pages.xml.bz2
21:01 < kanzure> also i think academic publications link to many of those pages
21:01 < kanzure> so... yeah the links should remain.
21:03 < yashgaroth> it's okay as a motley collection of some labs' random internal protocols, not sure what the end goal is but some of the procedures are decent
21:03 < kanzure> ultimately the goal of "get biologists to use computers" has yet to succeed :)
21:03 < kanzure> forcing igem groups to have a webpage seems to work reasonably well
21:03 < juul> hehe yeah true
21:04 < juul> well, i'm hoping the bionet will be more biologist-friendly
21:04 < kanzure> juul: i have been doing one-sentence summaries of igem group activities http://diyhpl.us/wiki/dna/projects/#igem-2013
21:05 < juul> oh very nice!
21:05 < juul> yashgaroth: what should the end goal be?
21:06 < yashgaroth> idk, I like eg the wolfson lab's page, they have a good collection of protocols http://wolfson.huji.ac.il/expression/index.html
21:06 < yashgaroth> I get if OWW wants to be "open" and not link to anything that doesn't have "wiki" in the title, but c'mon guys it's biology not programming
21:08 < yashgaroth> if wolfson kept their shit updated a little better I wouldn't need to go anywhere on the internet, aside from expasy blast uniprot pdb etc
21:09 < kanzure> "aside from the kajillion highly fragmented databases of doom"
21:10 < yashgaroth> gotta keep them all open in tabs and flit back and forth with sequences on my clipboard
21:11 < yashgaroth> clustalo, jpred, nebcutter, whatever sequence analysis software I'm using, a few company websites
21:12 < yashgaroth> note that none of those are discussion forums since all biology forums are absolute shit, I guess since people hoard knowledge and/or people ask an overwhelming amount of stupid shit that to answer them would only encourage terrible fuckups
21:12 < kanzure> yashgaroth: polymerase is really slow, i think no matter what we're going to have to figure out a reasonable way to do dna ligation :(
21:12 < kanzure> 1000 nt/sec is just terrible. there's no way that will work without ligation, for genome printing etc.
21:13 < kanzure> the biology forums are shit because nobody has bootstrapped a good one yet. the way to do that would be to get 10-20 professors signed up and responding daily all the time. the problem is that biologists hate computers.
21:13 < yashgaroth> well it's gotta hang out waiting for the right nucleotide, error-check, other protein stuff
21:13 < yashgaroth> it's hard enough to get professors to answer a question when you're doing an experiment for them in their lab
21:13 < kanzure> plus their impossible travel schedules, can't forget that
21:14 < yashgaroth> much less some random dude on the internet who says "crispr?!" every sentence
21:14 < yashgaroth> travel, mentally abusing postdocs, it's a packed day
21:14 < kanzure> i think that even if you paid a bunch of biology sexperts to sit around on a forum all day, even then you would not be able to bootstrap a biology forum :)
21:15 < kanzure> right you forgot about postdoc psychotorture rituals
21:15 < yashgaroth> mhm, I mean I occasionally get a search result on researchgate's forums and half the answers are totally wrong, and the other half they totally misunderstand the question, with the same result
21:17 < kanzure> juul has agreed to write our electronic polymerase paper for us
21:17 < yashgaroth> sick, thx juul
21:17 < kanzure> :P
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21:19 < juul> but how will i have time to catch all the pokiemans?
21:19 < yashgaroth> honestly I'd pay monthly for a curated/updated collection of protocols and tools, hell I'd spray money for someone to archive every grad student's webapp that does something totally awesome and then dies when they graduate
21:22 < yashgaroth> even a better version of bitesizebio, which is half articles with critically wrong information and half "top 10 reasons not to kill yourself because you're in grad school, part 17"
21:22 < yashgaroth> ok I'm done complaining
21:25 < kanzure> never stop complaining
21:26 < yashgaroth> yeah who am I kidding
21:27 < kanzure> these things:
21:27 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Genetically%20encoding%20photoswitchable%20click%20amino%20acids%20in%20Escherichia%20coli%20and%20mammalian%20cells%20-%202015.pdf
21:28 < kanzure> "DNA sequencing using electrical conductance measurements of a DNA polymerase" https://ir.nctu.edu.tw/bitstream/11536/22351/1/000319979400018.pdf
21:29 < kanzure> https://www.google.com/patents/US20150017655
21:29 < kanzure> https://www.google.com/patents/US20150065353
21:29 < kanzure> now to pick a polymerase and a few amino acids to photoswitch
21:31 < kanzure> vent polymerase is probably the right choice
21:31 < kanzure> but i can't find a structure for it
21:34 < ebowden> kanzure, norton blocked that website.
21:35 < ebowden> Malicious Web Site Blocked
21:35 < ebowden> You attempted to access:
21:35 < ebowden>  http://diyhpl.us/~bryan/papers2/bio/Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells - 2015.pdf
21:35 < ebowden> This is a known malicious web site. It is recommended that you do NOT visit this site. The detailed report explains the security risks on this site.
21:35 < ebowden> For your protection, this web site has been blocked. Visit Symantec to learn more about phishing and internet security.
21:36 < kanzure> you... use norton?
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21:39 < juul> yashgaroth: i'm hoping the bionet will solve this by having sandboxed versioned web apps stored in the database together with the associated data
21:40 < juul> though I haven't implemented the sandboxing yet
21:42 < kanzure> "containerize all the things"?
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21:44 < ebowden> kanzure, it was a cheap package deal with my computer.
21:47 < kanzure> you should install linux
21:49 < nmz787_i> kanzure: this was the retracted/bad paper: (9:28:06 PM) kanzure: "DNA sequencing using electrical conductance measurements of a DNA polymerase" https://ir.nctu.edu.tw/bitstream/11536/22351/1/000319979400018.pdf
21:49 < kanzure> wasn't retracted
21:49 < kanzure> unspecified "fraud investigation"
21:49 < kanzure> but since the pacbio patent seems to be something similar, i'm not particularly concerned
21:50 < nmz787_i> well the pacbio paper is a bit different I think
21:50 < kanzure> the "fraud" could be anything, who knows. it's unspecified. it could be something like "the performance is overstated" or "there's no error bars on any of the numbers" or something.
21:51 < kanzure> the pacbio patent on electronic polymerase-based sequencing?
21:52 < nmz787_i> /me checking it for deets
21:52 < juul> kanzure: client side only sandboxing first then when i have time add server side containers for the continually shrinking pool of stuff that can't run client side
21:52 < nmz787_i> I guess what I mean is, having a patent doesn't mean producing it via what that patent says is feasible
21:52 < kanzure> juul: great but how do you convince all the biologists to write compatible tools ?
21:53 < kanzure> nmz787_i: sure. that's true.
21:53 < nmz787_i> kanzure: problem with the 'fraud' paper IMO was it hand-waved on 'antibody' and 'nanoparticle'
21:53 < kanzure> their antibody protein transistor stuff was from another prior paper, true
21:53 < yashgaroth> find where they live and demand the source code; not just for archiving, but also I don't wanna wait two days for their 486 to crunch my data
21:54 < kanzure> conjugation of a protein to a CMOS circuit is somewhat trivial i think.... even if you don't use an antibody/immunoglobulin.
21:54 < kanzure> oh look at this guy living like a king with his 486
21:54 < nmz787_i> /me is meeting the author of that ramana single-nucleotide paper tomorrow
21:55 < juul> kanzure: yeah that's a problem. one way would be by making it really easy to re-use these widget-type sandboxed web apps that people write for common data types so it becomes easier to extend a sandboxed app that someone else wrote for a similar experiment than to do it on your own
21:55 < kanzure> yashgaroth: soo anyway my point above was that we should probably anticipate that we need to come up with some crazy dna ligase stuff :(
21:55 < juul> i'm gonna make it and see if anyone will use it
21:55 < kanzure> juul: make it a requirement for igem participation
21:55 < yashgaroth> the octamer assembly one, or just in general?
21:55 < kanzure> juul: all the igem software
21:56 < kanzure> yashgaroth: in general, like for ligating 1 kb strands etc in an efficient way. enzymatically.
21:56 < juul> kanzure: yes that might be doable. it will of course need to be nice and stable before I even attempt that conversation with Randy
21:56 < kanzure> oh i thought drew had secret mind control powers over randy
21:56 < kanzure> i must be confused about how that works
21:57 < nmz787_i> kanzure: why is 1000nt /sec slow? just do things in parallel.. its tiny as hell
21:57 < kanzure> nmz787_i: still takes months for a genome
21:57 < kanzure> if you do things in parallel then you need amazingly good ligation
21:57 < kanzure> we do not have amazingly good ligation
21:57 < yashgaroth> yeah ligase atm is just "put in 5 trillion DNAs and ligases overnight", surely ripe for improvement maybe some ssDNA binding protein on the sticky ends that reversibly dimerizes to help them along, idk
21:57 < juul> i will not claim to understand that relationship
21:57 < nmz787_i> 1000 nt/sec * 1000 rxns * 1000 seconds= gigabase in 16 minutes
21:58 < kanzure> nmz787_i: yes but you need to stitch them together correctly :)
21:58 < nmz787_i> so what
21:58 < nmz787_i> double the time
21:58 < nmz787_i> 32 mins
21:58 < kanzure> i am saying that there's no solution yet
21:58 < kanzure> and we will have to make one
21:58 < nmz787_i> that is a blanket statement in general though
21:58 < kanzure> gibson doesn't work. we'll need an engineered dna ligase of some kind.
21:59 < nmz787_i> gibson does work
21:59 < kanzure> not for 1000 separate sequences
21:59 < nmz787_i> why do they sell kits where people have succes?
21:59 < kanzure> it's 10 strands max
21:59 < nmz787_i> so, recursion
21:59 < yashgaroth> if your fragments are long enough, you need quite a bit of overlap
21:59 < nmz787_i> why is parallelization hard to understand?
21:59 < kanzure> recursion doesn't work if you want to use only one reaction chamber
21:59 < nmz787_i> why wouldn't there be 1000 chambers?
22:00 < nmz787_i> for gibson alone
22:00 < kanzure> because if you have a good enzymatic solution you don't need chambers
22:00 < nmz787_i> along with 1000 for basic-synthesis of short strands
22:01 < nmz787_i> kanzure: that is a good long-term goal, but don't try to optimize the enzymes when there are easier physical solutions first... if we get 16 mins per gigabase then it makes engineering your amaze-balls enzyme that much easier
22:01 < nmz787_i> idea formation is fine, I just don't want to rat-hole into premature optimization
22:01 < kanzure> "easier".... ahem, a million valves on a chip ain't easier.
22:02 < nmz787_i> multiplexer valves seem to work fine, and I've been thinking mostly valveless for majority of operations
22:02 < nmz787_i> just use electrophoresis
22:02 < nmz787_i> it /is/ DNA
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22:05 < kanzure> i'm also not sure why 1000 nt/sec is the best performance we have out of polymerase
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22:05 < kanzure> wouldn't biologists want to optimize this to much higher rates? it would mean less time spent in the lab..
22:06 < nmz787_i>  well I didn't know about that e.coli parallelization until you recently posted about it
22:06 < kanzure> no, you knew about replication forks, surely. just not that ecoli is slow.
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22:07 < kanzure> church did his "2x faster lab bacteria to replace ecoli" thing recently, maybe someone will get the hint and do the same for taq polymerase mutants
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22:12 < kanzure> "Statement in response to the report by the World Anti-Doping Agency" http://en.kremlin.ru/events/president/news/52537
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