2016-07-20.log

--- Log opened Wed Jul 20 00:00:02 2016
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archelshttp://66.media.tumblr.com/f22fe3161da0458db54827743950303b/tumblr_oa2j8f2YOa1rom810o1_500.jpg02:48
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kanzure.tw https://twitter.com/jhewitt123/status/75403503949145702608:39
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)08:39
kanzure.tw https://twitter.com/eboyden3/status/75398099632910336008:41
yoleauxSynthNeuro grad student Jake Bernstein will defend his PhD thesis, "Scalable Neural Recording," 11A July 27, MIT Media Lab room E14-633. (@eboyden3)08:41
kanzurehttp://reviverestore.org/ is the long now foundation's genetic rescue and storage thingy08:42
kanzurehttp://biohackacademy.github.io/biofactory/participants/documentation/08:48
kanzurehttp://biohackacademy.github.io/bha2/participants/documentation/08:48
kanzurehttp://biohackacademy.github.io/bha3/participants/documentation/08:48
kanzurehttp://biohackacademy.github.io/bha2/08:48
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chris_99that looks very interesting08:54
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kanzure"A movie of RNA Polymerase II transcription" https://www.youtube.com/watch?v=WlMV_l88Lus10:00
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kanzure"Molecular dynamics of the catalytic and translocation cycle of RNA polymerase" https://www.youtube.com/watch?v=XUn0m-gbVvU10:06
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_810:06
kanzure"Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue" https://www.youtube.com/watch?v=woplf2nlxlw10:07
kanzure"Poliiovirus RNA-dependent RNA Polymerase" https://www.youtube.com/watch?v=TPjCjxxNlTU10:09
SloanOnLinuxWhat 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=yTdQ7Qwarr810:09
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kanzure"Ribosome Molecular Dynamics Simulation Animation Site" https://www.youtube.com/watch?v=KVFKk2d2lV010:12
kanzureseminar on molecular dynamics simulations https://www.youtube.com/watch?v=vN4RKPNOsEc10:12
kanzureand one on gromacs https://www.youtube.com/watch?v=KEfMuHMTBQU10:13
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kanzureSloanOnLinux: what would you like to know about crispr? not sure what you need.10:23
kanzure"saudi human genome project" http://shgp.kacst.edu.sa/site/PDF/Phases.pdf10:27
nmz787_iFWIW I heard they'd be harder to sell on synthesis (Saudis)10:27
nmz787_ibut there's supposed to be a pretty amazing startup/VC opportunity there10:28
nmz787_i'mecca valley'10:28
nmz787_ior is it 'silicon mecca'10:28
nmz787_inot sure what the exact program names are unfortunately...  but this seems related10:32
nmz787_ihttp://www.arabnews.com/node/941821/saudi-arabia10:32
nmz787_i.title10:32
yoleauxDeputy Crown Prince Mohammed takes Vision 2030 to Silicon Valley | Arab News10:32
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kanzurehttp://www.gromacs.org/Documentation/Acceleration_and_parallelization10:52
kanzurehttp://www.gromacs.org/GPU_acceleration10:53
kanzurehm there's a pdb2gmx11:12
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kanzurehttp://manual.gromacs.org/programs/gmx-pdb2gmx.html11:14
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kanzure"Convergence and Reproducibility in Molecular Dynamics Simulations of Nucleic Acids" https://www.youtube.com/watch?v=JBYfQ9mUFo811:23
nmz787_ikanzure: be on the lookout for API/GUIs with ability to "delete all nodes/atoms further than 3 Amino-Acids from any  DNA atoms"11:23
kanzurewhy's that?11:24
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nmz787_ikanzure: 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'11:47
nmz787_iI might also want to say something more complex like "show aminos touching DNA or that are adjacent with an unobstructed path between"11:48
nmz787_iin other words, aminos whose charge/electronics wouldn't be shielded by other atoms11:49
nmz787_ibut aren't directly touching either11:49
kanzurethat's a visualization issue not a simulation issue11:51
kanzurether'es probably a plugin to VRD (or whatever it's called) or mayavi211:52
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nmz787_iI'm just saying keep an eye open, and FWIW mayavi2 was a ball of compile-headaches12:01
nmz787_iI 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 mind12:02
nmz787_i(if your RAM is big enough)12:02
kanzurei dunno about performance of this thing but spinning up a giant ec2 server for a few minutes is definitely doable12:03
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nmz787_iI actually meant mental RAM, for you to keep a lookout for that kind of API/calls/features12:12
kanzureokay i emailed zren@uic.edu he was very helpful12:15
kanzurehttp://diyhpl.us/~bryan/papers2/polymerase/zhong-ren-molecular-events-during-200/12:15
nmz787_ire:?12:15
kanzuremovies from his paper12:15
kanzurehe sent over those large gifs12:15
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nmz787_iamaz-some12:16
nmz787_iPDBs available somewhere?12:16
nmz787_i(I will check the PDFs too)12:16
nmz787_ig2g now12:17
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kanzurewow 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...13:13
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kanzurehttp://source.rcsb.org/jfatcatserver/15:06
kanzurersb 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%3A2OWOAe15:07
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kanzurerev1 has a whole bunch of molecular pores and tunnels16:13
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 ΞΆ (Rev3/Rev7)."16:14
kanzurehttp://www.rcsb.org/pdb/explore/explore.do?structureId=3OSP16:14
kanzureprimase-helicase also looks pretty weird in pymol http://www.rcsb.org/pdb/explore/explore.do?structureId=1Q5716:19
kanzuredna-directed rna polymerase http://www.rcsb.org/pdb/explore/explore.do?structureId=2WB116:28
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kanzuresomewhat useful index of pdb files for dna polymerase things http://proteopedia.org/wiki/index.php/DNA_polymerase16:54
nmz787_ikanzure: what is the 'same' color in that diff?17:03
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kanzurehttp://proteopedia.org/wiki/index.php/RNA_polymerase17:21
kanzurenmz787_i: hm?17:21
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nmz787_ikanzure: 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 motif18:29
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kanzureapparently ligase has something called a "polymerase domain"18:41
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kanzure"RNA recognition motif" http://pfam.xfam.org/family/PF0007619:03
kanzure"DNA-binding domain" http://pfam.xfam.org/family?acc=PF1389219:03
kanzurehttp://pfam.xfam.org/family?acc=PF0075119:04
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kanzurethis is nasty https://en.wikipedia.org/wiki/DNA_polymerase_III_holoenzyme19:41
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kanzurei think pfu polymerase would be an interesting candidate, since it has proofreading19:51
kanzurepfu dna polymerase http://www.rcsb.org/pdb/explore.do?structureId=2jgu19:51
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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/s00792-014-0706-120:05
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kanzurei 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.20:39
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kanzurealternatively 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 place20:39
kanzuremultiple 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 event20:42
kanzure(such as to block the attachment of the next nucleotide while you are incorporating)20:42
juulkanzure and others: What should happen to OpenWetWare.org ? Is it still relevant? Should it be restructured? Rebooted? Something else?20:47
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kanzurejuul: well the content should be preserved20:59
kanzurealso i might have rooted you guys, so i might have a backup already, not sure20:59
juulalright20:59
kanzureoh it was a mediawiki dump that i have21:00
kanzurenot root :(21:00
kanzureSpecial:Dumpsomethingsomething21:00
kanzure144 MB openwetware.org/oww-pages.xml.bz221:00
kanzurealso i think academic publications link to many of those pages21:01
kanzureso... yeah the links should remain.21:01
yashgarothit'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 decent21:03
kanzureultimately the goal of "get biologists to use computers" has yet to succeed :)21:03
kanzureforcing igem groups to have a webpage seems to work reasonably well21:03
juulhehe yeah true21:03
juulwell, i'm hoping the bionet will be more biologist-friendly21:04
kanzurejuul: i have been doing one-sentence summaries of igem group activities http://diyhpl.us/wiki/dna/projects/#igem-201321:04
juuloh very nice!21:05
juulyashgaroth: what should the end goal be?21:05
yashgarothidk, I like eg the wolfson lab's page, they have a good collection of protocols http://wolfson.huji.ac.il/expression/index.html21:06
yashgarothI 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 programming21:06
yashgarothif wolfson kept their shit updated a little better I wouldn't need to go anywhere on the internet, aside from expasy blast uniprot pdb etc21:08
kanzure"aside from the kajillion highly fragmented databases of doom"21:09
yashgarothgotta keep them all open in tabs and flit back and forth with sequences on my clipboard21:10
yashgarothclustalo, jpred, nebcutter, whatever sequence analysis software I'm using, a few company websites21:11
yashgarothnote 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 fuckups21:12
kanzureyashgaroth: 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
kanzure1000 nt/sec is just terrible. there's no way that will work without ligation, for genome printing etc.21:12
kanzurethe 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
yashgarothwell it's gotta hang out waiting for the right nucleotide, error-check, other protein stuff21:13
yashgarothit's hard enough to get professors to answer a question when you're doing an experiment for them in their lab21:13
kanzureplus their impossible travel schedules, can't forget that21:13
yashgarothmuch less some random dude on the internet who says "crispr?!" every sentence21:14
yashgarothtravel, mentally abusing postdocs, it's a packed day21:14
kanzurei 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 :)21:14
kanzureright you forgot about postdoc psychotorture rituals21:15
yashgarothmhm, 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 result21:15
kanzurejuul has agreed to write our electronic polymerase paper for us21:17
yashgarothsick, thx juul21:17
kanzure:P21:17
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juulbut how will i have time to catch all the pokiemans?21:19
yashgarothhonestly 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 graduate21:19
yashgarotheven 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
yashgarothok I'm done complaining21:22
kanzurenever stop complaining21:25
yashgarothyeah who am I kidding21:26
kanzurethese things:21:27
kanzurehttp://diyhpl.us/~bryan/papers2/bio/Genetically%20encoding%20photoswitchable%20click%20amino%20acids%20in%20Escherichia%20coli%20and%20mammalian%20cells%20-%202015.pdf21:27
kanzure"DNA sequencing using electrical conductance measurements of a DNA polymerase" https://ir.nctu.edu.tw/bitstream/11536/22351/1/000319979400018.pdf21:28
kanzurehttps://www.google.com/patents/US2015001765521:29
kanzurehttps://www.google.com/patents/US2015006535321:29
kanzurenow to pick a polymerase and a few amino acids to photoswitch21:29
kanzurevent polymerase is probably the right choice21:31
kanzurebut i can't find a structure for it21:31
ebowdenkanzure, norton blocked that website.21:34
ebowdenMalicious Web Site Blocked21:35
ebowdenYou 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.pdf21:35
ebowdenThis 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
ebowdenFor your protection, this web site has been blocked. Visit Symantec to learn more about phishing and internet security.21:35
kanzureyou... use norton?21:36
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juulyashgaroth: i'm hoping the bionet will solve this by having sandboxed versioned web apps stored in the database together with the associated data21:39
juulthough I haven't implemented the sandboxing yet21:40
kanzure"containerize all the things"?21:42
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ebowdenkanzure, it was a cheap package deal with my computer.21:44
kanzureyou should install linux21:47
nmz787_ikanzure: 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.pdf21:49
kanzurewasn't retracted21:49
kanzureunspecified "fraud investigation"21:49
kanzurebut since the pacbio patent seems to be something similar, i'm not particularly concerned21:49
nmz787_iwell the pacbio paper is a bit different I think21:50
kanzurethe "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.21:50
kanzurethe pacbio patent on electronic polymerase-based sequencing?21:51
nmz787_i/me checking it for deets21:52
juulkanzure: 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 side21:52
nmz787_iI guess what I mean is, having a patent doesn't mean producing it via what that patent says is feasible21:52
kanzurejuul: great but how do you convince all the biologists to write compatible tools ?21:52
kanzurenmz787_i: sure. that's true.21:53
nmz787_ikanzure: problem with the 'fraud' paper IMO was it hand-waved on 'antibody' and 'nanoparticle'21:53
kanzuretheir antibody protein transistor stuff was from another prior paper, true21:53
yashgarothfind 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 data21:53
kanzureconjugation of a protein to a CMOS circuit is somewhat trivial i think.... even if you don't use an antibody/immunoglobulin.21:54
kanzureoh look at this guy living like a king with his 48621:54
nmz787_i/me is meeting the author of that ramana single-nucleotide paper tomorrow21:54
juulkanzure: 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 own21:55
kanzureyashgaroth: 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
juuli'm gonna make it and see if anyone will use it21:55
kanzurejuul: make it a requirement for igem participation21:55
yashgaroththe octamer assembly one, or just in general?21:55
kanzurejuul: all the igem software21:55
kanzureyashgaroth: in general, like for ligating 1 kb strands etc in an efficient way. enzymatically.21:56
juulkanzure: yes that might be doable. it will of course need to be nice and stable before I even attempt that conversation with Randy21:56
kanzureoh i thought drew had secret mind control powers over randy21:56
kanzurei must be confused about how that works21:56
nmz787_ikanzure: why is 1000nt /sec slow? just do things in parallel.. its tiny as hell21:57
kanzurenmz787_i: still takes months for a genome21:57
kanzureif you do things in parallel then you need amazingly good ligation21:57
kanzurewe do not have amazingly good ligation21:57
yashgarothyeah 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, idk21:57
juuli will not claim to understand that relationship21:57
nmz787_i1000 nt/sec * 1000 rxns * 1000 seconds= gigabase in 16 minutes21:57
kanzurenmz787_i: yes but you need to stitch them together correctly :)21:58
nmz787_iso what21:58
nmz787_idouble the time21:58
nmz787_i32 mins21:58
kanzurei am saying that there's no solution yet21:58
kanzureand we will have to make one21:58
nmz787_ithat is a blanket statement in general though21:58
kanzuregibson doesn't work. we'll need an engineered dna ligase of some kind.21:58
nmz787_igibson does work21:59
kanzurenot for 1000 separate sequences21:59
nmz787_iwhy do they sell kits where people have succes?21:59
kanzureit's 10 strands max21:59
nmz787_iso, recursion21:59
yashgarothif your fragments are long enough, you need quite a bit of overlap21:59
nmz787_iwhy is parallelization hard to understand?21:59
kanzurerecursion doesn't work if you want to use only one reaction chamber21:59
nmz787_iwhy wouldn't there be 1000 chambers?21:59
nmz787_ifor gibson alone22:00
kanzurebecause if you have a good enzymatic solution you don't need chambers22:00
nmz787_ialong with 1000 for basic-synthesis of short strands22:00
nmz787_ikanzure: 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 easier22:01
nmz787_iidea formation is fine, I just don't want to rat-hole into premature optimization22:01
kanzure"easier".... ahem, a million valves on a chip ain't easier.22:01
nmz787_imultiplexer valves seem to work fine, and I've been thinking mostly valveless for majority of operations22:02
nmz787_ijust use electrophoresis22:02
nmz787_iit /is/ DNA22:02
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kanzurei'm also not sure why 1000 nt/sec is the best performance we have out of polymerase22:05
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kanzurewouldn't biologists want to optimize this to much higher rates? it would mean less time spent in the lab..22:05
nmz787_i well I didn't know about that e.coli parallelization until you recently posted about it22:06
kanzureno, you knew about replication forks, surely. just not that ecoli is slow.22:06
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kanzurechurch did his "2x faster lab bacteria to replace ecoli" thing recently, maybe someone will get the hint and do the same for taq polymerase mutants22:07
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kanzure"Statement in response to the report by the World Anti-Doping Agency" http://en.kremlin.ru/events/president/news/5253722:12
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