--- Log opened Wed Jun 08 00:00:23 2016 00:26 -!- fictor_de_aljabr [uid159228@gateway/web/irccloud.com/x-emhodeevabhwjuio] has quit [Quit: Connection closed for inactivity] 00:28 -!- augur [~augur@2601:645:c100:63f1:2493:4fb1:b88:4358] has quit [Remote host closed the connection] 00:30 -!- esmerelda [~andares@unaffiliated/jacco] has joined ##hplusroadmap 00:31 -!- fictor_de_aljabr [uid159228@gateway/web/irccloud.com/x-uipvufqbuizqczlk] has joined ##hplusroadmap 01:10 -!- Gurkenglas [Gurkenglas@dslb-178-000-182-226.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 01:18 -!- cluckj [~cluckj@pool-108-16-231-242.phlapa.fios.verizon.net] has quit [Read error: Connection reset by peer] 01:18 -!- cluckj [~cluckj@pool-108-16-231-242.phlapa.fios.verizon.net] has joined ##hplusroadmap 01:20 -!- irseeyou [~irseeyou@c-67-168-101-20.hsd1.wa.comcast.net] has left ##hplusroadmap [] 01:22 -!- Gurkenglas [Gurkenglas@dslb-178-000-182-226.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 02:14 -!- esmerelda [~andares@unaffiliated/jacco] has quit [Ping timeout: 276 seconds] 02:22 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rrdyncspcowynrhx] has joined ##hplusroadmap 02:47 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 02:52 -!- esmerelda [~andares@172.58.40.66] has joined ##hplusroadmap 02:52 -!- esmerelda [~andares@172.58.40.66] has quit [Changing host] 02:52 -!- esmerelda [~andares@unaffiliated/jacco] has joined ##hplusroadmap 02:58 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-yulmjsbxzkzjngjz] has joined ##hplusroadmap 03:01 -!- Orpheon [~Orpheon@46.140.52.182] has quit [Read error: Connection reset by peer] 03:06 -!- fictor_de_aljabr [uid159228@gateway/web/irccloud.com/x-uipvufqbuizqczlk] has quit [Quit: Connection closed for inactivity] 05:42 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rrdyncspcowynrhx] has quit [Quit: Connection closed for inactivity] 06:09 -!- nildicit_ [~nildicit@gateway/vpn/privateinternetaccess/nildicit] has joined ##hplusroadmap 06:13 -!- nildicit [~nildicit@gateway/vpn/privateinternetaccess/nildicit] has quit [Ping timeout: 252 seconds] 06:16 < kanzure> bloop 06:20 < JayDugger> bluup 06:25 -!- jtimon [~quassel@4.28.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 06:50 < kanzure> "Chemoenzymatic transformations in nucleoside chemistry" http://diyhpl.us/~bryan/papers2/DNA/Chemoenzymatic%20transformations%20in%20nucleoside%20chemistry.pdf 06:51 < kanzure> http://hackteria.org/wiki/index.php/DIY_Micro_Laser_Cutter 06:53 < chris_99> cool 07:04 < kanzure> "A two-neuron system for adaptive goal-directed decision-making in Lymnaea" http://www.nature.com/ncomms/2016/160603/ncomms11793/full/ncomms11793.html 07:08 -!- eudoxia [~eudoxia@r167-57-125-140.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 07:25 -!- eudoxia [~eudoxia@r167-57-125-140.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 07:34 -!- nildicit__ [~nildicit@unaffiliated/nildicit] has joined ##hplusroadmap 07:36 -!- nildicit_ [~nildicit@gateway/vpn/privateinternetaccess/nildicit] has quit [Ping timeout: 244 seconds] 08:04 < kanzure> "Scheme 20 is nice it adds an acyl group. Rutgers 2014 igem project used an acyl group to protect dNTPs. They used ammonia to remove it. I believe ammonia does not require protecting groups on nucleotide bases in fact it's sometimes used to remove them. However scheme 20 only works for bases a and t. I wonder if you could modify the enzyme to work on c and g. Scheme 17 only works on a u base." 08:04 < kanzure> "Well I've thought about this at length actually. Two posable strategies for alternative blocking groups have occurred to me. The first it may, just may, be posable to use a disaccharide synthase to add a sugar based compound to the 3 prime position of a dNTP. You can see scheme 31 in that paper shows a way of using a disaccharide synthase to add at the 5 prime position but there are a lot of disaccharides in nature and lots of different ... 08:04 < kanzure> ... enzymes to make them. You'd have to screen a lot of disaccharide synthases till you found one with week activity for 3 prime addition then do directed evolution to get something that could give you dNTPs blocked by joining another monosaccharide to the ribose. To the best of my knowledge all disaccharides break down into monosaccharides in sufficiently hot water. So you could make your own thermal liable blocked dNTP. It won't be ... 08:04 < kanzure> ... cheeper to do this than buy cleanamp." 08:04 < kanzure> "So the question in my mind is how hard would it be to make a dirty dNTP chemically with out an enzyme. Is there a reagent I could add to dNTPs and phosphoric acid that would attach PO4H2 to the 3 prime location with out the base or 5 prime end needing protecting groups. There are 4 OH groups hanging off the phosphors at the 5 prime end so can we expect some PO4H2 groups added here? What if I turned the phosphoric acid into a free ... 08:04 < kanzure> "The other option might be to use dirty ends. When dna breaks it doesn't always leave clean 3 prime ends. Often you get a lot of 3 prime ends with PO4H2 groups on them. You can't polymerise off this. But there is an enzyme PNKP that nips off the PO4H2 group so polymerisation can continue. If you used dirty dNTPs and used PNKP instead of heat to deblock that might be an option. However the only simple way I can think of to get dirty dNTPs ... 08:05 < kanzure> ... is to get a DNA sample, subject it to lots of oxygen, possibly ozone. Use exonucleases to break it down into clean and dirty dNMPs painstakingly purify out the dirty dNMPs turn them into dirty dNTPs using NDP / NMP kinases then separate them by base. This will also not be cheeper or easier than buying cleanamp." 08:05 < kanzure> ... radical before adding it using electrical discharge? All things I've considered. Basically I'm a sucky chemist and it takes a very talented chemist to do serious organic synthesis only using reagents you can purify out of things you can buy at your local supermarket or buy from amazon." 08:05 < kanzure> "And again none of this is going to be cheeper or easier than cleanamp. But as I said a cheep solution is unrealistic this method is aimed at those who a) want a learning experience or b) can't get industry made DNA sequences." 08:06 -!- Orpheon [~Orpheon@194.78.62.81.dynamic.wline.res.cust.swisscom.ch] has joined ##hplusroadmap 08:06 -!- Orpheon [~Orpheon@194.78.62.81.dynamic.wline.res.cust.swisscom.ch] has quit [Remote host closed the connection] 08:11 -!- Orpheon [~Orpheon@194.78.62.81.dynamic.wline.res.cust.swisscom.ch] has joined ##hplusroadmap 08:14 -!- augur [~augur@2601:645:c100:63f1:456d:e718:bf73:e22c] has joined ##hplusroadmap 08:15 -!- fictor_de_aljabr [uid159228@gateway/web/irccloud.com/x-qnqsfuuyifrxalbr] has joined ##hplusroadmap 08:48 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Quit: Leaving] 08:49 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 09:03 -!- Orpheon [~Orpheon@194.78.62.81.dynamic.wline.res.cust.swisscom.ch] has quit [Remote host closed the connection] 09:52 -!- psyreal [~psyreal@mail.transworldhealth.com] has joined ##hplusroadmap 10:23 < fictor_de_aljabr> I'd be interested in hearing why a group like this would be for or against Hilary Clinton 10:24 < kanzure> well if you pay us, we might suddenly have an opinion 10:24 < kanzure> also: why are you here. get lost. 10:44 < fictor_de_aljabr> What? 10:47 < fictor_de_aljabr> Who the hell..? 10:49 -!- mode/##hplusroadmap [+o kanzure] by ChanServ 10:49 -!- fictor_de_aljabr was kicked from ##hplusroadmap by kanzure [fictor_de_aljabr] 11:05 < Jawmare> kanzure : can you summarize your question? 11:06 <@kanzure> my what 11:07 -!- psyreal [~psyreal@mail.transworldhealth.com] has quit [Ping timeout: 240 seconds] 11:07 < Jawmare> or whatever you said 3 hours ago? 11:07 <@kanzure> i was quoting something from the diybio mailing list 11:07 <@kanzure> Jawmare: it was from the author of http://diyhpl.us/~bryan/papers2/DNA/A%20hypothetical%20protocol%20for%20DIYBIO%20DNA%20synthesis.pdf 11:07 < Jawmare> oh ok 11:13 -!- bsm1175321 [~mcelrath@38.121.165.30] has quit [Ping timeout: 246 seconds] 11:16 -!- ArturShaik [~ArturShai@37.218.162.209] has quit [Ping timeout: 250 seconds] 12:00 -!- Darius [~quassel@cpe-158-222-160-123.nyc.res.rr.com] has joined ##hplusroadmap 12:29 < ybit_> https://www.youtube.com/watch?v=Yth7O6yeZRE 12:29 < ybit_> .title 12:29 < yoleaux> Decentralized Web Summit - Live From The Internet Archive - YouTube 12:41 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-yulmjsbxzkzjngjz] has quit [Quit: Connection closed for inactivity] 12:50 -!- Aurelius_Work [~cpopell@209.48.69.2] has quit [Ping timeout: 240 seconds] 12:50 -!- augur [~augur@2601:645:c100:63f1:456d:e718:bf73:e22c] has quit [Remote host closed the connection] 12:50 -!- augur [~augur@c-73-202-137-143.hsd1.ca.comcast.net] has joined ##hplusroadmap 12:51 <@kanzure> https://www.hodinkee.com/articles/interview-meet-dan-spitz-anthrax-guitarist-turned-master-watchmaker 12:51 <@kanzure> http://danspitz.com/spitz-bench/ 12:55 -!- augur [~augur@c-73-202-137-143.hsd1.ca.comcast.net] has quit [Ping timeout: 260 seconds] 12:59 -!- Aurelius_Work [~cpopell@209.48.69.2] has joined ##hplusroadmap 13:05 -!- Orpheon [~Orpheon@213.200.193.129] has joined ##hplusroadmap 13:07 -!- sandeepkr_ [~sandeep@111.235.64.4] has joined ##hplusroadmap 13:09 -!- sandeepkr [~sandeep@111.235.64.4] has quit [Ping timeout: 250 seconds] 13:26 -!- nildicit_ [~nildicit@unaffiliated/nildicit] has joined ##hplusroadmap 13:29 -!- sandeepkr__ [~sandeep@111.235.64.4] has joined ##hplusroadmap 13:30 -!- nildicit__ [~nildicit@unaffiliated/nildicit] has quit [Ping timeout: 252 seconds] 13:31 -!- sandeepkr_ [~sandeep@111.235.64.4] has quit [Ping timeout: 260 seconds] 13:33 -!- jaboja [~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 13:56 -!- namespace [irssi@2600:3c00::f03c:91ff:fe89:ddeb] has quit [Quit: ZNC 1.6.2 - http://znc.in] 13:59 < archels> kanzure: reposting this but, what's good mindmapping software that does different views like timeline and spatial (graph/network?) organisation? 14:01 < archels> slide based presentations should be a subset of mind mapping software too 14:03 <@kanzure> dunno. i hate mindmapping software. i think there was one called "mindmapper" that people liked. 14:03 <@kanzure> .tw https://twitter.com/BoredElonMusk/status/556184760721371136 14:03 < yoleaux> Move Fast and Break Rockets. (@BoredElonMusk) 14:04 < archels> are you still using textfiles for mind mapping 14:05 -!- nildicit_ is now known as nildicit 14:06 <@kanzure> i'm not sure i am doing any mindmapping at all. what signs would i have to look for to decide whether that's happening ? 14:08 < archels> I'm using a textfile for my todo list/braindump, I thought you were doing similar things 14:09 <@kanzure> oh is that a mindmap? 14:09 < archels> close enough 14:09 < chris_99> heh i thought mindmaps where graphy things? 14:15 -!- Aurelius_Work2 [~cpopell@209.48.69.2] has joined ##hplusroadmap 14:17 < maaku> I use mindmaps but never found software useful for it 14:18 -!- Aurelius_Work [~cpopell@209.48.69.2] has quit [Ping timeout: 244 seconds] 14:20 <@kanzure> chris_99: i think they are the things where you have lots of "links" between things. 14:20 <@kanzure> i could spend hours enumerating links between concepts but i'm not sure there's any point... semantic web stuff has never worked out positively for me. 14:25 < chris_99> hmm it seems they're forming many hierarchies as i understand it from wiki? i guess you could represent that similarly just by using multiple levels of headings in text 14:28 < maaku> chris_99: not sure what you're describing but it's not a mindmap 14:28 < maaku> mindmap is just an arbitrarily structured graph of idea space 14:28 < chris_99> yeah, where the subgraphs form hierarchies 14:28 < maaku> it's a way of thinking about something larger than your working memory 14:29 < maaku> chris_99: arbitrary graph, not hierarchies 14:29 <@kanzure> i would just sit there all day adding links. not a good use of time. 14:30 < maaku> chris_99: e.g. cycles are ok (and common in fact) 14:30 < chris_99> ah, the ones i was looking at didn't have cycles 14:30 < maaku> i've only found it to be useful for a specific task, often scoping problems 14:31 < maaku> chris_99: probably because if you're googling 'mindmap' you get a bunch of mindmap software, most of which don't know how to handle cycles (part of why I say mindmap software is junk) 14:31 <@kanzure> why scoping in particular 14:32 < maaku> kanzure: let's take the canonical example of "moving overseas" 14:33 < maaku> if I mindmap that I'll end up with a huge graph of things that need to be done in relation to pulling off sucha move, with clusters related to acquiring visas and updated passports, finding accomodation, schools for kids, setting up forwarding, hiring movers, packing up my belongings, etc. 14:34 < maaku> and all the dependencies between these items, represented as linkages, etc. 14:34 < maaku> it's way too big of a task to keep in memory, and a hierarchical text document will not allow the cyclical or non-hierarchical cross dependencies to be adequately documented 14:35 < maaku> *way to big a project (too many tasks) 14:35 < maaku> mindmapping is just "assisted cognition" -- a way of dumping thoughts so you can focus on specific pieces at a time 14:36 < maaku> I typically only do it at the start of a project to identify all the moving parts and interdependencies however 14:36 < chris_99> could always have goto's in the text document ;) 14:37 < xentrac_> yeah, that's what I do 14:49 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rbobufwqvmvbszto] has joined ##hplusroadmap 15:05 -!- strangewarp [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has joined ##hplusroadmap 15:09 -!- strangewarp_ [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has quit [Ping timeout: 244 seconds] 15:27 -!- augur [~augur@2601:645:c100:63f1:dca6:4191:b97e:3ee2] has joined ##hplusroadmap 15:53 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 276 seconds] 16:07 -!- strangewarp [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has quit [Read error: Connection timed out] 16:08 -!- strangewarp [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has joined ##hplusroadmap 16:31 -!- CuriousCat [~CuriousCa@2602:30a:2c94:5460:cdcf:15b0:6113:fa04] has joined ##hplusroadmap 16:31 -!- CuriousCat [~CuriousCa@2602:30a:2c94:5460:cdcf:15b0:6113:fa04] has quit [Changing host] 16:31 -!- CuriousCat [~CuriousCa@unaffiliated/wye-naught/x-8734122] has joined ##hplusroadmap 17:12 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 17:42 -!- mz_o___ is now known as mz_o__ 18:09 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 18:29 -!- abetusk [~abram@c-98-216-104-129.hsd1.ma.comcast.net] has quit [Ping timeout: 276 seconds] 18:41 -!- abetusk [~abram@c-98-216-104-129.hsd1.ma.comcast.net] has joined ##hplusroadmap 18:42 -!- abetusk is now known as Guest97171 18:45 <@kanzure> bloop 18:52 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has joined ##hplusroadmap 18:52 -!- yash [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 18:54 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Read error: Connection reset by peer] 18:55 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Ping timeout: 258 seconds] 19:13 -!- mz_o__ [~drop_shot@68.232.180.123] has quit [Ping timeout: 240 seconds] 19:18 -!- mz_o__ [~drop_shot@68.232.180.123] has joined ##hplusroadmap 19:19 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 19:21 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 19:22 -!- Guest97171 is now known as abetusk 19:22 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 20:36 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has quit [Read error: Connection reset by peer] 20:36 -!- ArturShaik [~ArturShai@37.218.162.209] has joined ##hplusroadmap 20:42 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rbobufwqvmvbszto] has quit [Quit: Connection closed for inactivity] 21:01 -!- Orpheon [~Orpheon@213.200.193.129] has quit [Read error: Connection reset by peer] 21:08 -!- mz_o__ is now known as ratnooirc 21:09 -!- ratnooirc is now known as mz_o__ 21:27 -!- jtimon [~quassel@4.28.134.37.dynamic.jazztel.es] has quit [Ping timeout: 240 seconds] 21:43 -!- Darius [~quassel@cpe-158-222-160-123.nyc.res.rr.com] has quit [Remote host closed the connection] 22:16 -!- nildicit_ [~nildicit@unaffiliated/nildicit] has joined ##hplusroadmap 22:20 -!- nildicit [~nildicit@unaffiliated/nildicit] has quit [Ping timeout: 260 seconds] 22:23 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-pakkcwuqnvvdfxmd] has quit [Ping timeout: 250 seconds] 22:23 -!- Joshchamp [sid159459@gateway/web/irccloud.com/x-nqjapmpsmpdjjral] has quit [Ping timeout: 272 seconds] 22:23 -!- proofoflogic [sid65184@gateway/web/irccloud.com/x-otvtcursyuknoknl] has quit [Ping timeout: 250 seconds] 22:24 -!- proofoflogic [sid65184@gateway/web/irccloud.com/x-hmatrzszillbzser] has joined ##hplusroadmap 22:25 -!- nickjohnson [sid789@gateway/web/irccloud.com/x-alvlbzcxnisscxbn] has quit [Ping timeout: 260 seconds] 22:25 -!- strages [sid11297@gateway/web/irccloud.com/x-gxvcdftzurxgnsal] has quit [Ping timeout: 272 seconds] 22:28 -!- Joshchamp [sid159459@gateway/web/irccloud.com/x-idnyztitzfeqtobb] has joined ##hplusroadmap 22:32 -!- nickjohnson [sid789@gateway/web/irccloud.com/x-eroflmzrtblewlhb] has joined ##hplusroadmap 22:33 -!- strages [sid11297@gateway/web/irccloud.com/x-eseaoysybiisfudm] has joined ##hplusroadmap 22:35 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-vizwuvtewuzrvpqr] has joined ##hplusroadmap 22:55 -!- yash [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:07 -!- augur [~augur@2601:645:c100:63f1:dca6:4191:b97e:3ee2] has quit [Remote host closed the connection] 23:19 -!- CuriousCat [~CuriousCa@unaffiliated/wye-naught/x-8734122] has quit [Quit: * * * * *] 23:23 -!- mz_o__ [~drop_shot@68.232.180.123] has quit [Ping timeout: 244 seconds] 23:31 -!- mz_o__ [~drop_shot@68.232.180.123] has joined ##hplusroadmap --- Log closed Thu Jun 09 00:00:24 2016