--- Log opened Fri Mar 06 00:00:18 2020 00:17 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 00:53 -!- strages [uid11297@gateway/web/irccloud.com/x-vobtlsutuvqvranf] has quit [Quit: Connection closed for inactivity] 01:32 < fltrz> hey, I'm not familiar with the biosynthesis pathways of humans, how do I interpret the colors and and directions of the arrows at https://www.genome.jp/kegg-bin/show_pathway?org_name=hsa&mapno=01230&mapscale=&show_description=hide&show_module_list=show ? 01:34 < fltrz> how can I deduce the essentiality of amino acids from this graph? the 9 essential ones don't look different from the non-essential ones in this graph 01:42 -!- jenelizabeth [~jenelizab@cpc155793-brmb11-2-0-cust474.1-3.cable.virginm.net] has quit [Remote host closed the connection] 01:46 -!- jenelizabeth [~jenelizab@cpc155793-brmb11-2-0-cust474.1-3.cable.virginm.net] has joined ##hplusroadmap 01:51 -!- jenelizabeth [~jenelizab@cpc155793-brmb11-2-0-cust474.1-3.cable.virginm.net] has quit [Ping timeout: 256 seconds] 01:52 -!- jenelizabeth [~jenelizab@cpc155793-brmb11-2-0-cust474.1-3.cable.virginm.net] has joined ##hplusroadmap 02:22 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 256 seconds] 02:59 < nmz787> fltrz: like this? https://www.genome.jp/kegg/kegg1c.html 02:59 < nmz787> .title 02:59 < saxo> KEGG Color Codes 03:00 < nmz787> essentiality might not be color-coded... it might just be something like an item that you can't click on (because it doesn't have a pathway in humans)... 03:02 < fltrz> nmz787, thanks for the color code legend! I still don't understand, I thought it would only show pathways that occur in the human body if I select Homo Sapiens 03:02 < fltrz> also the arrow head directions are still unclear, is it pointing to dependency or products? 03:03 < fltrz> also not sure what is meant with "reference pathways" 03:03 < fltrz> nmz787, also thanks for pointing out the nodes are clickable 03:15 -!- helleshin [~talinck@98.29.27.253] has joined ##hplusroadmap 03:18 -!- hehelleshin [~talinck@98.29.27.253] has quit [Ping timeout: 258 seconds] 03:19 -!- jenelizabeth [~jenelizab@cpc155793-brmb11-2-0-cust474.1-3.cable.virginm.net] has quit [Quit: Leaving...] 03:28 < nmz787> fltrz: sorry, not sure, you'd have to read up on KEGG a bit... maybe search on google scholar and sort by date, then filter the earliest hits (to find a paper talking about *what* KEGG is, how it works, etc) 03:28 < nmz787> presumably they have another legend somewhere on their site 03:28 < nmz787> there's also this http://biochemical-pathways.com/#/map/1 03:29 < nmz787> and maybe something you might find useful here, idk, https://www.expasy.org/ 03:30 < nmz787> or this, for metabolic pathways specifically: https://metacyc.org/ 03:31 < nmz787> hey, they even have a guide RIGHT THERE on their main webpage: https://metacyc.org/MetaCycUserGuide.shtml 03:32 < nmz787> unfortunately it doesn't /appear/ that they have a human specific one for amino acids... but maybe I'm wrong https://metacyc.org/META/new-image?object=Amino-Acid-Biosynthesis 03:34 * nmz787 sleeps 03:39 -!- faceface is now known as facefaceface 03:40 -!- CRM114 is now known as Urchin 03:49 -!- spaceangel [~spaceange@ip-89-177-23-46.net.upcbroadband.cz] has joined ##hplusroadmap 04:02 -!- helleshin [~talinck@98.29.27.253] has quit [Read error: Connection reset by peer] 04:02 -!- helleshin [~talinck@98.29.27.253] has joined ##hplusroadmap 04:04 -!- nsh [~lol@wikipedia/nsh] has quit [Remote host closed the connection] 04:06 -!- facefaceface [~faceface@unaffiliated/faceface] has quit [Ping timeout: 265 seconds] 04:06 -!- andytoshi [~apoelstra@unaffiliated/andytoshi] has quit [Ping timeout: 265 seconds] 04:07 -!- facefaceface [~faceface@unaffiliated/faceface] has joined ##hplusroadmap 04:07 -!- andytoshi [~apoelstra@wpsoftware.net] has joined ##hplusroadmap 04:07 -!- andytoshi [~apoelstra@wpsoftware.net] has quit [Changing host] 04:07 -!- andytoshi [~apoelstra@unaffiliated/andytoshi] has joined ##hplusroadmap 04:07 -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap 04:16 < adlai> maaku: so what's the plan? [for values of 'plan' significantly less formalised than "writing up a proposal", yet slightly too verbose to fit within a single IRC message] 04:21 -!- darsie [~kvirc@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 04:35 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 256 seconds] 04:43 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 04:51 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 256 seconds] 04:54 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 05:24 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 258 seconds] 06:00 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 06:05 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 256 seconds] 06:12 -!- Human_G33k [~HumanG33k@62.147.242.8] has quit [Read error: Connection reset by peer] 06:44 -!- HumanG33k [~HumanG33k@62.147.242.8] has joined ##hplusroadmap 06:45 -!- agile_prg [~nyb@50.227.202.42] has joined ##hplusroadmap 06:46 -!- HumanG33k [~HumanG33k@62.147.242.8] has quit [Remote host closed the connection] 06:47 < agile_prg> Hi all, I am in an online hackathon to create a corona virus vaccine and drug treatments, we have a harvard virology & bioinformatics consultant helping us, if you want to join come to this slack url: https://join.slack.com/t/wuhan2020/shared_invite/enQtOTQxMTU4MzgyNTYwLWIxMTMyNWI4NWE2YTk3NGRjZGJhMjUzNmJhMjg1MDQ3OTEzNDE5NGY4MWFhMjRlYWU4MmE3ZGQyOGU4N2YwMzY 06:47 < agile_prg> we are in channel #autovax 06:47 -!- HumanG33k [~HumanG33k@62.147.242.8] has joined ##hplusroadmap 06:47 < agile_prg> any help is appreciated :> 06:48 < kanzure> agile_prg: welcome. someone in here is working on a plasmid vaccine. 06:51 -!- yashgaroth [~ffffffff@172.58.19.169] has joined ##hplusroadmap 06:51 < yashgaroth> it's me 06:51 < agile_prg> oh wow! 06:52 < agile_prg> can you please tell me more about this approach? 06:53 < yashgaroth> sure, it's basically what Inovio is doing - get a plasmid that expresses the Covid spike protein, electroporate it into skin cells, and stimulate inflammation near the injection site so you develop antibodies to the spike protein 06:54 < agile_prg> is there any bioinformatics involved? 06:54 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 06:55 < yashgaroth> nothing I'd really need help with, but yeah there's a little 06:55 < agile_prg> I guess creating the plasmid part would use bioinformatics 06:56 < yashgaroth> so is the slack group actually working on a vaccine? I don't see any mention of that in the github page or the channel list 06:56 < agile_prg> go to #autovax 06:56 < agile_prg> you can see it in the channel description 06:58 < agile_prg> what channel are you in? 06:59 < yashgaroth> I'm viewing the autovax channel, I haven't joined it yet 06:59 < agile_prg> we have a trello with tasks to review papers etc.. releated to creating a vaccine that the Harvard Consultant gave us 06:59 < agile_prg> can I invite you to our trello board? 07:00 < agile_prg> she is actually working on the vaccine right now 07:00 < agile_prg> China sent 150 million to Harvard & MIT in grant money to help with the corona virus 07:00 < agile_prg> if we do well, we can probably get some of that grant money 07:02 < yashgaroth> is there a page with information on this autovax software that I can review? 07:02 < fltrz> nmz787, thank you *very* much for your links 07:02 < agile_prg> we have a web page mockup right now that is all, that is the goal of the hackathon to create this software 07:02 < agile_prg> does that make sense? 07:03 < agile_prg> there is a powerpoint on the github 07:03 < yashgaroth> it makes sense in principle but not in practice 07:05 < yashgaroth> do you have a direct link to the powerpoint? I can't seem to find it 07:06 < agile_prg> I have it on my hardrive can I email it to you? 07:08 -!- CRM114 [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 07:10 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Ping timeout: 260 seconds] 07:26 < kanzure> agile_prg: are you xp_prg 07:31 -!- CryptoDavid [uid14990@gateway/web/irccloud.com/x-ojhdkcxtgalgshvg] has joined ##hplusroadmap 07:34 < agile_prg> yes 07:35 < kanzure> well that explains everything. 07:55 < agile_prg> in what way are you referring exactly? 07:55 < adlai> why are yall trying to synthesize vaccines from scratch? can't you just ask nicely for an antibody donation from a few dozen survivors? 07:56 < agile_prg> adlai I am new to vaccines, it sounds like a great idea however 07:57 < adlai> i realize that being able to bioinformaticize vaccines out of raw nucleotide sequences is a cool project for your CV, but if you want to actually have a deployable vaccine on a short timeframe, copy nature. 07:57 < agile_prg> I am curious what an antibody really is, is it a cell, is it a protein, what is it? 07:57 < adlai> agile_prg: i'm quite certain this is how early immunities were conferred. 07:59 < agile_prg> can the CAR T approach work? 07:59 < agile_prg> take a person's t cell's out and reprogram them? 08:16 < adlai> agile_prg: you're welcome to continue thinking aloud re: "reprogramming" a T-cell, although I'm a little at a loss as to how you'd go about doing that. if you'd like a software simile, T-cells are roughly as reprogrammable as... an AR15's upper receiver. 08:16 * adlai may have originally intended to give the analogy of a mining chip, although that's much less programmable 08:20 < kanzure> paperbot: doi:10.1126/science.aba0672 09:00 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 09:05 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 258 seconds] 09:40 -!- CryptoDavid [uid14990@gateway/web/irccloud.com/x-ojhdkcxtgalgshvg] has quit [Quit: Connection closed for inactivity] 10:16 -!- jtimon [~quassel@206.160.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 10:33 < maaku> adlai: The plan is simple: develop a theory-derived grammar that is basically a spoken form of neo-Davidsonian event semantics, develop a novel mechanism for noun phrase constructions, then use modern machine learning based NLP tools to group concepts into words and assign phonemes. 10:35 < juri_> kanzure: https://www.youtube.com/watch?v=APRswiwIRFA 10:35 < adlai> in no part of that plan do i perceive the need for a new language, provided that you are working within a host language that has sufficient flexibility 10:35 < juri_> ^-- me, giving a 45 minute presentation on ImplicitCAD. 10:36 < maaku> adlai: I prototyped (played around) with a new grammar on top of English vocabulary, but I found it too difficult to no lapse into English-based ambiguity 10:37 < maaku> if you have a different approach, I'd like to hear it 10:38 < juri_> not that it really matters.. but i thought you'd like to know who you're working with. you know, when you work with 3d printer happy people. :) 10:38 < adlai> maaku: before I continue, should I read about [neo]Davidsonian semantics? 10:40 < maaku> adlai: maybe? it's a bit in the weeds. but here's my preferred reference (there's a youtube video of this course too, if you search for it) https://www.nyu.edu/projects/champollion/eventsemantics/nyu_2016_course.pdf 10:41 * adlai has only formally studied latin and ancient greek, although is familiar germanic and semitic languages as the signalbearing background 10:42 < adlai> the reason i ask that specific question is that reading about that is quite likely to change my answer. 10:42 < maaku> the relevance is this: loglan/lojban is spoken predicate logic. but it turns out first-order logic *doesn't* capture many things we say. "event semantics" on the other hand is a specific logical interpretation that can describe the semantics of, say, any English sentence 10:43 < maaku> Lucas Champollion's event semantics, specifically. He (very recently) unified two branches of event semantics, and the unified result is general enough to assign precise meaning to all speech. 10:44 -!- CRM114 is now known as Urchin 10:46 < maaku> So whereas lojban is spoken predicate logic with a bunch of ad-hoc, unformalized pragmatic additions, a spoken event semantics could be kept more "pure", and therefore more precise 10:51 < adlai> before reading the linked document: your emphasis is on creating a language for scientific discourse. although human speech likely did not emerge from such a need, it has been greatly shaped by it in recent history. your goal would be better served by improving the process of existing languages' evolution, rather than searching for unexplored regions in the space of all languages 10:55 < maaku> adlai: I found a few emails I wrote that explained what I'm doing in a bit more detail. let me throw them into a google doc 10:58 < maaku> adlai: https://docs.google.com/document/d/1-BclijZ_tgUPlibEUjazQmf8jg04w3IDX8Nzkm6L2io/edit?usp=sharing 11:04 < maaku> I disagree, and point to programming languages as an intuition pump. 11:04 < maaku> Should we continue evolving C into C++, C++ into C++11/14/20, etc., or try something radically new like side-effect-free Haskell? 11:04 < maaku> Removing imperative constructs entirely, as Haskell does, gets a benefit that is not realizable by incremental improvements to evolved languages like C++. 11:05 < maaku> And even though the world didn't move to Haskell, experimenting with novel pure constructs is paying dividends now with the emergence of Rust, which incorporates all the lessons learned in Haskell in a more familiar, but still pure language. 11:06 < juri_> the world hasn't moved to haskell yet. 11:07 < juri_> I'm still hopeful. :) 11:07 < maaku> the world is moving to Rust 11:07 * adlai reads further before exploring the example of spoken languages vs written instructions for input to compilers 11:07 < maaku> and every new C++ version is incrementally closer to Haskell :P 11:08 < maaku> If I stretch this analogy, Lojban is like the first LISP, or one of the other early radical departures from the algol family. 11:08 < maaku> But there hasn't been (yet) a constructed language that is both complete and maintains its purity, like Haskell or Miranda were. I think that's necessary to realize the potential, whether it gets widespread adoption or not. 11:12 < maaku> adlai: permissions on the doc should be fixed 11:12 < maaku> I meant for it to be world-viewable with the link. 11:20 < adlai> should I read the google doc instead of skimming the course? 11:22 < maaku> before reading the linked document: your emphasis is on creating a language for scientific discourse. <-- I hope it's clear from what I wrote above that this is not my intent. 11:22 < maaku> yes, read the google doc. it describes what I'm trying to do and why 11:23 * adlai got that intent from your phrase "unambiguous grammar for scientific thought" 11:23 < adlai> spoken languages tend to be primarily useful for conversation, although I do see that there's a difference between your original phrase and my incorrect recollection. 11:25 < maaku> So what I'm trying to create is a universal language for communication. But one which prioritizes clarity and unambiguous interpretation of meaning. 11:25 < maaku> Which of course is highly useful in scientific discourse, but (I claim) would be highly useful in daily life too. 11:51 < adlai> maaku: I am intentionally making my edits suggestions, rather than accepted changes to the document, since I'm uncertain of your precise intent. 11:51 < adlai> specifically, see the last paragraph. 11:51 < adlai> regrettably, this google docs thing doesn't let you conditionalize the way actual version control systems do 11:53 < nmz787> agile_prg: antibodies are pretty much just proteines 12:10 < lsneff> maaku: after reading the culture series, I've been casually interested in designed languages. As such, I'd like to contribute to this project. 12:53 < agile_prg> nmz787 want to join our project in the hackathon? 12:55 < nmz787> agile_prg: not really... yashgaroth is probably on top of it... I have too many projects already 12:56 < agile_prg> nmz787 well can you be a consultant at least? 12:56 < nmz787> plus I'd have to like, sign up for slack or whatever 12:58 < lsneff> slack bad 12:58 < agile_prg> I hate slack too 12:59 < agile_prg> maaku you are a rascal with haskeel 12:59 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 272 seconds] 13:05 -!- pepesza [~pepesza@185.83.218.228] has quit [Ping timeout: 260 seconds] 13:06 -!- pepesza [~pepesza@185.83.218.228] has joined ##hplusroadmap 13:08 -!- adlai [~adlai@unaffiliated/adlai] has quit [Quit: Not all who wander are lost] 13:09 -!- adlai [~adlai@unaffiliated/adlai] has joined ##hplusroadmap 13:11 -!- Netsplit *.net <-> *.split quits: traumsch1le, HEx1, gwillen, otoburb, pasky, ptrcmd, drolmer, berndj, fenn 13:12 -!- Netsplit over, joins: gwillen, berndj, otoburb, drolmer, HEx1, pasky, ptrcmd, traumsch1le, fenn 13:13 -!- drolmer [~drolmer@unaffiliated/drolmer] has quit [Max SendQ exceeded] 13:13 -!- traumsch1le [~traumschu@mehl.schokokeks.org] has quit [Max SendQ exceeded] 13:13 -!- traumschule [~traumschu@mehl.schokokeks.org] has joined ##hplusroadmap 13:17 -!- drolmer [~drolmer@unaffiliated/drolmer] has joined ##hplusroadmap 13:49 < maaku> lsneff: your assistance and youthful enthusiasm would be appreciated 13:58 < lsneff> Youthful enthusiasm is one of my most prized skills. 14:06 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 14:10 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 14:10 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Ping timeout: 258 seconds] 14:22 -!- shmeebegek [62cf5a17@c-98-207-90-23.hsd1.ca.comcast.net] has joined ##hplusroadmap 14:34 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 255 seconds] 14:48 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 14:49 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-babonjbwpjdhsfne] has quit [Ping timeout: 245 seconds] 14:50 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-bxequggfbvyiuyaz] has joined ##hplusroadmap 14:53 -!- Urchin [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 15:22 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 256 seconds] 15:26 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 15:32 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 15:41 -!- spaceangel [~spaceange@ip-89-177-23-46.net.upcbroadband.cz] has quit [Ping timeout: 255 seconds] 17:52 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 18:00 -!- N-time [~Mark@212.225.172.60] has joined ##hplusroadmap 18:15 -!- sivoais [~zaki@unaffiliated/sivoais] has quit [Ping timeout: 265 seconds] 18:43 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 240 seconds] 18:51 -!- N-time [~Mark@212.225.172.60] has quit [Quit: Leaving] 19:12 < kanzure> .tw https://twitter.com/kanzure/status/1236052909885923328 19:12 < saxo> Announcing the release of python-bitcoinlib v0.11.0, now with segwit and segwit examples: // 1) P2WPKH: https://github.com/petertodd/python-bitcoinlib/blob/master/examples/spend-p2wpkh.py // 2) P2WSH: https://github.com/petertodd/python-bitcoinlib/blob/master/examples/spend-p2wsh-txout.py // https://twitter.com/peterktodd/status/1235668662108946432 (@kanzure) 19:13 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 20:05 -!- darsie [~kvirc@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 256 seconds] 20:24 -!- agile_prg [~nyb@50.227.202.42] has quit [Disconnected by services] 20:24 -!- agile_prg [~nyb@96.70.252.186] has joined ##hplusroadmap 20:24 -!- agile_prg [~nyb@96.70.252.186] has quit [Disconnected by services] 20:25 -!- yashgaroth [~ffffffff@172.58.19.169] has quit [Quit: Leaving] 20:25 -!- agile_prg [~nyb@96.70.252.186] has joined ##hplusroadmap 20:27 -!- agile_prg [~nyb@96.70.252.186] has quit [Disconnected by services] 20:27 -!- agile_prg2 [~nyb@96.70.252.186] has joined ##hplusroadmap 22:07 -!- jtimon [~quassel@206.160.134.37.dynamic.jazztel.es] has quit [Ping timeout: 268 seconds] 22:23 -!- ShellcatZero [~ShellcatZ@cpe-76-93-142-197.san.res.rr.com] has quit [Ping timeout: 268 seconds] 22:41 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 240 seconds] 23:39 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap --- Log closed Sat Mar 07 00:00:15 2020