| --- Log opened Wed Oct 17 00:00:58 2012 | ||
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| @kanzure | "Dear to whom it may concern: Lateen chemicla Co., ltd is here, Exporting sucralose with high quality and low price." | 06:04 |
|---|---|---|
| @kanzure | spam is the best | 06:04 |
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| @kanzure | http://www.slideshare.net/ptmvanboheemen/igem-europe-diybio-meetup | 06:16 |
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| @kanzure | nmz787: hi | 07:28 |
| chido | kanzure: what kind of job did yash get in the end? I can't seem to be able to align our IRC schedules :) | 07:31 |
| @kanzure | i think he's doing similar work for another pharma company | 07:34 |
| @kanzure | not sure where or who or what | 07:34 |
| @kanzure | in fact i know nothing | 07:34 |
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| @kanzure | oh dear | 07:58 |
| @kanzure | now the genome compiler guy is starting 'diybio holy land' | 07:58 |
| @kanzure | (israel) | 07:58 |
| nmz787 | lol | 07:58 |
| Urchin | lol | 08:05 |
| @kanzure | http://www.guardian.co.uk/technology/shortcuts/2012/aug/19/grinders-cult-of-man-machine | 08:07 |
| @kanzure | "next stage in mankind's evolution" i wish people would stop saying these things | 08:07 |
| @kanzure | whether or not it is "evolution" has no bearing on the topic | 08:07 |
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| gnusha | diyhpluswiki.git: dac7199 add omri as a contact for diybio-israel | 08:27 |
| @kanzure | so i know about NEURON and i've heard about GENESIS, but what is MOOSE and NEST? | 08:31 |
| @kanzure | and why are these all in caps | 08:31 |
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| archels | NEST focuses on large-scale simulation of relatively simple neurons | 08:33 |
| archels | MOOSE I do not know much about, let alone come across it in the literature | 08:33 |
| archels | "MOOSE is the rewritten core code for GENESIS" | 08:34 |
| @kanzure | i see, hm | 08:35 |
| @kanzure | archels: so, i'm curious why no up-and-coming professor has tried to mimic blue brain project with some sort of public repository of neuron models and ion channels | 08:36 |
| @kanzure | the formats already exist, but nobody seems to be doing the work converting old neurophysiology studies into these formats | 08:36 |
| archels | Define mimicking the BBP... lots of labs are building models of cortical columns. In fact, I might be doing a PhD on just that. | 08:37 |
| @kanzure | my understanding is that markram's slaves are just typing up models for pNEURON | 08:38 |
| archels | What I detest is how all these models live in something of a void--each does its own little thing well enough to publish, but it's impossible to combine these models into something coherent that does more than one thing well. | 08:38 |
| @kanzure | why not just dump all the ion channel formulas into a simulator http://channelpedia.epfl.ch/ | 08:39 |
| @kanzure | on the left in the drop-down click 'ion channels' | 08:39 |
| @kanzure | then go find a sodium or potassium channel | 08:39 |
| archels | yes, and then what | 08:39 |
| @kanzure | oh hm a few of these seem to be blank, one moment | 08:40 |
| @kanzure | http://channelpedia.epfl.ch/ionchannels/1 | 08:40 |
| @kanzure | scroll down to 'models' | 08:40 |
| archels | I mean, what are you hoping to achieve by throwing some disembodied PDEs into a simulator? | 08:40 |
| @kanzure | http://channelpedia.epfl.ch/ionchannels/1/hhmodels/18.channelml | 08:41 |
| archels | or disem-neuroned ion channels for that matter :P | 08:41 |
| @kanzure | well, i agree that ion channels without neurons makes useless data and useless models | 08:41 |
| @kanzure | i don't have any particular goal except wondering why there's no open source cortical simulation project | 08:42 |
| archels | because the search space is so ridiculously massive, and there is not nearly enough experimental data to constrain it | 08:42 |
| @kanzure | i think there's a neuroml database that records some attributes of specific neuron types, but iirc it didn't include models to necessary detail | 08:42 |
| @kanzure | well, i wouldn't mind if someone just started with one type of neuron in the visual cortex for instance | 08:43 |
| @kanzure | pyramidal glutamatergic something or other | 08:43 |
| archels | you need at least two types of inhibitory neuron to get anything that remotely resembles what is actually going on | 08:43 |
| @kanzure | sure | 08:44 |
| archels | but say you did this | 08:44 |
| archels | you would probably need to throw in some plasticity rules to get it to do something interesting/useful | 08:44 |
| @kanzure | yes, eventually | 08:44 |
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| @kanzure | just summarizing popular models of plasticity is, i'm sure, at least one grad student for a year or something | 08:45 |
| archels | then perhaps you want it to generate brain waves | 08:45 |
| @kanzure | what is a brain wave | 08:45 |
| archels | large-scale oscillations, rhythms | 08:45 |
| archels | alpha/theta/mu/gamma and what have you | 08:45 |
| archels | oh, and then there's the thought (which I am tempted to share) that a cortex in isolation is pretty useless | 08:45 |
| @kanzure | i'm sure it is useless | 08:46 |
| archels | if it's not being fed into, and kept in check by, subcortical structures, it's useless | 08:46 |
| @kanzure | i think it has some advantages though, like helping us build out infrastructure for brain simulation | 08:46 |
| @kanzure | you're not just going to magically wish this stuff into existence | 08:46 |
| archels | meh, the problem is not so much the infrastructure as knowing what to put into one's model | 08:47 |
| archels | NEURON is pretty good at simulating the (computationally salient) bits of neurons | 08:47 |
| archels | and it scales well, too | 08:47 |
| @kanzure | it still requires lots of configuration to get anything resembling a study | 08:47 |
| @kanzure | i don't think saying "well, just use neuron" gets you anywhere :P | 08:47 |
| archels | that's not configuration of the simulator/infrastructure, that's constraining your model | 08:48 |
| archels | The problem is, no one really knows what to simulate. :) | 08:48 |
| @kanzure | seems to be some good equations inside http://channelpedia.epfl.ch/ionchannels/1/hhmodels/18.channelml | 08:49 |
| @kanzure | "Kv1.1 channel, with rate equations expressed in tau and inf form" | 08:49 |
| archels | And how many of those do you need on your neuron (for each type)? And where on the spines, dendrite, soma, axon, boutons? | 08:50 |
| @kanzure | this isn't the per-neuron file, that's in another database called neuroml or something | 08:50 |
| @kanzure | neuromodeldb? | 08:50 |
| archels | NeuroML is a "unified" XML modelling language | 08:50 |
| @kanzure | modeldb | 08:50 |
| archels | yes, modeldb houses NEURON models | 08:50 |
| @kanzure | (what an awful, generic name) | 08:50 |
| @kanzure | and NEURON is an awful name too | 08:51 |
| @kanzure | fuck these people | 08:51 |
| archels | heh, heh | 08:51 |
| @kanzure | i'm confused | 08:51 |
| @kanzure | http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=144416&file=\YamazakiNagaoPONE11\sum.rb | 08:51 |
| @kanzure | what is ruby code doing here? | 08:51 |
| archels | Admittedly there are some good models for single pyramidal cells... but putting everything together in the right way, that's another thing. | 08:51 |
| @kanzure | i mean why is this source code here | 08:52 |
| @kanzure | maybe i have misunderstood modeldb | 08:52 |
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| archels | maybe they use Ruby to invoke NEURON? shrug | 08:52 |
| archels | I think the authors are supposed to put everything in there to make their simulation go. | 08:52 |
| @kanzure | oh but it's always unique software, not something that works in a framework? | 08:53 |
| archels | It's the scripts that the authors hacked together to make things work :) | 08:54 |
| @kanzure | hm http://senselab.med.yale.edu/modeldb/FindBySimulator.asp | 08:54 |
| archels | (but most of it should be hoc, i.e. NEURON's language) | 08:54 |
| @kanzure | so why aren't these version controlled repositories | 08:54 |
| archels | oh, I guess they support more simulators now too. Excellent. | 08:54 |
| archels | Hey, you should be glad it came this far... scientists are notoriously uneager to share their data/software. | 08:56 |
| @kanzure | it looks like the NEURON stuff at least might possibly work together | 08:57 |
| archels | Because it's written in the same language? | 08:58 |
| archels | I wouldn't hold my breath. | 08:58 |
| @kanzure | i thought the whole idea of NEURON files were that they were independent modules that could be stacked on top of each other by adding them to a simulation instance | 08:59 |
| archels | In principle maybe, but you know how it goes with software. :P | 08:59 |
| archels | I mean, if a bunch of people in the same lab are working on their NEURON models, I'm sure they'll coordinate to such a degree that they can put them together in the same instance. | 09:01 |
| archels | But taking two random models from labs across the globe, and hoping for seamless integration? | 09:01 |
| @kanzure | this stuff is awful | 09:01 |
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| archels | NeuroML is an attempt to make it all a bit more interchangable. | 09:03 |
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| @kanzure | Juul: hi | 10:28 |
| Juul | kanzure, hi | 10:29 |
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| @kanzure | 11:50 < Swizzy> I seriously thought github created git | 11:51 |
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| @kanzure | there's probably a vulnerability on http://www.chemspider.com/chemistry-news/ but i'm too lazy to check | 13:57 |
| @kanzure | http://www.rsc.org/publishing/journals/rssfeed.asp | 13:59 |
| @kanzure | http://www.rsc.org/robots.txt is interesting | 13:59 |
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| @kanzure | oh wow, what? rsc passwords are just your birthdate | 14:25 |
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| @kanzure | there are way too many conferences: | 14:31 |
| @kanzure | http://www.rsc.org/ConferencesAndEvents/conference/eventsbymonth.cfm?month=11&year=2012 | 14:31 |
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| @kanzure | damn these guys are evil www.rsc.org/Advertising/direct-mailing.asp | 14:33 |
| @kanzure | i mean, http://www.rsc.org/Advertising/direct-mailing.asp | 14:33 |
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| @kanzure | oh neat. they have google search appliance and forgot to turn off the cache feature. | 14:46 |
| @kanzure | so a lot of their pdfs are accessible. | 14:46 |
| @kanzure | example: http://google.rsc.org/search?site=default_collection&q=cache%3Awww.rsc.org%2Febooks%2F2009%2FBK9780854041992%2FBK9780854041992-00151.pdf&btnG.x=0&btnG.y=0&btnG=Search&output=xml_no_dtd&sort=date%3AD%3AL%3Ad1&lr=&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=10&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=11&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=0&btnG.y=9&client=default_frontend&btnG.x=0&btnG.x=0&btnG.x= | 14:47 |
| @kanzure | that's "Detection of DNA Damage in Drosophila and Mosue" | 14:48 |
| @kanzure | *Mouse | 14:48 |
| @kanzure | this is sorta unreadable though | 14:48 |
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| @kanzure | oh look people are quoting the text i wrote on wikipedia :-/ | 15:27 |
| @kanzure | http://www.mindthesciencegap.org/2012/10/11/3944/ | 15:27 |
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| @kanzure | oh nice http://apache.org/server-status | 15:34 |
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| ThomasEgi | nice | 16:11 |
| ThomasEgi | ah. wrong tab | 16:11 |
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| @kanzure | http://www.ioccc.org/2012/hamano/hamano.c | 17:17 |
| ThomasEgi | epic win | 17:18 |
| ThomasEgi | my informatic professor would've killed me for commiting such code tho. :D | 17:19 |
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| @kanzure | ThomasEgi: as he should have! | 17:21 |
| @kanzure | i mean, should have if you would have | 17:21 |
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| ThomasEgi | hehe. some of my teammates in the info-class produce horrible code. | 17:24 |
| ThomasEgi | no style at all, brackets all over the place, no unified indetation | 17:24 |
| ThomasEgi | often a mix of copy-pasted stuff from other people. | 17:24 |
| not_unoriginal | http://www.modsimmer.metu.edu.tr/en/index.php?option=com_content&view=article&catid=58:Seminars&id=121:functional-near-infrared-spectroscopy-fnir-for-noninvasive-monitoring-of-brain-activity&Itemid=144 | 17:24 |
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| skorket | evening all | 18:13 |
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| @kanzure | ooh venter has been working on a dna synthesizer product? | 19:27 |
| jrayhawk | huh, i would've assumed he'd go for a services model | 19:28 |
| skorket | link? | 19:28 |
| @kanzure | no link.. it's somewhere in the news though | 19:29 |
| @kanzure | i got it by email | 19:29 |
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| @kanzure | hi necine | 19:54 |
| necine | hey there | 19:55 |
| necine | i'm trying to get into diybio, and getting started resources? | 19:59 |
| @kanzure | http://diyhpl.us/wiki/diybio/faq | 20:00 |
| necine | thanks | 20:02 |
| yashgaroth | oh hey so I went to the annual san diego diybio meeting last night | 20:10 |
| @kanzure | how'd that go? | 20:10 |
| @kanzure | hey also, could you show up at an office for me? | 20:10 |
| yashgaroth | 7 people, good talk | 20:10 |
| @kanzure | at 2768 Carlsbad | 20:11 |
| yashgaroth | yes probably I can visit some place | 20:11 |
| yashgaroth | aww carlsbaaaaaad? | 20:11 |
| @kanzure | no? okay. | 20:11 |
| yashgaroth | well what is it/am I doing there | 20:11 |
| @kanzure | stalking people | 20:11 |
| yashgaroth | I will be up there when the genentech guy from the diybio meeting does a tour of his 17,000 liter bioreactors and stuff | 20:12 |
| yashgaroth | but yes I'm free to stalk, as long as it's outside of regular business hours | 20:13 |
| yashgaroth | also this uh kinda looks like a residential address | 20:14 |
| not_unoriginal | Carlsbad? Swanky. | 20:15 |
| yashgaroth | ehh it's still cheaper than north san diego | 20:15 |
| yashgaroth | also neither todd nor carlo from the conference attended this meeting, but they're in contact | 20:15 |
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| * ybit3 tickles not_unoriginal | 20:33 | |
| not_unoriginal | Teehee. | 20:33 |
| not_unoriginal | http://www.modsimmer.metu.edu.tr/en/index.php?option=com_content&view=article&catid=58:Seminars&id=121:functional-near-infrared-spectroscopy-fnir-for-noninvasive-monitoring-of-brain-activity&Itemid=144 | 20:33 |
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| --- Log closed Thu Oct 18 00:00:59 2012 | ||
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