| --- Log opened Sat Jan 26 00:00:41 2013 | ||
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| kanzure | paperbot: http://www.jove.com/video/2032/experimental-models-for-study-retinal-pigment-epithelial-physiology | 01:32 |
|---|---|---|
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Experimental%20Models%20for%20Study%20of%20Retinal%20Pigment%20Epithelial%20Physiology%20and%20Pathophysiology.pdf | 01:32 |
| kanzure | eleitl: ping^ | 01:32 |
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| juri_ | uwah. | 03:03 |
| juri_ | just got done with some truely hideous javascript. | 03:04 |
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| chris_99 | nmz787, are you about per chance? | 08:17 |
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| kanzure | paperbot: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0053760 | 10:40 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Telomerase%20Reverse%20Transcriptase%20Synergizes%20with%20Calorie%20Restriction%20to%20Increase%20Health%20Span%20and%20Extend%20Mouse%20Longevity.pdf | 10:40 |
| kanzure | http://www.theatlantic.com/magazine/archive/2012/11/hacking-the-presidents-dna/309147/1/ | 10:41 |
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| seba- | kanzure cool | 11:41 |
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| Urchin[Emacs] | hi | 12:46 |
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| kanzure | what text editor leaves myfile.LCK files everywhere? | 16:13 |
| kanzure | vim seems to use .swo and .swp, but recently i've been finding a bunch of files left on webservers as .whatever.swn (instead of swp or swo) | 16:13 |
| kanzure | aha. dreamweaver leaves .lck files. | 16:14 |
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| kanzure | dunno what's going on here http://downloadpaper.ir/ | 16:26 |
| kanzure | not much in here http://www.gigapaper.ir/Articles/ | 16:26 |
| Urchin[Emacs] | I'm checking out my old transhumanist blog | 16:26 |
| kanzure | the ieee folder has some papers | 16:26 |
| Urchin[Emacs] | not much stuff there | 16:26 |
| Urchin[Emacs] | I haven't posted since 2006 | 16:28 |
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| eudoxia | so some guy started a new hplus forum http://thetranshumanist.com/forum/ | 17:32 |
| eudoxia | getting koen de paus to advertise your new h+ forum to his followers... i should have thought about that | 17:33 |
| eudoxia | meh it will be filled with useless philosophers anyways | 17:33 |
| yashgaroth | wtf is a koen de paus | 17:33 |
| kanzure | it's a sign of respect, i think, between mob bosses | 17:34 |
| yashgaroth | haha | 17:34 |
| eudoxia | some guy on g+ who occasionally talks about transhumanism and has like 20k followers | 17:34 |
| nmz787 | kanzure: did you try the code ? | 17:44 |
| kanzure | nmz787: yours? no not yet. i have been busy writing other things. | 17:50 |
| kanzure | "You have selected a resource that is licensed for the exclusive use of Wyoming citizens." | 17:50 |
| eudoxia | w-w-well see if i c-care, Wyoming ;_; | 17:59 |
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| kanzure | http://www.cypherpunks.ru/static/goam.txt | 19:18 |
| kanzure | their character encoding is wrong | 19:18 |
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| kanzure | ParahSailin: am i reading this right? http://www.i-nobel.com/bbs/read.php?tid-433188.html | 19:51 |
| kanzure | they want me to send in photo id to register? | 19:51 |
| kanzure | ... to share papers? | 19:51 |
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| kanzure | http://madhadron.com/?p=263 "I’m leaving bioinformatics to go work at a software company with more technically ept people and for a lot more money. This seems like an opportune time to set forth my accumulated wisdom and thoughts on bioinformatics. My attitude towards the subject after all my work in it can probably be best summarized thus: “Fuck you, bioinformatics. Eat shit and die.”" | 21:44 |
| nmz787 | wow | 21:46 |
| yashgaroth | looks about right | 21:46 |
| brownies | well that's inspiring. | 21:48 |
| kanzure | http://news.ycombinator.com/item?id=5123022 | 21:48 |
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| brownies | "Instead of verifying a single implementation, it's often better for somebody to reimplement the idea from scratch; if a second implementation in a different language written by a different programmer gets the same results, this is a much more thorough validation of the software than going over prototype software line by line." | 22:15 |
| brownies | wat | 22:15 |
| kanzure | yeah that's just the tip of the iceberg of the crazy | 22:16 |
| brownies | it seems that the problem is that biologists should have all thought "oh, let's learn to program!" and instead they procured lots of extra grant money and said "oh, let's hire programmers!" | 22:16 |
| brownies | s/the problem/one of the problems/ | 22:17 |
| yashgaroth | biologists didn't spend 15 years in grad school to learn more things | 22:17 |
| yashgaroth | after, that is | 22:17 |
| brownies | you know what they say | 22:24 |
| brownies | "once you learn a certain amount, you can stop learning forever!" | 22:24 |
| yashgaroth | also they're probably secretly peeved that programmers make more than they do | 22:25 |
| * kanzure throws out his nodejs documentation | 22:26 | |
| kanzure | secret? it's no secret. nobody likes to make $30k/year. | 22:26 |
| brownies | yeah, well, if they'd stop spending grant money on paying programmers whose time they don't know how to fully utilize (!!!) maybe they wouldn't have to pay themselves subsistence wages. | 22:27 |
| brownies | "Also, I've seen way too many software engineers come in with an enterprisey attitude of establishing all sorts of crazy infrastructure and get absolutely no work done." | 22:27 |
| brownies | where do they get this crap? | 22:27 |
| juri_ | you know, this is funny to read, given that i'm a (rock star motherfuckka!) computer/mechanical/electrical engineer, wishing i had biological skills. | 22:29 |
| juri_ | ... and i can't find enough work in the free software industry to make double minimum wage. ;P | 22:30 |
| yashgaroth | regarding that comment you quoted, the UCSC genome browser is one of the best/few useable bioinformatics tools, and it's still annoying as shit | 22:31 |
| juri_ | maybe bioinformatics tools wouldn't suck, if every person who hired a programmer didn't insist on keeping the secret sauce secret. | 22:33 |
| brownies | yashgaroth: what's annoying about it? | 22:34 |
| yashgaroth | a million settings, and none of them change what you want them to | 22:34 |
| brownies | ah. UX problems. no surprise. | 22:35 |
| yashgaroth | idk it's not that bad for gov't funded programming, I'm sure | 22:35 |
| nmz787 | kanzure: we chose the same pic for inobel | 22:35 |
| yashgaroth | juri_ what do you mean? most bioinfo software, especially grant-funded, is open source | 22:38 |
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| juri_ | yash: i don't know bioinformatics software, i just know the requests in all industries that i as a software developer get. I've got standing offers to make six figures as a non-free software developer, but instead make barely enough to live developing free software, as the price of making non-free software is just too high. | 22:58 |
| yashgaroth | ok | 22:59 |
| brownies | bad priorities. got it. | 23:02 |
| juri_ | people are my priority. | 23:03 |
| brownies | yashgaroth: holy hell. http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source | 23:04 |
| brownies | have these people never heard of ./configure ? | 23:04 |
| yashgaroth | I've no idea what that or you are talking about :/ | 23:05 |
| yashgaroth | juri_ why not take the job with dem sixfigz and pay two programmers to do free software | 23:05 |
| brownies | me? | 23:05 |
| yashgaroth | yes, the text on that page or what a ./configure is | 23:06 |
| brownies | yashgaroth: it's the "open source building instructions" for the Genome Browser you mentioned | 23:06 |
| brownies | yes, that's the problem. | 23:06 |
| brownies | they haven't exactly made it easy for other people to contribute work back to it, to help improve it, to build upon what's already there | 23:06 |
| yashgaroth | see, you could've said it was anything and I'd believe you | 23:06 |
| brownies | then that's also the problem! =P | 23:06 |
| brownies | where is kanzure? he can help me rant about this. | 23:06 |
| yashgaroth | heh | 23:06 |
| brownies | i have this little pet hypothesis that all of science would be drastically improved if we could just convince every working academic to put their code on github every time they publish a paper | 23:07 |
| juri_ | yash: i've actually tried that, when i was working for walmart. my work made walmart stronger, where the development i paid for didn't really help anyone. I'm a very good software developer. ;) | 23:07 |
| juri_ | i helped walmart roll out stores in mexico which they are still facing charges about. I'm not proud of those days, its the greatest black mark on my work. | 23:09 |
| yashgaroth | well find a company that's less mind-fuckingly evil than walmart | 23:09 |
| juri_ | oddly, it seems the eviler they are, the more they pay. | 23:10 |
| juri_ | and that still doesn't solve the 'i write code better than the people i can hire' problem. ;) | 23:11 |
| yashgaroth | well work at some innocuous company in silicon valley making the next facegram...r | 23:11 |
| yashgaroth | they still pay insane money apparently | 23:12 |
| kanzure | brownies: i think academics should submit themselves to code reviews | 23:12 |
| kanzure | they believe in peer review, so why not code review. | 23:13 |
| kanzure | code review makes better programmers. and they don't do it. | 23:13 |
| yashgaroth | are we still talking about bioinformatics here | 23:13 |
| kanzure | academic programming of any sort. | 23:13 |
| kanzure | i wrote some bioinformatics software when i was stationed in two different academic labs | 23:14 |
| kanzure | and nobody ever wanted to look over my code. | 23:14 |
| juri_ | i was barely talking about it in the first place. while some of the algorithms i use/maintain are used in that field, i don't work in it myself. | 23:14 |
| kanzure | at the time, i could have really used some code review from people who actually knew bioinformatics and programming. | 23:14 |
| brownies | the problem is that there probably wasn't anyone qualified to both review code AND the bio ideas contained therein | 23:14 |
| brownies | the code review system works because it's basically apprenticeship ... which means there already exist people who know wtf is going on. | 23:15 |
| kanzure | one of the programs i built was extremely simply- i was optimizing which codons to use for encoding certain proteins in a genome to make a biofuel process suck less | 23:15 |
| kanzure | i think bioperl or biopython has a module that does that, but i didn't know about it at the time and apparently nobody wanted to tell me either. | 23:15 |
| brownies | =/ | 23:15 |
| juri_ | for code review with accademic papers, you would think the paper would cover enough of the knowlege to help a programer review the code. | 23:15 |
| yashgaroth | kanzure: oh I hope you weren't just changing every codon to the single most commonly used one for highly expressed genes | 23:16 |
| juri_ | if anyone needs review of free software, associated with an accademic paper, i think i can find some time. | 23:17 |
| kanzure | yashgaroth: no it was based on metabolism | 23:17 |
| yashgaroth | ah good | 23:18 |
| kanzure | pfft come on man | 23:18 |
| yashgaroth | just checkin' | 23:18 |
| kanzure | i find your lack of faith disturbing, long and prosper | 23:18 |
| yashgaroth | the tRNA depletion, maaaan | 23:18 |
| kanzure | (because jj abrams is doing both, all quotes must henceforth be mixed from both SW and ST) | 23:18 |
| kanzure | speaking of which, i should go back and comment on cathal's code | 23:19 |
| yashgaroth | these aren't the droids you're uh...shit I don't watch star trek much | 23:19 |
| brownies | "the paper would cover enough ... knowledge to help a programmer review the code" <= laughably wrong | 23:19 |
| kanzure | https://github.com/cathalgarvey/PySplicer | 23:19 |
| brownies | the paper usually barely covers enough knowledge to help a working specialist review the paper | 23:19 |
| kanzure | i helped him clean up the code a few months ago (years?) but it's probably lapsed a bit | 23:20 |
| kanzure | plus it's completely non-installable | 23:20 |
| juri_ | brownies: to assist in reviewing the code? got an example? | 23:20 |
| kanzure | "lib" what is "lib" this does not belong in a python project | 23:20 |
| juri_ | i write code based on accademic papers, in the image recognition field. | 23:21 |
| kanzure | re-implementing an algorithm from a paper is the most annoying shit | 23:22 |
| kanzure | for stress relief i recommend printing out a physical copy of the paper and burning it | 23:22 |
| juri_ | i leave physical copies of papers in the restroom. what is done with them there is an exercise left to the reader. ;) | 23:22 |
| brownies | i think we've all written code based on papers; that is not really the point | 23:23 |
| brownies | the point is that the paper should come with a polished, well-commented, documented version of the exact code used in producing the paper | 23:23 |
| brownies | so that thousands of people don't have to sit around like jackasses implementing code based on papers -_- | 23:23 |
| kanzure | juri_: btw, one of the things the free software community desperately needs is an actually open source implementation of a nurbs manipulation library. brlcad has been struggling along without one for years. | 23:23 |
| kanzure | juri_: opencascade has a questionable license, and their source code is unmaintainable garbage (french + english + russian) with bugs all over the place. and tracing things properly across >200 submodules is nearly impossible even with grep. | 23:24 |
| kanzure | juri_: this would be very very helpful with things like hardware packaging standards because we could just use a nurbs representation of models and parametrically re-use parts in other models that build on other pieces of open source hardware. | 23:25 |
| * juri_ takes a peek. | 23:25 | |
| kanzure | http://brlcad.org/ | 23:26 |
| kanzure | http://opencascade.org/ | 23:26 |
| juri_ | I've been watching implicitcad with more than some interest. | 23:27 |
| juri_ | they're looking at constraints support, ATM. | 23:27 |
| kanzure | i somehow convinced fenn to try out implicitcad, http://fennetic.net/irc/rail_meshlab.png | 23:29 |
| kanzure | 12:04 < fenn> kanzure: implicitcad works as intended, but it needs a lot of work to be usable. the constant size sampling grid for example makes things slow at larger absolute dimensions | 23:30 |
| kanzure | 12:04 < fenn> rendering time scales ~ as the cube of the dimension | 23:30 |
| kanzure | 12:05 < kanzure> "size sampling grid" what? | 23:30 |
| kanzure | 12:05 < fenn> a simple script to watch the source file for changes and re-render it at increasing resolution would be nice | 23:30 |
| kanzure | if implicitcad could be replaced with nurbs manipulation under the hood, you could dump output to standard formats for proprietary cad tools and start to sucker in people from the actual engineering fields. | 23:35 |
| kanzure | https://github.com/stepcode/stepcode | 23:36 |
| juri_ | kanzure: i think this is a good answer to the question i asked you the other day. | 23:37 |
| kanzure | sometimes it takes me a while. | 23:37 |
| juri_ | a good answer is worth the wait. | 23:38 |
| -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has quit [Quit: Leaving] | 23:44 | |
| --- Log closed Sun Jan 27 00:00:42 2013 | ||
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