| --- Day changed Tue Oct 28 2008 | ||
| ppk | howdy xp | 00:01 |
|---|---|---|
| xp_prg | ppk did you finish what is up? | 00:09 |
| ppk | hey xp | 00:54 |
| ppk | hey xp | 01:44 |
| kanzure_ | Server froze for a while there. | 02:34 |
| kanzure_ | Anything I miss? | 02:34 |
| splicer | na | 02:41 |
| fenn | hmph. pptx2ppt.com errors out with 'The file input type "pptx" is not supported.' | 03:26 |
| fenn | http://www.boston.com/bigpicture/2008/10/enceladus_up_close.html check out the flyby animation | 04:02 |
| splicer | Planet Hoth | 04:06 |
| kanzure_ | fenn: maybe it's some sort of political stand. "pptx2ppt: impossible rawr!" | 04:10 |
| fenn | i could think of more direct ways of saying so.. | 04:11 |
| kanzure_ | yes, but not more annoying | 04:12 |
| xp_prg2 | ppk you here man? | 04:30 |
| Sparn | anyone have any experience with GENESIS? | 04:41 |
| kanzure_ | Sparn: sort of. | 04:41 |
| kanzure_ | I haven't ran many simulations with it. | 04:42 |
| kanzure_ | run | 04:42 |
| kanzure_ | but it is installed at least :) | 04:42 |
| Sparn | lol | 04:42 |
| ppk | hey xp | 04:48 |
| xp_prg2 | ppk you here man? | 05:40 |
| ppk | sup xp | 05:45 |
| ppk | gtg to bed | 05:59 |
| -!- jookos is now known as nsh | 08:52 | |
| faceface | With regards to the synthesis of DNA I'd like to let you know that this is a multi-step process, of course, which details largely are proprietary of GENEART. The basis is the synthesis of oligonucleotides (http://en.wikipedia.org/wiki/Oligonucleotides) which are subsequently assembled to the full-length sequence. You can learn about the oligo synthesis in relevant biotechnology text books and papers. | 08:54 |
| faceface | I'll reply "WOW THANKS FOR THE INFORMATION!!!!!" | 08:54 |
| nsh | proprietary my arse | 08:55 |
| nsh | you [they] mean "secret" | 08:56 |
| faceface | nsh, yeah | 08:58 |
| faceface | bkero, indeed, PDB is my specialty... kinda | 08:58 |
| faceface | speciality | 08:59 |
| faceface | I hope this information is useful to you. Please don't hesitate to get in touch again if you have any further queries. | 09:00 |
| faceface | do you think I should send an honest reply? | 09:00 |
| faceface | "Dear sirs, you have done nothing but spew out the measly bit of information that is already on your website. Do you think I can't read? Further more...." | 09:01 |
| faceface | no point I guess... not sure what I hoped to learn... I need to hit the toolkit actually :D | 09:01 |
| faceface | UtopiahGHML, unfortunately I did some work on a presentation instead of the BioCourse thingy... also I watched a show about zombies. | 09:02 |
| faceface | This evening I have some other work to do too... I'll see what I can do during today. | 09:02 |
| nsh | s/during // | 09:19 |
| faceface | not an inclusionist then? | 09:31 |
| faceface | you guys heard of rainbow tables? | 09:31 |
| faceface | http://thelinuxsociety.org.uk/content/rainbow-tables-slides-from-talk | 09:31 |
| faceface | they seem pretty cool (although see WP for the meat). | 09:31 |
| faceface | nsh, ... hmmm... can't think of any redundancies ... | 09:32 |
| * nsh smiles | 09:42 | |
| UtopiahGHML | faceface: to be completely straight, don't worry I stoped building caste in the sky made out of people's promises ;) | 10:49 |
| UtopiahGHML | if you do something, cool, we use it and move on, if you don't, well that's our lost but I can't complain since I didn't do it either. | 10:50 |
| kanzure_ | woah | 11:58 |
| fenn | 'sup neo | 11:59 |
| kanzure_ | So on the singularity mailing list, (the one right next to the agi mailing list), there are people now telling me that the 'singularity' is about predicting the financial markets | 11:59 |
| kanzure_ | Joshua Fox in particular. | 11:59 |
| fenn | baka darou | 11:59 |
| kanzure_ | so he's linking over to Peter Thiels etc. | 11:59 |
| kanzure_ | I don't know how they could say these things with a straight face | 12:00 |
| kanzure_ | many of the technologies they talk about easily make 'money' irrelevant | 12:00 |
| kanzure_ | if you're infinitely intelligent, what does money mean to you ? | 12:00 |
| kanzure_ | "Sorry Mr. Jupiter Brain, your bank account has simply run dry." | 12:01 |
| fenn | it is a possibility.. | 12:01 |
| fenn | but it has nothing to do with singularity or singularity-ism | 12:01 |
| kanzure_ | on the other hand, I should have expected some of this | 12:02 |
| kanzure_ | considering that many 'futurists' (*cough* Ray ol' buddy) are in it for predicting the future to make a buck | 12:02 |
| fenn | is that true? i thought ray made keyboards or OCR software | 12:03 |
| kanzure_ | he's an "inventor" | 12:03 |
| fenn | a "speak n read" for the blind is one of his latest projects | 12:04 |
| kanzure_ | I'm not claiming that he's financially unstable and needs to make a buck predicting what people want to hear or something. | 12:04 |
| kanzure_ | remember some of the things from the /fernhout/ notes to kurzweil re: him kind of looking into the future and seeing his own reflection, stock markets, economics of growths and what not | 12:05 |
| fenn | yes of course, simple observer bias | 12:05 |
| fenn | that does not make technological singularity about predicting stock markets | 12:05 |
| fenn | it's about fundamental problem of predicting a system that is more intelligent than yourself | 12:07 |
| fenn | dont whine at me for saying intelligent, you can restate it as "agent with more information" | 12:07 |
| kanzure_ | nah, that's just the Anissimovian hijacking of the singularity concepts .. I thought we agreed that even a self-replicating singularity could lead to intelligence/oh-shit-predictability barriers. | 12:07 |
| fenn | hm. yes. | 12:08 |
| fenn | that's just regular old unpredicability in complex systems though :) | 12:08 |
| kanzure_ | whenever PeerInfinity shows up again we should ask him about these things. | 12:08 |
| kanzure_ | apparently he contributes money to singinst .. I wonder if it's economically motivated | 12:09 |
| fenn | if what is economically motivated? | 12:09 |
| kanzure_ | anywho, did you hear that Hod Lipson is coming to UT? | 12:09 |
| kanzure_ | his financial contributions to singinst | 12:09 |
| kanzure_ | his 'philanthropy' | 12:09 |
| fenn | um, that doesnt make sense | 12:09 |
| fenn | (tell hod lipson that he should just kill fab@home and switch to reprap) | 12:10 |
| kanzure_ | hod is fab@home? | 12:10 |
| fenn | ya | 12:10 |
| kanzure_ | I should go back and read up on him :) | 12:10 |
| kanzure_ | I sent an email to the ADL doc saying Hod was showing up, and he had a two minute turn around to get an email out to all of his lab-students something like "most important lecture of the year if you don't go head on a stick rawr" | 12:11 |
| * kanzure_ goes down to eat. | 12:12 | |
| fenn | lol | 12:12 |
| kanzure_ | http;//open-innovation-projects.org/ <-- yet another HTTP-HTML-only directory interface. | 12:38 |
| fenn | i thought it was a pretty good start | 12:38 |
| fenn | the "browse" kinda sucks | 12:39 |
| * fenn waits on slow computer.. | 12:40 | |
| fenn | but look at the metadata fields! http://open-innovation-projects.org/projects/show/66/bug-labs | 12:40 |
| fenn | (too bad they are mostly empty) | 12:41 |
| fenn | ew @ http://open-innovation-projects.org/terms-of-use | 12:42 |
| fenn | "Please check "Outsourced" whenver an external party is paid for supplying components." | 12:44 |
| kanzure_ | what's wrong with 'outsourced'? sounds like debian's "free vs. nonfree" distinctions | 12:46 |
| fenn | i just thought it was interesting because they are considering supply chain closure | 12:47 |
| fenn | is there some kind of FOSS javascript thingy that will display a table and let you sort by columns? | 12:49 |
| kanzure_ | No. userscripts.org might have it if it did exist. | 12:50 |
| fenn | i dont really understand why people release things this way: http://www.mattkruse.com/javascript/sorttable/source.html | 12:52 |
| fenn | "you may not redistribute in any way except through use" | 12:52 |
| fenn | like that even means anything? | 12:52 |
| kanzure_ | maybe there's some weird situation where your ignorance of the existence of the item causes it to proliferate more | 12:52 |
| UtopiahGHML | anybody did stats on his Firefox SQL data? | 16:47 |
| UtopiahGHML | or anything useful based on personal data basically | 16:47 |
| UtopiahGHML | like top sites, top time spent, patterns, etc? | 16:47 |
| UtopiahGHML | eventually use it to suggest new patterns based on good practices? | 16:48 |
| UtopiahGHML | (like transforming your FF to a teacher ;) | 16:48 |
| kanzure_ | Hi UtopiahGHML. | 16:48 |
| UtopiahGHML | hey kanzure_ | 16:48 |
| kanzure_ | Yes, so, as to what you're looking for, that's, optimally, what I should have been doing for the past three or four years | 16:48 |
| fenn | what are you hoping to learn from the data? "i spend too much time trolling on slashdot"? | 16:48 |
| kanzure_ | Instead I just have this crappy ADR file of all bookmarks (2.8 MB at this point) | 16:48 |
| kanzure_ | http://heybryan.org/bookmarks/ | 16:49 |
| kanzure_ | fenn: that's about all that you'd get | 16:49 |
| kanzure_ | I'd be less interested in personal stats | 16:49 |
| kanzure_ | and more interested in pathways / patterns like that | 16:49 |
| kanzure_ | i.e., down the fifth branch and to the left, becomes a pattern and then maybe compartmentalize that as a 'command' or something. | 16:49 |
| kanzure_ | i.e. so that I don't loose track in my tabbing sessions | 16:49 |
| kanzure_ | *lose | 16:49 |
| * kanzure_ just got back | 16:49 | |
| kanzure_ | guess this isn't what UtopiahGHML is wanting .. but I figure it'd be somewhat more usable than just timewastegraphs | 16:50 |
| fenn | i've got three years of timewastegraphs if anyone is interested | 16:50 |
| kanzure_ | sleeplogs? | 16:50 |
| kanzure_ | or are you actually timing how long you look at a webpage? | 16:50 |
| fenn | http://fennetic.net/sleep/ | 16:50 |
| kanzure_ | heh | 16:50 |
| fenn | both | 16:50 |
| kanzure_ | :) | 16:51 |
| fenn | and other stuff, like what i eat | 16:51 |
| kanzure_ | how complete? | 16:51 |
| fenn | chronologically complete, lacking in some resolution of course (to avoid the diary dilemma) | 16:51 |
| faceface | UtopiahGHML, yup | 16:51 |
| kanzure_ | fenn: do you go wild if you can't log what you ate for the da y, or some such? | 16:51 |
| kanzure_ | *day | 16:51 |
| UtopiahGHML | :) | 16:52 |
| kanzure_ | "Today, we all vow to change the galaxy, and indeed the galaxy will one day be free." | 16:52 |
| fenn | go wild? no i just get sort of anxious about having to keep track of bits of paper | 16:52 |
| kanzure_ | hrm | 16:52 |
| UtopiahGHML | kanzure_: well bookmark data is cool but Im more interested in behavior and as you said patterns | 16:52 |
| fenn | instead of second-naturedly writing in my familiar text console | 16:52 |
| kanzure_ | right | 16:52 |
| fenn | or if i'm being chased through the woods by a swamp monster and have no time to keep logs, then yeah i guess i'd go wild | 16:53 |
| kanzure_ | I gthe issue I have with this is that I'd be anxious about "starting late", i.e. "Randomly, one day in October, Bryan decided to start keeping track." wtf? | 16:53 |
| fenn | and that your data is incomplete for previous years? | 16:53 |
| kanzure_ | right. | 16:53 |
| kanzure_ | would need some sort of formal metadata for expressing known incompleteness maybe? | 16:54 |
| UtopiahGHML | guess you can start with sth imprecise/vague then refine it based on needs | 16:54 |
| UtopiahGHML | and eventually an adapted tool for notation. | 16:54 |
| kanzure_ | I guess if I keep track of incompleteness, that's not bad | 16:54 |
| UtopiahGHML | Bit by bit you improve it. | 16:54 |
| fenn | i should have been more explicit about energy levels/ moods but they're hard to quantify | 16:54 |
| kanzure_ | but incompleteness, by nature, is incomplete | 16:54 |
| kanzure_ | fenn: I like the stats that ICUs in hospitals do. | 16:54 |
| fenn | so i will just try to infer from what i did instead | 16:54 |
| kanzure_ | erm, not stats, but the beeping and the graphing etc. | 16:54 |
| kanzure_ | what the hell. | 16:55 |
| kanzure_ | I accidentally missed a few seconds of a cut scene | 16:55 |
| kanzure_ | some integral, important part of the story | 16:55 |
| kanzure_ | and there's no way to go back | 16:55 |
| kanzure_ | yay "autosave" | 16:55 |
| fenn | always burning ahead on the razor's edge of the present | 16:55 |
| kanzure_ | poetry? | 16:56 |
| fenn | can you feel the angst? | 16:56 |
| kanzure_ | I wonder what they were thinking. | 16:57 |
| fenn | it takes about a minute to parse the logs and output images, so its too slow for a casual grep 'foo' | ./logparse.py | 16:59 |
| fenn | i'm wondering if writing a gtk frontend is worth the effort | 16:59 |
| UtopiahGHML | Suggesting for going further based on the personal data your browser daily collects : http://seedea.free.fr/wiki/index.php?n=Utopiahanalysis.Pim#pimderivedidea | 17:00 |
| kanzure_ | "Quick! A massive space station still under construction! Plot a course for the outer rim!" | 17:00 |
| fenn | is "pim" your tachikoma thing? | 17:00 |
| kanzure_ | "okay." | 17:00 |
| kanzure_ | yay understanding of geometry | 17:01 |
| fenn | what's "outer rim"? | 17:01 |
| kanzure_ | of the galaxy | 17:01 |
| fenn | oh | 17:01 |
| UtopiahGHML | nop I just use PIM for "Personal Internet Memory" locally | 17:01 |
| fenn | kanzure_: i suppose they have FTL then | 17:01 |
| kanzure_ | hrm. | 17:01 |
| kanzure_ | oh, Star Wars? yes | 17:01 |
| UtopiahGHML | fenn: but... I guess it could also use the tachikoma as a visual way to represent the teacher, right. | 17:02 |
| * fenn notes that the degree of FTL technology is inversely proportional to the amount of melancholic poetry | 17:02 | |
| fenn | UtopiahGHML: too bad surfraw never quite made it.. | 17:03 |
| kanzure_ | yeah :( | 17:04 |
| UtopiahGHML | surfraw? | 17:04 |
| kanzure_ | the most awesome thing ever | 17:04 |
| fenn | UtopiahGHML: you could do stuff like 'google foobar' and it would dump the results to stdout | 17:04 |
| kanzure_ | As everything should. | 17:04 |
| fenn | or 'define squidgyboo' | 17:04 |
| UtopiahGHML | hmmm like some Webdav thing? | 17:05 |
| kanzure_ | Hey, what is the definition of squidyboo anyway? I hear it mentioned in these contexts often. | 17:05 |
| kanzure_ | No. | 17:05 |
| kanzure_ | It's just a scrape.r | 17:05 |
| kanzure_ | *scraper. | 17:05 |
| kanzure_ | Not even SOAP. | 17:05 |
| fenn | i use youtubedl.py instead of in a browser because it works so much better in mplayer than flash plugin | 17:05 |
| fenn | kanzure_: simpsons reference, they're playing scrabble | 17:05 |
| kanzure_ | originated there too? Huh. | 17:06 |
| UtopiahGHML | so it would be like a command line API to the web? | 17:06 |
| UtopiahGHML | like wget but "just for data"? | 17:06 |
| fenn | am spelling it wrong and google isnt helping | 17:06 |
| fenn | Surfraw provides a fast unix command line interface to a variety of | 17:07 |
| fenn | popular WWW search engines and other artifacts of power. It reclaims | 17:07 |
| UtopiahGHML | hard to see how this could be faster than Vimperator though. | 17:07 |
| fenn | google, altavista, dejanews, freshmeat, research index, slashdot and | 17:07 |
| fenn | many others from the false-prophet, pox-infested heathen lands of | 17:07 |
| fenn | html-forms, placing these wonders where they belong, deep in unix | 17:07 |
| kanzure_ | Terrible paste. | 17:07 |
| fenn | heartland, as god loving extensions to the shell. | 17:07 |
| fenn | when firefox takes 2 minutes to start you start to hate it | 17:08 |
| kanzure_ | Vimperator sucks because firefox sucks | 17:08 |
| kanzure_ | otherwise vimperator is fine | 17:08 |
| fenn | i wish i could use ubiquity from the shell and just tell FF to fuck off | 17:08 |
| kanzure_ | ubiquity? | 17:08 |
| fenn | ff commandline plugin | 17:08 |
| fenn | sorta like hyperwords (?) | 17:09 |
| xp_prg2 | ppk u here? | 17:09 |
| kanzure_ | ugh | 17:10 |
| faceface | bkero, PDB question? | 17:10 |
| UtopiahGHML | well then I guess you could build a local GET meta-API that would be an abstraction for all the APIs of the websites you like (eventually with scrappers for websites that don't provide APIs) you like then query it with wget, no? | 17:11 |
| xp_prg2 | kanzure_ I did some work on the script last night man! | 17:11 |
| UtopiahGHML | eventually make it community based to have faster adoption rate of new innovate websites | 17:11 |
| fenn | UtopiahGHML: that was the idea behind surfraw | 17:11 |
| xp_prg2 | kanzure_ quick question what os do we want to target for this? | 17:11 |
| UtopiahGHML | fenn: oh. ok, well then it was a cool idea :P | 17:11 |
| fenn | problem was that the websites changed faster than coders could keep up | 17:11 |
| xp_prg2 | windows, linux? | 17:11 |
| UtopiahGHML | hmmm yes but since then we have wider RSS adoptions, more public APIs and sometimes webservices, no? | 17:12 |
| fenn | i guess :\ | 17:12 |
| kanzure_ | xp_prg2: Target operating systme? | 17:12 |
| kanzure_ | *system? | 17:12 |
| kanzure_ | libsbml compiles on all systems known to man as far as I can tell | 17:12 |
| * fenn drags out the mac plus "it doesnt have a compiler! yay" | 17:13 | |
| kanzure_ | gcc cross compiling? | 17:13 |
| fenn | damn, i guess that would work | 17:13 |
| UtopiahGHML | hmmm Im adding surfraw to my PIM article, pretty cool, thanks | 17:14 |
| xp_prg2 | kanzure_ well, the problem is you have to install libsmbl so its not "easy" to setup | 17:14 |
| xp_prg2 | then you have to set the dynamic library path | 17:14 |
| kanzure_ | guess this isn't for flash then huh | 17:14 |
| kanzure_ | geeze | 17:14 |
| xp_prg2 | well the back end is not in flash and never was going to be | 17:15 |
| UtopiahGHML | (talking of which I still didn't write the API for my website so no LINK>>PIMarticle<CR> possibility, damn | 17:15 |
| xp_prg2 | just wondering if you want the back end to be easily setup is all | 17:15 |
| UtopiahGHML | fuck lazyness) | 17:15 |
| xp_prg2 | what os do you use kanzure_ ? | 17:15 |
| kanzure_ | debian | 17:15 |
| xp_prg2 | awsome ok | 17:15 |
| kanzure_ | look, all I need is the mapping between the element names and the API calls | 17:15 |
| bkero | faceface: Just wondering what a good PDB viewer was | 17:15 |
| kanzure_ | I'll figure out everything else, okay? | 17:15 |
| xp_prg2 | kanzure_ ok, I am working on that | 17:16 |
| kanzure_ | at this point I don't really trust you for anything more than that heh' | 17:16 |
| xp_prg2 | heh | 17:16 |
| xp_prg2 | well, remember things are a compromise, you want what you want, I want what I want, we meet in the middle and get what we both want | 17:16 |
| xp_prg2 | I am learning a huge amount!!! | 17:16 |
| kanzure_ | there's nothing to learn really . | 17:16 |
| xp_prg2 | there is for me! | 17:16 |
| kanzure_ | nothing to compromise either .. either it's there or it isn't | 17:16 |
| kanzure_ | it's not like this requires specialized domain knowledge | 17:17 |
| faceface | bkero, oh | 17:18 |
| faceface | I wrote the FAQ on that one ;-) | 17:18 |
| bkero | Haha | 17:18 |
| bkero | There doesn't seem to be much in the portage tree--at least that I can see. | 17:18 |
| faceface | http://pdbwiki.org/index.php/PDB_FAQ | 17:18 |
| xp_prg2 | kanzure_ you have to be able to understand the input/output to make a program man, without that you mine as well give it to a blind person and say draw me castle | 17:18 |
| faceface | bkero, the best viewer imho is rasmol, because its so simple | 17:19 |
| kanzure_ | I did tell her to draw me a castle, and it was beautiful. What do you know of being blind? | 17:19 |
| faceface | you should ask on #bioinformatics too | 17:19 |
| * kanzure_ grumbles about people talking about the blind. | 17:19 | |
| UtopiahGHML | "Please.please understand thoroughly about this artificial, virtual money market in western world and then you will realize you are part of booby trap laid by certain western capitalists to retain their hegemony." http://renjithmn.wordpress.com/2008/10/25/global-economic-downturn-and-indian-reality/ | 17:19 |
| bkero | faceface: Thanks, rasmol is in the portage tree too. :) | 17:19 |
| faceface | what is the portage tree? | 17:20 |
| fenn | bkero: ghemical maybe? | 17:20 |
| faceface | l8r dudes | 17:21 |
| bkero | Are thos compatible with 2.3 and 3.0 specs? | 17:21 |
| -!- xp_prg2 is now known as xp_prg | 17:22 | |
| fenn | UtopiahGHML: if people are feeling uptight because they realize their "financial instrument" is a sack of shit, that's a real phenomenon | 17:22 |
| fenn | it affects how generous they are with resource allocation | 17:23 |
| UtopiahGHML | well, doesn't being serious with resource allocation usually result in optimizations? | 17:25 |
| fenn | renjithm is a whiny bitch, tell him to go study some math | 17:25 |
| UtopiahGHML | well you tell him yourself Im just skimming through his writting | 17:25 |
| UtopiahGHML | gather other PoW. | 17:26 |
| xp_prg | kanzure_ you here? | 17:26 |
| xp_prg | can I get a login to your debian box? | 17:26 |
| kanzure_ | yes | 17:26 |
| kanzure_ | I'm on it | 17:26 |
| ppk | hey xp | 17:30 |
| xp_prg | ppk! | 17:30 |
| xp_prg | ppk I have questions about what you sent me got a sec? | 17:31 |
| ppk | yeah | 17:32 |
| fenn | bah - "Access to PyMOL Documentation (Paid Subscribers Only)" | 17:33 |
| xp_prg | I am writing it to pastebin one sec | 17:33 |
| xp_prg | http://pastebin.com/d14301512 | 17:35 |
| ppk | ok | 17:36 |
| fenn | that's going to be a lot of menus | 17:37 |
| fenn | arent there a couple thousand biobricks? | 17:37 |
| xp_prg | ppk wow you know what you did do this right, my bad | 17:37 |
| xp_prg | didn't understand cuz you didn't indent | 17:38 |
| ppk | I couldn't in gmail | 17:38 |
| ppk | it was annoying | 17:38 |
| xp_prg | now did you do terminators? | 17:38 |
| ppk | no | 17:38 |
| ppk | I don't really know the difference between them | 17:38 |
| xp_prg | dude I need terminators! | 17:38 |
| ppk | and the purpose of having diff terminators | 17:38 |
| kanzure_ | what the hell are you doing, anyway, xp_prg ? | 17:38 |
| ppk | so I can't choose cool/popular ones | 17:38 |
| xp_prg | well ask questions, I don't know either :> | 17:38 |
| xp_prg | kanzure_ working on my interface, I need a login to your debian box to work on the back end, is that cosure? | 17:39 |
| kanzure_ | what the fuck/ | 17:39 |
| kanzure_ | ? | 17:39 |
| kanzure_ | no? | 17:39 |
| xp_prg | why not? | 17:39 |
| kanzure_ | because you have a computer yourself? | 17:39 |
| xp_prg | sbml is being a bitch to setup on my mac :( | 17:40 |
| xp_prg | I know how to do it on linux though | 17:40 |
| kanzure_ | know how to do what | 17:40 |
| xp_prg | get libsbml compiled and integrated with python to make the backend script | 17:41 |
| kanzure_ | just tell me what API functions to call | 17:41 |
| kanzure_ | that's all you have to do | 17:41 |
| kanzure_ | I'll take care of the rest | 17:41 |
| kanzure_ | there's already a python module anyway | 17:41 |
| xp_prg | I don't know the answer to that without working with the code I need a place to work with the code | 17:43 |
| kanzure_ | How could you not know the answer to that? | 17:43 |
| kanzure_ | I even gave you the link to the API docs | 17:43 |
| kanzure_ | really at this point it's me being lazy and that's why you're (supposedly) doing it instead of me.; | 17:44 |
| xp_prg | well, I want to do it, anyway, I will work on setting it up on my mac no big deal | 17:44 |
| kanzure_ | uh, why? | 17:44 |
| xp_prg | why what? | 17:45 |
| kanzure_ | why set it up? | 17:45 |
| kanzure_ | when you just have to give me the list? :) | 17:45 |
| fenn | kanzure_: i need to login to your debian box to browse your porn collection, is that cool? | 17:45 |
| xp_prg | kanzure_ I don't understand your method of coding, I don't code that way, I don't understand api docs that way, I work with code to understand api's etc... | 17:45 |
| kanzure_ | fenn: yeah | 17:45 |
| xp_prg | ppk you here man? | 17:45 |
| kanzure_ | you don't have to code xp_prg | 17:45 |
| ppk | I'm here | 17:46 |
| kanzure_ | I don't trust you to code anything any more | 17:46 |
| xp_prg | ok | 17:46 |
| kanzure_ | just give me teh lists | 17:46 |
| xp_prg | ppk, lets talk about those terminators man | 17:46 |
| ppk | if I can find out why there are so many different kinds | 17:46 |
| xp_prg | can anyone help ppk for a sec? | 17:47 |
| kanzure_ | ppk: that's the sort of things that biobricks are supposed to contain | 17:47 |
| kanzure_ | since that information isn't presently maintained in their information set, we're going to ignore it for now | 17:47 |
| kanzure_ | and maybe also go yell at them while we're at it :) | 17:47 |
| ppk | well I mean I see different terminators in pre-made completed parts | 17:48 |
| ppk | on partsregistry.org | 17:48 |
| kanzure_ | that's because they were done by hand | 17:48 |
| ppk | termination seems like a simple task to me | 17:48 |
| procto | kanzure_: see my gelbox-o-matic? | 17:48 |
| ppk | which is why I don't understand why there are so many different kinds | 17:48 |
| kanzure_ | procto: I commented on it yesterday btw :) I like. | 17:48 |
| ppk | you made the gel box laser cutting schematics? | 17:49 |
| procto | yah | 17:49 |
| ppk | that's cool | 17:49 |
| ppk | I don't know how to view the file | 17:50 |
| procto | well, the generator for the schematics | 17:50 |
| procto | it's a .py file | 17:50 |
| procto | you run it | 17:50 |
| ppk | but I intend on using those, soon | 17:50 |
| kanzure_ | ppk: SVG? firefox or opera | 17:50 |
| procto | run electrophoresis.py --help if you need help | 17:50 |
| kanzure_ | heh | 17:50 |
| fenn | procto: where? | 17:50 |
| procto | if you're on windows and have inkscape installed in its default location, it should open it in inkscape by default | 17:50 |
| procto | fenn: http://logarchy.org/electrophoresis.py | 17:50 |
| fenn | hm i was close | 17:51 |
| procto | you can use the -d parameter to specify path to alternative viewer | 17:51 |
| kanzure_ | fenn: you're not on diybio? | 17:51 |
| procto | for example, you can put in -d display, if you have imagemagick installed on a linux machine | 17:51 |
| kanzure_ | procto: ew, automatic viewer opening? | 17:51 |
| procto | if you don't like it, put -s or --silent | 17:51 |
| kanzure_ | and by default? | 17:51 |
| procto | yes. the default user story has the user converting it to DXF in inkscape right away | 17:52 |
| fenn | why must length >= 16*thickness ? | 17:54 |
| procto | because of the way it needs to fit with it | 17:55 |
| procto | when you are setting the gel, the inner box is turned sideways, and the walls of the big one maintain edges | 17:55 |
| procto | then it slides into the center of the big one | 17:56 |
| procto | in order for the hooks that make it hang to fit into the big box | 17:56 |
| procto | that's the minimum size | 17:56 |
| fenn | i keep getting sh: /home/fenn/sandbox/electrophoresis.svg: Permission denied | 17:56 |
| procto | hm, at what stage? | 17:57 |
| procto | try running it with -s | 17:58 |
| fenn | after it dumps the struct | 17:58 |
| fenn | -s silenced the error, seems to work fine either way | 17:59 |
| xp_prg | ok ppk, I put in your changes, I need those terminators, got any? | 17:59 |
| procto | I think it's mostly that you're not on windows :> | 17:59 |
| procto | fenn: I'll modify the next version | 17:59 |
| * kanzure_ still doesn't understand what xp_prg is doing. | 18:00 | |
| xp_prg | creating an input front end to make an sbml interface | 18:00 |
| fenn | and the resulting box is massively huge in inkscape relative to the page | 18:00 |
| xp_prg | based on interface1.php, I need Promoter, RBS, Coding DNA, and Terminators | 18:00 |
| kanzure_ | then why ask for a list of specific terminators | 18:00 |
| kanzure_ | yes, so why ask for a list? | 18:00 |
| kanzure_ | you jnuyst need a single line of input\ | 18:01 |
| xp_prg | to make it easy on the user | 18:01 |
| kanzure_ | no, don't bother with that | 18:01 |
| procto | xp_prg is correct | 18:01 |
| kanzure_ | I'll handle that bullshit ok? | 18:01 |
| procto | but the list needs to be loaded dynamically | 18:01 |
| kanzure_ | correct | 18:01 |
| kanzure_ | but in fact | 18:01 |
| kanzure_ | if any of you asshats had been listening yesterday, | 18:01 |
| xp_prg | hahah | 18:01 |
| kanzure_ | one thing that we can do is make it abstract so that the user doesn't have to see them at all | 18:01 |
| xp_prg | ppk where are you man?! | 18:02 |
| xp_prg | what are you doing? | 18:02 |
| xp_prg | I need this last part! | 18:02 |
| xp_prg | is anyone alive in here, what happened? | 18:14 |
| fenn | our satellite uplink is being jammed by KGB agents | 18:15 |
| xp_prg | ppk you still here, someone give me some good terminators real quick | 18:15 |
| xp_prg | that is the last thing I need right now | 18:15 |
| xp_prg | fenn anyone, hello? | 18:18 |
| kanzure_ | we already gave you the lists | 18:19 |
| xp_prg | well which ones would specifically apply to the ones in my menu for now? | 18:24 |
| xp_prg | http://pastebin.com/d14301512 | 18:24 |
| kanzure_ | what menu | 18:25 |
| kanzure_ | why is there a menu | 18:25 |
| ppk | back | 18:25 |
| ppk | so xp_prg, why don't you mock up a pre-made plasmid | 18:26 |
| ppk | from partsregistry.org | 18:26 |
| kanzure_ | why | 18:26 |
| kanzure_ | ppk: what does that have to do with his task? | 18:26 |
| ppk | if you want to get non-working stuff in there asap | 18:26 |
| ppk | I'm guessing it's easier for him to do stuff if he has tangible examples of parts in biobench | 18:27 |
| kanzure_ | but you see, he already does | 18:27 |
| ppk | ./shrug | 18:27 |
| kanzure_ | do you do any programming? | 18:27 |
| ppk | not really | 18:27 |
| kanzure_ | aha | 18:27 |
| kanzure_ | that explains all of this .. | 18:28 |
| fenn | ./shrug.py > /dev/null | 18:28 |
| xp_prg | ppk what? | 18:28 |
| xp_prg | we can't just terminator parts? | 18:29 |
| xp_prg | just use? | 18:29 |
| ppk | nevermind | 18:29 |
| xp_prg | ppk, dude explain to me where we are on the terminator parts menu please? | 18:30 |
| ppk | there are plasmids in partsregistry.org | 18:30 |
| kanzure_ | this is so stupid.. | 18:30 |
| ppk | you could mock up an actual one | 18:30 |
| kanzure_ | fenn: help me :( | 18:30 |
| ppk | with the graph::easy stuff | 18:30 |
| kanzure_ | fenn: like, even if it's yelling at me for feeding the troll | 18:30 |
| kanzure_ | Why oh why did I feed the troll? | 18:30 |
| fenn | kanzure_: please provide me complete specifications on how to help you | 18:30 |
| kanzure_ | Heh. | 18:30 |
| xp_prg | ppk, I don't understand what your saying, can you help me to understand? | 18:30 |
| fenn | you must state the answer in the form of a question | 18:31 |
| fenn | or was it the other way around? | 18:31 |
| fenn | kanzure_: i really think someone, maybe me, should try to get the data from open-innovation-projects.org or whatever | 18:32 |
| kanzure_ | write a crawler? | 18:32 |
| kanzure_ | or go knocking? | 18:33 |
| kanzure_ | Well this is a disappoint. The game is over already? | 18:35 |
| kanzure_ | *disappointment | 18:35 |
| kanzure_ | "Do you want to restart the game now with all your powers, costumes and upgrades unlocked? This will overwrite your saved game." | 18:35 |
| * kanzure_ suddenly remembers why arcade games are the win | 18:36 | |
| * bkero wins. | 18:39 | |
| kanzure_ | You're an arcade game? | 18:39 |
| bkero | Just win | 18:39 |
| kanzure_ | "{Your dad} is now following you on twitter!" <- Crap. | 18:40 |
| bkero | haha | 18:41 |
| bkero | AnandTech started following me the other day | 18:41 |
| kanzure_ | Who now? | 18:41 |
| * kanzure_ goes for lunch | 18:42 | |
| bkero | Me | 18:43 |
| bkero | The winner | 18:43 |
| UtopiahGHML | "{Your dad} is now following you on twitter!" :) | 18:43 |
| UtopiahGHML | technology, yeah! | 18:43 |
| UtopiahGHML | does he also twitt? | 18:44 |
| fenn | is your dad a twitt? | 18:44 |
| * xp_prg is stuck and ppk won't talk to him anymore :( | 18:45 | |
| xp_prg | anyone want to help me with the terminator question please? | 18:46 |
| UtopiahGHML | Sarah Connor? | 18:47 |
| xp_prg | the terminators for a biobrick part | 18:47 |
| fenn | "TwoWayMirroringWithRsync : How to keep identical copies of a wiki on two systems, one hosted and the other local," | 18:47 |
| UtopiahGHML | well, at least I tried. | 18:48 |
| * fenn grumbles about ikiwiki | 18:48 | |
| xp_prg | how do you pick the terminator for a bio brick part? | 18:49 |
| fenn | UtopiahGHML: instead of Rsync you might want to use Unison (or even dump the wiki backend into git somehow, then merge changes) | 18:50 |
| fenn | instead of overwriting local changes | 18:50 |
| UtopiahGHML | fenn: http://seedea.free.fr/wiki/index.php?n=Seedea.RemoteInstall | 18:51 |
| UtopiahGHML | Rsync was a bad idea, I just added it because it was an already existing pmwiki module | 18:51 |
| UtopiahGHML | problem is, it's not just the backend though | 18:51 |
| UtopiahGHML | but yes Ill soon start to use a real *VS soon for the modules and packaging it | 18:52 |
| UtopiahGHML | still dunno on what though, GIT, Trac, etc... :/ | 18:52 |
| UtopiahGHML | (checking Unison) | 18:53 |
| fenn | there are a lot of ~meaningless choices, and they will all become interoperable eventually | 18:53 |
| UtopiahGHML | yep, especially since ideally I want the whole thing to be self contained anway | 18:53 |
| fenn | except for backwater sludge like svn of course | 18:53 |
| UtopiahGHML | but bit by bit I should just go first a working option and move on. | 18:54 |
| fenn | yes | 18:54 |
| UtopiahGHML | (updated with Unison) | 18:55 |
| UtopiahGHML | uhhh... I started to think about the API and changes propagation over several installs based on different underlying wiki and... Id rather not think about it and go cook sth really :/ | 19:00 |
| fenn | this is why a real RCS like git is better than unison/rsync | 19:02 |
| bkero | git++ | 19:02 |
| bkero | There's a trac-git plugin | 19:03 |
| UtopiahGHML | thanks for the tip, Ill think about it, bbl | 19:04 |
| ppk | any of you know what the following parameters are and how they're useful for measuring terminators? | 19:09 |
| ppk | forward_efficiency0.309[CC] | 19:09 |
| ppk | reverse_efficiency-0.368[CC] | 19:09 |
| kanzure_ | Games aren't very much fun anymore. I'll just sit down and "teh win" and then be sad. | 19:28 |
| kanzure_ | ppk: Context? Where did you find those parameters? | 19:29 |
| ppk | partsregistry.org, on terminators | 19:29 |
| kanzure_ | Is it in the biobrick XML format? | 19:30 |
| ppk | it's just on the terminator part description page | 19:30 |
| kanzure_ | *expressed in the | 19:30 |
| ppk | http://partsregistry.org/wiki/index.php?title=Part:BBa_B0012 | 19:30 |
| ppk | what do you think? | 19:34 |
| kanzure_ | That doesn't answer my question. | 19:35 |
| kanzure_ | Here, look here: | 19:35 |
| kanzure_ | http://heybryan.org/books/biobricks/ | 19:35 |
| kanzure_ | I downloaded all biobrick information. | 19:36 |
| bkero | You got all of it? | 19:37 |
| bkero | Snazzy | 19:38 |
| kanzure_ | Yes. | 19:38 |
| kanzure_ | Also, you should see the scripts there too. I don't actually expect anybody to ever read them, so I might have my SSN in there or something. | 19:38 |
| ppk | I don't see anything on forward/reverse efficiency in here | 19:39 |
| kanzure_ | Then the biobrick people suck. So ignore that information for now. | 19:40 |
| ppk | I'd still like to know what that means | 19:41 |
| kanzure_ | efficiency? | 19:41 |
| ppk | google only finds MIT affiliated sites when searching for those terms though | 19:41 |
| fenn | i think a terminator works because the polymerase falls off the strand, so it probably falls off more reliably when going in one particular direction | 19:41 |
| ppk | hmm | 19:42 |
| fenn | http://en.wikipedia.org/wiki/Terminator_sequence | 19:42 |
| fenn | polyadenylation is what i'm remembering | 19:43 |
| ppk | still not sure about this | 19:44 |
| fenn | what are you doing? | 19:44 |
| ppk | I guess I'd have to ask somebody who's worked with the parts before | 19:45 |
| ppk | nothing in particular, just want to learn what those parameters mean | 19:45 |
| ppk | your explanation seems plausible | 19:45 |
| fenn | ah. well, perhaps you can convince whoever made them to add some more info | 19:45 |
| ppk | yeah | 19:45 |
| kanzure_ | "HOPE: it hasn't killed Apple [yet]" | 19:46 |
| fenn | wasnt Linux supposed to kill Apple? | 19:46 |
| fenn | i mean, the only thing keeping them going was that they were the microsoft alternative | 19:47 |
| kanzure_ | huh | 19:47 |
| bkero | what | 19:48 |
| procto | hm, the dow is up over 800 and holding | 19:59 |
| bkero | Over 8000? | 20:11 |
| kanzure_ | Hi ppk, Nade, splicer | 20:21 |
| splicer | hi kanz | 20:22 |
| kanzure_ | "You may call it a dungeon, but to me it's a giant mazetoilet." | 20:27 |
| bkero | wtf | 20:30 |
| UtopiahGHML | Programming Bits and Atoms http://www.youtube.com/watch?v=w8ubXgXM7kk | 21:30 |
| xp_prg | ok I have biobench .003 who wants it?! | 21:46 |
| UtopiahGHML | what can I do with it? | 21:47 |
| xp_prg | use biobricks in a graphical way | 21:49 |
| xp_prg | give me your email if you want it! | 21:50 |
| xp_prg | I am about to send it so let me know now | 21:52 |
| xp_prg | too late | 21:53 |
| UtopiahGHML | what could I do using biobricks in a graphical way? | 21:55 |
| xp_prg | you could design e-coli or yeast organisms to do novel things | 21:55 |
| UtopiahGHML | once the design is done how can I test the result? | 21:56 |
| xp_prg | with the compile/simulation abilities | 21:57 |
| UtopiahGHML | and when it's ready? | 21:58 |
| xp_prg | what do you mean? | 21:58 |
| UtopiahGHML | compiled and tested? what do I d with the result? | 21:59 |
| xp_prg | you can simulate it, then you could create it physically by either doing it yourself or sending it to company like blue heron to make it for you:http://www.blueheronbio.com/index.html | 22:00 |
| UtopiahGHML | how could I do it myself? | 22:00 |
| xp_prg | with centrifuges, chemicals, cells, petri dishes etc... | 22:01 |
| UtopiahGHML | what have you personnaly done with it so far? | 22:02 |
| xp_prg | I am creating the software only right now, but we have successfully built an e-coli plasmid that will generate a flourescent protein | 22:03 |
| UtopiahGHML | nice | 22:03 |
| UtopiahGHML | is your result public too? let's imagine that Id like BlueheronBio to make it for me, what would I need? | 22:05 |
| xp_prg | this is opensource software gpl'd free | 22:05 |
| xp_prg | just send them the dna :> | 22:05 |
| xp_prg | and the cell you want it in | 22:05 |
| UtopiahGHML | have you tried it yet? the whole process | 22:06 |
| xp_prg | no, still learning how it works | 22:06 |
| xp_prg | I want to though | 22:06 |
| UtopiahGHML | to do what ultimately? | 22:06 |
| UtopiahGHML | your wild long term goal let's say :) | 22:07 |
| xp_prg | create a biologically based cpu similar to a retina | 22:07 |
| UtopiahGHML | a retina? | 22:08 |
| xp_prg | http://thalamus.wustl.edu/course/eyeret.html | 22:09 |
| xp_prg | F. Signal processing in the retina - the center-surround receptive field. | 22:09 |
| UtopiahGHML | ok so similar in what sense? | 22:10 |
| xp_prg | a retina behaves like a silicon based cpu | 22:10 |
| xp_prg | but biologically based | 22:10 |
| UtopiahGHML | what similarities? it can compute? it can schedule? it can access memory? | 22:12 |
| xp_prg | yes all of the above | 22:12 |
| UtopiahGHML | isn't it connected neurones behind it that do that? connected to the optical nerve? | 22:13 |
| xp_prg | yes the neuronal structures that do the signal processing are in the retina | 22:13 |
| UtopiahGHML | and why do you want it for? replace a normal eye but with embeded augmented reality functionalities? | 22:14 |
| xp_prg | to create cheap cpus | 22:17 |
| UtopiahGHML | and why are you especially interested in the retina instead of classical neural networks? | 22:19 |
| xp_prg | because the retina does not re-configure itself, it is static neuronal structures | 22:20 |
| UtopiahGHML | nice, so when will I be able to try it? | 22:22 |
| kanzure_ | sense when the fuck is biobench about a retina? | 22:25 |
| kanzure_ | *since | 22:25 |
| kanzure_ | Argh. | 22:25 |
| kanzure_ | This is like a bad horror story. | 22:25 |
| xp_prg | UtophiahGHML you can try it now but it is not complete :> | 22:27 |
| xp_prg | kanzure I just released biobench .003! | 22:27 |
| xp_prg | do you want it? | 22:27 |
| kanzure_ | I read the backlog. | 22:27 |
| kanzure_ | yes | 22:27 |
| kanzure_ | I thought you were sending it to me anyway ?? | 22:27 |
| xp_prg | kanzure_ I wasn't sure you wanted it anymore you seem upset and stuff | 22:27 |
| kanzure_ | I am very upset. Doesn't mean I don't rabbidly archive .. even the shitstuff. :( | 22:28 |
| xp_prg | UtophiahGHML what is your email? | 22:28 |
| UtopiahGHML | Id rather check it on your website/wiki if you don't mind | 22:28 |
| xp_prg | ok | 22:29 |
| xp_prg | maybe kanzure_ will post it | 22:29 |
| UtopiahGHML | you don't have a website? | 22:29 |
| kanzure_ | he's on a mac | 22:29 |
| kanzure_ | and apparently doesn't have server software | 22:29 |
| xp_prg | ok sent it! | 22:29 |
| UtopiahGHML | eh... so what? you don't have to host your own website locally | 22:30 |
| kanzure_ | :) | 22:30 |
| kanzure_ | "You are what you cache." | 22:30 |
| UtopiahGHML | (dunno how I feel about Dojo...) | 22:30 |
| kanzure_ | Dojo the js thingy? | 22:31 |
| UtopiahGHML | yep | 22:31 |
| xp_prg | post it kanzure_ so UtopiaGHML can see it! | 22:31 |
| UtopiahGHML | xp_prg: did you make some in-use screenshots? | 22:31 |
| xp_prg | no | 22:31 |
| UtopiahGHML | are you doing some right now? | 22:32 |
| kanzure_ | xp_prg: I haven't received the email. | 22:32 |
| xp_prg | I sent it | 22:32 |
| kanzure_ | That does not mean I have received it. | 22:33 |
| UtopiahGHML | maybe both of you lied... | 22:36 |
| kanzure_ | ? | 22:36 |
| UtopiahGHML | maybe he didn't send it and maybe you did receive it. | 22:37 |
| UtopiahGHML | That will be my conclusion for tonight, bye guys. | 22:40 |
| gene_ | are you there Kanzure? | 22:54 |
| kanzure_ | yes | 22:54 |
| xp_prg | hi ppk!!! | 23:06 |
| xp_prg | ppk did you try it yet? | 23:06 |
| ppk | yeah | 23:06 |
| xp_prg | what do you think? | 23:06 |
| xp_prg | http://www.umassigem.org/biobench/biobench.html | 23:08 |
| xp_prg | check it out everyone! | 23:08 |
| kanzure_ | we don't have flash | 23:09 |
| kanzure_ | we've been telling you. | 23:09 |
| xp_prg | so get it | 23:09 |
| kanzure_ | uh, it doesn't work on the terminal | 23:09 |
| xp_prg | you can get codeweaver for free for year today | 23:09 |
| kanzure_ | I'm not interested in commercial systems | 23:09 |
| xp_prg | well there is osflash | 23:09 |
| xp_prg | it fully opensourced | 23:10 |
| kanzure_ | does it work in the terminal? | 23:10 |
| xp_prg | no | 23:10 |
| xp_prg | works in a web page though | 23:10 |
| kanzure_ | uh? | 23:10 |
| kanzure_ | not necessarily | 23:10 |
| kanzure_ | for instance, I have elinks, links, links2, w3m, and lynx | 23:10 |
| kanzure_ | and flash does not work in these. | 23:10 |
| xp_prg | kanzure_ your cool, never met anyone who doesn't use X | 23:10 |
| xp_prg | your missing out but ok | 23:11 |
| kanzure_ | I use X when it's convenient :) running X on the server is a bad idea | 23:11 |
| xp_prg | kanzure_ can you help me to understand more about what an effector is, I think I saw it on interface2.php | 23:11 |
| kanzure_ | What difference would it make whether it was X or Y? | 23:13 |
| xp_prg | cuz it will help me to understand how they relate to the SBML modeling file | 23:15 |
| kanzure_ | Really? How? | 23:15 |
| xp_prg | so I can understand the output correctly | 23:15 |
| kanzure_ | You don't see "effectors" already in the pregenerated SBML examples from the synbioss designer? | 23:15 |
| xp_prg | yes the example does have an effector in it | 23:16 |
| kanzure_ | Okay, then what's so hard about that? | 23:16 |
| kanzure_ | Now you know. | 23:16 |
| xp_prg | I don't know what it does | 23:16 |
| kanzure_ | You don't have to. | 23:16 |
| xp_prg | well I want to, you won't tell me why? | 23:21 |
Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!