--- Day changed Fri Apr 10 2009 00:06 < kanzure> hm, the OCR isn't working for the 1970s Nature papers 01:01 < fenn> hehehe.. the-tan, scientology mascot 01:02 < fenn> please tell anonymous 01:08 < genehacker> scientology mascot? 01:09 < genehacker> oh i get it 01:37 -!- PeerInfinity [n=someone@216.36.180.162] has quit [] 03:29 -!- genehacker [n=chatzill@wireless-128-62-96-128.public.utexas.edu] has quit [Read error: 110 (Connection timed out)] 04:18 -!- genehacker [n=chatzill@wireless-128-62-96-128.public.utexas.edu] has joined #hplusroadmap 04:58 -!- any25439579 [n=someone@75-120-4-84.dyn.centurytel.net] has joined #hplusroadmap 05:12 -!- genehacker [n=chatzill@wireless-128-62-96-128.public.utexas.edu] has quit ["ChatZilla 0.9.84 [Firefox 3.0.8/2009032609]"] 05:16 -!- katsmeow-afk [n=someone@75-120-34-77.dyn.centurytel.net] has quit [Read error: 110 (Connection timed out)] 05:48 -!- any25439579 is now known as katsmeow-afk 06:47 -!- jm|space [n=jm@p57B9EA8E.dip.t-dialin.net] has joined #hplusroadmap 07:04 -!- jm [n=jm@p57B9E73D.dip.t-dialin.net] has quit [Read error: 110 (Connection timed out)] 07:07 -!- any55560268 [n=someone@75-120-4-84.dyn.centurytel.net] has joined #hplusroadmap 07:20 -!- katsmeow-afk [n=someone@75-120-4-84.dyn.centurytel.net] has quit [Nick collision from services.] 07:21 -!- any55560268 is now known as katsmeow-afk 08:34 < kanzure> hurray, it's now separated into somewhat reasonably sized folders 08:59 -!- jm|space [n=jm@p57B9EA8E.dip.t-dialin.net] has quit [Read error: 113 (No route to host)] 09:08 * kanzure needs to hunt down "An information-bearing seed for nucleating algorithmic self-assembly" in the March 24th issue of PNAS 09:26 < kanzure> oh boy. now diybio is turning into a job forum. ugh 09:53 < kanzure> http://news.slashdot.org/comments.pl?sid=1194963&cid=27530751 "Oh! I get it! Nice work." 10:36 -!- samrose [n=samrose@adsl-99-147-182-70.dsl.lgtpmi.sbcglobal.net] has joined #hplusroadmap 11:34 < bkero> kanzure: are employers trolling it, or kids who just graduated? 11:35 < fenn> it was just two posts that ought to have been off-list 11:37 < kanzure> true, but there has also been past occurences 11:37 < kanzure> let's all post our resumes, yay jobs for everyone 11:39 < kanzure> have any of you checked out mendeley yet? 11:39 < kanzure> I want to try out the group sharing feature 11:40 < fenn> i looked, didnt see anything interesting 11:44 < kanzure> http://heybryan.org/books/papers/microfluidics/microfluidics.20090410.bib 11:44 < fenn> how does it 'extract' metadata anyway? 11:45 < kanzure> well after having it completely fail to OCR the Nature publications, I'm thinking now that maybe it doesn't 11:45 < kanzure> it pays special attention to anything that has a DOI number 11:46 < kanzure> it completely fails (like everything else) in reading 'fl' and 'fi' next to each other in the titles in the paper 11:46 < kanzure> a clear sign that it's OCRing. 11:46 < fenn> of course it wouldn't do OCR 11:46 < fenn> oh, it does? 11:46 * kanzure nods 11:46 < fenn> uh, why 11:46 < kanzure> it would be amazingly useful if I could train it on datasets and draw rectangles of where a title is on a page that it doesn't know how to process.. 11:46 < kanzure> what? 11:47 < kanzure> because people just keep PDF files on their hard drives and they don't have the metadata 11:47 < kanzure> so it extracts it. 11:48 < fenn> so you download this application that runs and it uploads the metadata to the website? 11:48 < kanzure> yes, but it has local export options as well 11:49 < kanzure> it wants to synchronize paper collections between multiple computers and possibly different people ("group sharing") 12:08 -!- PeerInfinity [n=someone@216.36.180.162] has joined #hplusroadmap 12:09 -!- PeerInfinity [n=someone@216.36.180.162] has quit [Client Quit] 12:09 -!- PeerInfinity [n=someone@216.36.180.162] has joined #hplusroadmap 12:16 < fenn> uh.. no drag and drop, i can only add one document at a time? 12:16 < fenn> oh there it goes 12:18 -!- PeerInfinity [n=someone@216.36.180.162] has quit [] 12:29 < fenn> that 'do you want to save metadata?' dialog is really annoying 12:30 < fenn> Referencer is a GNOME application to organise documents or references, and 12:31 < fenn> ultimately generate a BibTeX bibliography file. 12:32 < fenn> oh this is handy http://www.zotero.org/support/pdf_fulltext_indexing 12:35 < fenn> i want a tagging metadata index with full text search 12:35 < fenn> not more hierarchical crap.. i can do that with a filesystem 12:38 < kanzure> are you "josef blousef" 12:38 < fenn> ja 12:39 < fenn> supposedly zotero does "Automatic synchronization of collections among multiple computers." 12:39 < fenn> so why is mendeley interesting? 12:40 < fenn> why not just make a torrent with all the individual pdf's 12:40 < fenn> people can pick and choose what they want, or get the whole thing 12:40 < kanzure> mostly for the automatic metadata extraction even if it does somewhat suck 12:40 < kanzure> sucks less than tesseract 12:40 < fenn> can't you just rename the files with the paper title? 12:41 < kanzure> I do 12:41 < fenn> it doesn't do OCR btw 12:41 < kanzure> it's also very painfully slow though to switch between reading a paper to figure out authors, publication, etc., to the file rename utility (whatever I happen to be using) 12:41 < fenn> i sniffed the binary, it doesnt have any ocr code 12:41 < fenn> well, you wouldnt do it by hand 12:42 < fenn> does bibtex include the filename? 12:42 < kanzure> at least zotero grabs metadata at point of download :) 12:42 < kanzure> no 12:42 < kanzure> erm, wait 12:44 < kanzure> phone 12:45 < fenn> the problem with these things is they don't play well with existing organization schemes 12:46 < fenn> so every time you switch metatada managers you have to basically start over 12:47 < kanzure> wtf is wrong with this woman 12:47 < kanzure> she calls me because she's throwing shit out of my room back at the death-house 12:47 < kanzure> and she can't be bothered to do a full inventory? jebus 12:48 < kanzure> anywho, the idea with zotero is that at least you can capture metadata at the time of download 12:48 < fenn> your stuff doesn't matter because you're dead anyway, right? 12:48 < kanzure> I would like to implement something with zotero such that the downloaded PDFs are put into a tar file next to a dot bib or metadata thingy. 12:48 < kanzure> oh right 12:48 < kanzure> but srsly. she scares me. 12:49 < kanzure> is it reasonable to expect to be able to randomly call somebody and then go through their entire room asking them what can be thrown away? 12:49 < fenn> uh, no comment 12:50 < fenn> 'at time of download' means there's some microformatting on the download page? 12:50 < kanzure> well, it looks like zotero has some custom download templates for scraping certain publisher websites 12:50 < fenn> blah 12:50 < kanzure> yeah :/ 12:50 < kanzure> but zotero might have that critical mass variable for it 12:50 < kanzure> i.e., with enough people using it, there's enough scraper-templates already implemented, or something 12:51 < fenn> the great thing about standards is that nobody uses them 12:51 < kanzure> hm, a large grasshopper just got on my window, 12 floors up 12:51 < fenn> they can fly 12:52 < fenn> plagues of locusts 12:52 < kanzure> does their flying ability automagically scale with body size? 12:53 < fenn> no 13:12 < kanzure> I think I invited you to a group in mendeley 13:24 < kanzure> http://heybryan.org/books/papers/microfluidics.20090410.bibliography.html 13:25 < fenn> oh, i'm already over it :\ 13:26 < fenn> i have enough projects to work on without reading obscure science papers 13:27 -!- samrose [n=samrose@adsl-99-147-182-70.dsl.lgtpmi.sbcglobal.net] has quit [Remote closed the connection] 13:33 < kanzure> heh 13:34 * kanzure waddles off to turn in paperwork by hand, because he's living in the stone age 13:57 -!- fenn_ [n=fenn@cpe-72-177-52-180.austin.res.rr.com] has joined #hplusroadmap 14:01 -!- fenn [n=fenn@cpe-72-177-52-180.austin.res.rr.com] has quit [Nick collision from services.] 14:02 -!- fenn [n=fenn@cpe-72-177-52-180.austin.res.rr.com] has joined #hplusroadmap 14:02 -!- fenn__ [n=fenn@cpe-72-177-52-180.austin.res.rr.com] has joined #hplusroadmap 14:04 -!- fenn__ [n=fenn@cpe-72-177-52-180.austin.res.rr.com] has quit [Client Quit] 14:14 -!- fenn_ [n=fenn@cpe-72-177-52-180.austin.res.rr.com] has quit [Read error: 110 (Connection timed out)] 15:01 -!- cis-action_ [n=cis-acti@c-66-31-201-117.hsd1.ma.comcast.net] has joined #hplusroadmap 15:44 -!- any65752339 [n=someone@99.194.249.112] has joined #hplusroadmap 16:03 -!- katsmeow-afk [n=someone@75-120-4-84.dyn.centurytel.net] has quit [Read error: 110 (Connection timed out)] 16:03 < bkero> waddler 16:14 -!- xp_prg [n=root@c-24-130-14-113.hsd1.ca.comcast.net] has joined #hplusroadmap 16:19 -!- wrldpc [n=worldpea@pool-173-48-214-204.bstnma.fios.verizon.net] has joined #hplusroadmap 16:33 -!- cis-action [n=cis-acti@c-66-31-201-117.hsd1.ma.comcast.net] has joined #hplusroadmap 16:33 -!- cis-action_ [n=cis-acti@c-66-31-201-117.hsd1.ma.comcast.net] has quit [Read error: 104 (Connection reset by peer)] 16:39 -!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has joined #hplusroadmap 17:06 -!- samrose [n=samrose@c-24-11-214-181.hsd1.mi.comcast.net] has quit [Remote closed the connection] 17:12 < kanzure> you take that back 17:12 < bkero> But I have evidence! 17:14 < kanzure> wtf mac, wtf 17:14 < kanzure> now when you want to talk to diy people you have to email nine different lists? 17:14 < kanzure> diybio-nyc, diybio, diybio-boston, diybio--seattle, diybio-sf, diybio-announce, diybio-chicago 17:15 * fenn wonders if that was directed at cis-action or not 17:15 < cis-action> oh 17:16 < cis-action> was that a faux pas 17:16 < cis-action> maybe I should have just used the main diybio list. 17:16 < cis-action> I got a little excited, I admit it. 17:17 -!- wrldpc_ [n=worldpea@pool-173-48-214-204.bstnma.fios.verizon.net] has joined #hplusroadmap 17:17 < kanzure> well, if you want, I'll send all future emails to all mailing lists 17:17 < kanzure> it's not a big deal for me, but most people hate crossposting 17:17 < kanzure> I also don't know why anyone has taken up interest in the automatic safety protocol generator/instruction work re: MSDS and skdb 17:17 < kanzure> but that's another rant :-p 17:18 < fenn> i've been thinking about it 17:18 < cis-action> hey, I'm interested 17:18 < kanzure> cis-action: do you remember it? 17:18 < kanzure> fenn: but you don't count because nobody listens to you (or me) 17:18 < fenn> well i havent really talked about it either 17:18 < cis-action> hmm, what I remember is wanting something like the cc licensing wizard to give you a safety badge for your digital lab notebook / website by asking a series of safety questions 17:19 < cis-action> obviously there would be liability issues there. 17:19 < kanzure> cis-action: that's one idea, but here's specifically what the emails were about 17:19 < kanzure> in particular, given diybio-certified "protocols" like pcr.xml, safety instructions could be automatically generated from a standard knowledge base of safety 17:19 < kanzure> even up to and including things like community checklists or something for various get-together occassions. I don't know how people would want to work that out 17:20 < fenn> "safety" in gen-engineering goes beyond actual safety precautions 17:20 < kanzure> but the big deal is getting people to help work on protocol encoding in XML format 17:20 < fenn> it's more like "containment" 17:20 < kanzure> that's true 17:20 < kanzure> a basic series of questions (FAQ) isn't enough IMHO- it's a good start but we already have that 17:20 < kanzure> it should be tailored to the experiment/instructable/thingy 17:20 < cis-action> Personally, I like it, but I'm afraid it might be conceptual overhead when what we need right now is something simpler 17:20 < fenn> in my mind the only way to contain bacteria is with BSL ratings 17:21 < kanzure> what overhead? 17:21 < cis-action> If you think this would be a productive and fruitful avenue for helping address the safety concerns outsiders have with garage labs, please make it happen. 17:21 < kanzure> well, I already began to do it but nobody really seemed interested in helping as I said 17:21 < kanzure> I spent a few hours on pcr.xml and nobody corrected my obvious errors 17:22 < fenn> you can't have a safety wizard unless you already have a protocol wizard in place 17:22 * kanzure nods 17:22 < kanzure> wizards are easy to write- it's really not that much overhead- the only bottleneck is in encoding the information and knowledge 17:22 < kanzure> maybe you could hook us up with somebody with some time and a good knowledge of protocols? 17:22 < kanzure> and a good knowledge of XML. 17:22 < kanzure> I mean, since it didn't really work when I posted to diybio 17:22 < fenn> doesn't have to be xml 17:22 < cis-action> It could be more general-purpose. NIH guidelines don't look at protocol-level of detail to classify work as bl1, 2, etc 17:23 < kanzure> computer-parseable is a mouthful 17:23 < fenn> formalized 17:23 < kanzure> but then they will think of beauracracy 17:23 < fenn> it doesnt even need to be computer parseable is the point 17:23 < kanzure> hm? 17:24 < fenn> massaging well structured text into XML-ish format is not difficult 17:24 < kanzure> that's parseable 17:24 < fenn> it can be delegated to a volunteer 17:24 < cis-action> half of the value comes from asking people to think about the safety concerns for themselves. If it's all automated, people might actually become less safe because they use less common sense 17:24 < fenn> people have no common sense 17:24 < cis-action> but I have to go now. I would recommend looking at the contributors to protocols on OWW and finding someone who has put a lot of time into basic protocols 17:24 < cis-action> bye 17:24 < fenn> ciao 17:24 < kanzure> :-/ 17:25 < fenn> oh nice, OWW actually has protocols 17:25 < kanzure> yes 17:26 < kanzure> in the typical overview-materials-procedure-notes-references format 17:26 < kanzure> hm, you know, if I was a masochist 17:26 < fenn> you'd massage that structured text into an xml-ish format? 17:26 < kanzure> I might be inclined to believe that steps in a procedure could be parsed for physical units 17:26 < fenn> uh, of course they can 17:26 < fenn> that's the whole point 17:26 < kanzure> but but it's never quite clear the relation between the physical units and the other words 17:27 < fenn> "electroporate - 12.5 kV/cm, pulse number of 10, puse interval of 500 ms, plasmid DNA concentration of 25 ng/ul" 17:27 < fenn> these are basically arguments to a function 17:27 < kanzure> "2 volumes EtOH" <- what the *fuck* 17:27 < kanzure> http://openwetware.org/wiki/DNA_Precipitation 17:27 < fenn> that's badly written from any perspective 17:28 < kanzure> oh, you know what would be even better 17:28 < kanzure> hrm, okay I see now 17:28 < kanzure> we will have to define function signatures 17:28 < fenn> yeah i think so 17:28 < kanzure> and then steps in a procedure formatted in a specific way will be parsed so that some parts are arguments and the other is the function name 17:29 < fenn> add A to B 17:29 < fenn> mix(x) 17:29 < fenn> same crap different domain 17:29 < kanzure> well in particular I'm thinking of those tagging interfaces where they do character-by-character suggestion 17:29 < kanzure> thus our 'protocol wizard' for parsing this shitty dataset 17:29 < kanzure> "did you mean ____ ?" 17:29 < fenn> protocol creation wizard 17:30 * kanzure nods 17:30 -!- wrldpc [n=worldpea@pool-173-48-214-204.bstnma.fios.verizon.net] has quit [Read error: 110 (Connection timed out)] 17:30 < fenn> i think there should also be another one for following the protocol 17:30 < kanzure> the reason I haven't written one is because I don't know enough about protocols 17:30 < kanzure> I've read many of them, but that doesn't help me to figure out exactly how to write a good creation wizard 17:30 < fenn> excuses excuses 17:30 < kanzure> yeah I agree 17:30 < kanzure> "did you mean to add water to acid, not acid to water? " 17:30 < fenn> i dont know the answer because i havent solved the problem yet 17:31 < fenn> hmm 17:31 < fenn> other way around 17:31 < kanzure> the paperclip is the mischevious symbolifier 17:32 < kanzure> so why isn't there a general "create an instance of an XML file from this given DTD" wizard app interface thingy? or anything for "creating an instantation of something that would conform to this given BNF grammar" 17:32 < fenn> because you dont know the search terms 17:33 < kanzure> "AutoTag makes it easy for non-technical people to create XPath select statements " 17:33 < kanzure> isn't this what code generation is about? 17:33 < kanzure> although that's mostly translation. 17:37 < kanzure> 17:36 < sproingie> sure, just run the wizard wizard wizard and you'll get a wizard wizard for your wizards 17:38 < kanzure> why did I bother with #python? surely I knew I was going to get a zen answer 17:39 < bkero> kanzure: I put a wizard in your wizard so I can easy while you're easing. 17:39 < kanzure> you know, if I go ask the perlmonks, they'll give it to me in a single line 17:41 * kanzure still likes txt2regex, a nice wizard. but for regexps. 17:42 < kanzure> fenn: so how about this? a few lists would be made: physical quantities, equipment, materials; you just type in the procedures, or some preliminary notes; at the end, the wizard will ask you whether or not there is conservation of some material (in terms of stuff that you have to deal with), etc. 17:43 < fenn> ok so basically you need to specify a grammar and then prompt the user for valid choices from that grammar 17:43 < kanzure> right 17:43 < fenn> conservation? 17:43 < fenn> i notice protocols leave out a lot of information 17:43 < kanzure> yes 17:43 < fenn> like "add this TO a 50mL beaker" 17:44 -!- cis-action [n=cis-acti@c-66-31-201-117.hsd1.ma.comcast.net] has quit [Read error: 110 (Connection timed out)] 17:44 < kanzure> and then at the end you have no more of "this" 17:44 < fenn> without that info your wizard/converter will have to use common sense, which has historically been difficult to program 17:44 < kanzure> bleh. 17:44 < fenn> no you still have it, it's in the beaker 17:44 < kanzure> hrm 17:45 < kanzure> so it's hard to distinguish between empty beakers and bottles too sometimes 17:45 < kanzure> I heart perl: http://search.cpan.org/search?query=wizard&mode=all 17:45 < fenn> if you're doing automatic safety checking, you need to have a chemical reaction simulation 17:45 < fenn> right? 17:45 < kanzure> I think safety starts with cleanliness 17:45 -!- any65752339 is now known as katsmeow-afk 17:45 < kanzure> but chemical reaction checking should be implemented 17:46 < kanzure> (perhaps as a future thingy to implement as a plugin) 17:46 < fenn> no xml creation wizard tho 17:47 < fenn> ah well, i'm sort of over DTD's anyway 17:47 < kanzure> http://search.cpan.org/~jwied/Wizard-0.1006/ 17:47 < kanzure> Text, TextArea 17:47 < kanzure> gah, those are defined by the HTML DTD 17:47 < kanzure> why isn't this abstracted 17:47 < fenn> what does Wizard do? 17:48 < kanzure> I don't know, but they do stuff like: "use Wizard(); my $wiz = Wizard->new(%attr); my $form = $wiz->Form(%attr); $wiz->Run($form);" 17:48 < kanzure> I'm not sure what benefit this adds.. 17:48 < fenn> # Wizard - A Perl package for implementing system administration 17:48 < fenn> # applications in the style of Windows wizards. 17:48 < kanzure> there's also a shell version though 17:48 < kanzure> http://search.cpan.org/~jwied/Wizard-0.1006/lib/Wizard/Shell.pm 17:49 < kanzure> oh look 17:49 < kanzure> http://search.cpan.org/~oesterhol/Term-Screen-Wizard-0.56/Wizard.pm 17:49 < kanzure> "PROMPT=>VARNAME, LEN=16 chars; ONLYVALID=>regexp here" 17:49 < kanzure> that's close. 17:50 < kanzure> ooh, what if onlyvalid can be sent to a function? 17:50 < kanzure> that would be really nice. 17:52 < kanzure> http://search.cpan.org/~zim/Tk-XML-WizardMaker-0.91/WizardMaker.pm "Tk::XML::WizardMaker - easy way to build the Software Assistants and Installation Wizards based on XML description." 17:53 < kanzure> hm, not quite. 17:55 < kanzure> http://pypi.python.org/pypi?%3Aaction=search&term=wizard&submit=search 17:55 -!- nsh [n=nsh@host217-43-230-27.range217-43.btcentralplus.com] has joined #hplusroadmap 17:56 < kanzure> nsh: know of any wizard wizards? 17:58 < kanzure> hm, yep, Term::Screen::Wizard allows validator functions 17:59 < kanzure> hm, that grasshopper is still there 18:08 < kanzure> I'm not sure what to ask the user 18:08 < kanzure> do we care about where to put stuff? 18:21 -!- cis-action [n=cis-acti@146-115-127-170.c3-0.smr-ubr1.sbo-smr.ma.cable.rcn.com] has joined #hplusroadmap 18:40 -!- wrldpc [n=worldpea@pool-173-48-214-204.bstnma.fios.verizon.net] has joined #hplusroadmap 18:45 -!- wrldpc_ [n=worldpea@pool-173-48-214-204.bstnma.fios.verizon.net] has quit [Read error: 110 (Connection timed out)] 19:53 < kanzure> http://www3.interscience.wiley.com/browse/?type=CURRENT_PROTOCOL 19:54 < kanzure> this is interesting: http://www.protocol-online.org/latest_breakthroughs.html 19:54 < kanzure> I have some of those papers 19:59 < kanzure> cis-action: you around? 19:59 < kanzure> cis-action: I was wondering if you could tell me what EXACT is 19:59 < cis-action> yes 20:00 < kanzure> http://groups.google.com/group/diybio/msg/e9acc67ca97312da 20:00 < cis-action> More context please. 20:00 < kanzure> where did EXACT come from? it's not exactly easy to search for 20:00 < kanzure> that link. 20:02 < kanzure> hm, there's this I guess: http://bioinformatics.oxfordjournals.org/cgi/content/full/24/13/i295 20:03 < kanzure> oh. http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/ 20:04 < cis-action> hmm ok good 20:04 < cis-action> I was searching for it 20:05 < cis-action> so it was mentioned in that bioinformatics article? I just scanned it again and missed it. 20:05 < kanzure> " 20:05 < kanzure> Examples of how parts of the Competant Cells protocol could be implemented in a programming language for validation/simulation purposes." 20:06 < kanzure> Larisa Soldatova just earned a new fan 20:06 < cis-action> Ha ha. I like the human-friendly syntax 20:10 * wrldpc is looking for website with .rar text book rapidshare links .. bio, robo, w/e 20:11 < kanzure> wrldpc: http://heybryan.org/docs/ check the .txt file with a list of book sharing sites 20:11 < wrldpc> ty 20:12 < kanzure> also, see http://heybryan.org/books/ since I probably have everything already anyway 20:12 < kanzure> I like the list of pre-conditions 20:31 < fenn> the haskell is the best parseable protocol i've seen so far 20:32 < fenn> i probably would have chosen "From" and "To" instead of "Start" and "End" 20:33 < kanzure> I'm not able to tell whether or not that haskell script (the first one (not Actions.hs)) generated that yeast protocol example file 20:33 < kanzure> I think it did, but if so, I'm not accustomed to how haskell works- I see no main() 20:33 < kanzure> I see a runState() actually 20:34 < fenn> which example file? 20:34 < kanzure> the yeast competent cells file 20:34 < kanzure> http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/yeast_Competent_cells_v1.txt 20:35 < fenn> no 20:35 < fenn> i dont know what that is 20:35 < kanzure> it looks like the output log of the file 20:35 < kanzure> see Actions.hs, there's a logging flag or somethign 20:35 < fenn> it would generate lines like this "Incubate " ++ name ++ " in " ++ equipment ++ " at " ++ (show temp) ++ " degC, " ++ (show rpm) ++ "rpm in order " ++ goal 20:37 < kanzure> instead I see: "experiment action: incubate \n object: competent cell culture flask\n equipment: shaking incubator \n rpm: 200 \n temp: 30C \n time: 30 mins" 20:37 < fenn> it does seem like that's in some kind of format 20:37 < fenn> you'd think they would say what format.. 20:38 < kanzure> I like the list of equipment at the end of the yeast_Competent_cells_v1.txt file 20:38 < kanzure> pre/post conditions are awesome too. 20:39 < fenn> meh 20:39 < kanzure> the extra \n's at the end make me wonder 20:39 < fenn> those should be automatically generated 20:39 < kanzure> right 20:39 < fenn> i dont want to have to go through and count the number of different beakers 20:39 < kanzure> (that's what I had to do anyway..) 20:39 < fenn> it should just count the number of beaker references 20:39 < kanzure> I mean, that's what it ended up turning into 20:39 < kanzure> erm, you should separately label all of your objects 20:39 < kanzure> and then declare the labels at the beginning 20:40 < fenn> oh pff 20:40 < fenn> did you learn that in C++ class? 20:40 < kanzure> no 20:40 < kanzure> you just need to distinguish between beakerA and beakerB in your protocol, is all I mean 20:40 < fenn> so what if some evil hacker inserts a step where you need a clean spork right in the middle of your protocol 20:40 < kanzure> error undefined reference? wizard failed. 20:41 < fenn> no, it's defined right there, myspork = Spork() 20:41 < kanzure> did you add the myspork object to @listofobjects? 20:41 < fenn> no, why would i do that 20:41 < kanzure> because you're *not* an evil hacker? 20:42 < fenn> sez who 20:42 < kanzure> just because you can read the wireshark man pages doesn't mean you're a leet hax0r 20:42 < fenn> anyway do you see what i'm getting at 20:42 < kanzure> no, would Spork's constructor add itself to the global list? 20:42 < fenn> um, maybe 20:43 < fenn> i think if you instantiate a physical object it should get counted somehow 20:43 < fenn> whether that's at creation or deletion doesn't really matter 20:45 < fenn> in C++ does a derived object call its parent class's constructor? 20:50 < kanzure> only if you don't provide your own constructor 20:50 < kanzure> or something 20:50 < kanzure> it's different with a virtual class (?) 20:54 * fenn is writing a DXF parser for some odd reason 20:58 < kanzure> huh, that grasshopper wasn't dead 20:59 < kanzure> just decided to stay put for 8 hours? 21:00 < kanzure> I like its style. 21:01 < kanzure> doesn't OCC have a DXF importer? 21:04 < fenn> yes 21:10 < kanzure> hm, I think I can do "all that" iff I am allowed to constrain the domain to volumetric-related lab protocols (i.e., moving volumes of liquid around) 21:10 < kanzure> what percentage or how many protocols would that give me access to? I figure it would give me at least a few 21:10 < kanzure> pipetting grammar heh 21:12 < kanzure> because volumes are easy to represent with pq 21:12 < kanzure> (and check/evaluate/expressions tags conditional checkies thingers) 21:22 < kanzure> you know, that really is a good domain constraint problem-wise I mean for skdb 21:22 < kanzure> what other physical quantities are you going to have, really? besides volumes. 21:22 < kanzure> maybe some temperatures, or something, but that's not a quantity 21:22 < kanzure> erm, I don't know how to say that. 22:05 < fenn> temperature is a physical quantity 22:06 < fenn> python is pissing me off 22:06 < fenn> i can't figure out how to do a simple pointer 22:32 < kanzure> why are you using a pointer? 22:32 < kanzure> http://lookherefirst.wordpress.com/2007/12/19/python-copy-by-reference-copy-by-value-shit-it-depends-on-what-you-copy/ 22:33 < kanzure> http://www.wellho.net/solutions/python-copying-an-object-copy-the-reference.html 22:34 * fenn grumbles something about alligators and swamps 22:35 < fenn> i dont know how to do that in this case 22:35 < fenn> i have a line defined by start and end points 22:35 < fenn> gah 22:36 < fenn> http://pastebin.ca/1388579 22:37 < fenn> if i try to get a reference to myline.start.x i just get the value 22:37 < fenn> if i try to set parameters[' 10'] it just changes the entry in parameters 22:38 < fenn> when i want to change myline.start.x 22:39 < fenn> i'm sure this is super interesting 22:41 < fenn> i bet it would work fine if i had a set() method 22:41 < fenn> but that gets old after the zillionth time 23:21 < kanzure> fenn, did we ever put some thought into the wizard interface to help package maintainers use skdb to find compatible components? I was always thinking of something like apt-cache search, and just adding parameters as we add new ways to search the metadata, does that still fly? 23:23 -!- any26898923 [n=someone@75-120-21-158.dyn.centurytel.net] has joined #hplusroadmap 23:29 < fenn> dunno. brain fried. bbiab or tomorrow 23:37 -!- cis-action [n=cis-acti@146-115-127-170.c3-0.smr-ubr1.sbo-smr.ma.cable.rcn.com] has quit [] 23:40 -!- katsmeow-afk [n=someone@99.194.249.112] has quit [Read error: 110 (Connection timed out)] 23:41 -!- genehacker [n=chatzill@wireless-128-62-99-202.public.utexas.edu] has joined #hplusroadmap 23:57 -!- cis-action [n=cis-acti@146-115-127-170.c3-0.smr-ubr1.sbo-smr.ma.cable.rcn.com] has joined #hplusroadmap 23:58 -!- cis-action [n=cis-acti@146-115-127-170.c3-0.smr-ubr1.sbo-smr.ma.cable.rcn.com] has quit [Client Quit]