Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-12-10

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All times shown according to UTC.

Time Nick Message
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07:21 jonathan_ some time ago I started 'robotics' module for lab automation.   but would like to get back to it.  anyone hear of interest in the project from outside?
08:53 kai I think we still use undergrads. they're cheaper than robots
08:54 kai kidding aside, what does the module do?
09:40 dbolser jonathan_: ppl in #hplusroadmap may have an interest
09:40 jonathan_ um
09:40 jonathan_ currently the module fails 100% perl tests. ha
09:40 jonathan_ but thats because it requires a benchtop robot.   it allows perl to control the robot.  pipette, arm, etc.
09:41 jonathan_ i've heard that undergrad comment before.  undergrads cant be trusted, I say.
09:42 jonathan_ imagine, the most advanced biotech research in the world has the gruntwork carried out by a hung over undergrad who is thinking more about the girl in the next lab than thinking about the measurement..  Hmm.  ha
10:00 dbolser jonathan_: I guess you know ross king?
10:01 jonathan_ name doesnt ring a bell
10:02 jonathan_ oh, robot scientist you mean right, only read the papers.
10:02 kai jonathan_: I don't see too much of a difference to having the gruntwork done by a robot that has been prepared by said hung over undergrad ;)
10:03 jonathan_ I had a more ambitious and next-gen plan in mind than what I've read about robot scientist
10:03 jonathan_ ah, except robot errors are quantitative.. whereas undergrad errors are qualitative
10:04 kai it'll produce more consistent errors
10:04 kai yeah
10:04 kai but the old bioinformatics adage of "garbage in, garbage out" still applies
10:06 jonathan_ consistent errors can be ok.  they can be modeled and filtered out, with enough samples.
10:09 jonathan_ many samples cost a lot though to run.  typical lab problem.
10:09 kai if I had enough data to model my stuff, I wouldn't bother with lab work :)
10:11 jonathan_ most of that data is based off only 1 or 2 experimental measurements.  no good.  need more samples and more controls.
10:59 dbolser jonathan_: yeah, #hplus will be happy to discuss this
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14:41 paul_in_pgh hi all
14:42 paul_in_pgh how can I extract (and write to a file) a specific Blast report from a Blast output file that can contain hundreds of Blast reports?
14:45 paul_in_pgh oops sorry forget that question
14:56 * dbolser erases
15:43 paul_in_pgh Why doesn't Bio::SearchIO::Writer::TextResultWriter output the Algorithm and Algorithm reference at the top of the Blast result?
15:44 paul_in_pgh The output starts with the Reference
15:45 paul_in_pgh so the person reading the output has no idea what algorithm (i.e. TBLASTX) was used to generate the output
15:45 paul_in_pgh thank you
16:48 dbolser paul_in_pgh: no clue
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17:32 paul_in_pgh dbolser, should I submit a bug for that?
17:37 dbolser paul_in_pgh: it won't hurt
18:06 paul_in_pgh submitted bug --> http://bugzilla.open-bio.org/show_bug.cgi?id=3160
18:41 dbolser paul_in_pgh: ++
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19:54 CIA-1 bioperl-live: hyphaltip master * r1fbee14 / t/SearchIO/Writer/TextWriter.t : text writer test - http://bit.ly/eo5oxH
19:54 CIA-1 bioperl-live: hyphaltip master * refb4918 / Bio/SearchIO/Writer/TextResultWriter.pm : bug #3160 - pcantalupo@gmail for writing the alg name at the top of the report -- this may need to be adjusted for multi-report output?? - http://bit.ly/exyQfQ
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