| Time |
S |
Nick |
Message |
| 02:18 |
|
|
searchbot` joined #sourcefu |
| 02:32 |
|
pdurbin |
"Almost every non-trivial software system suffers from the accumulation of technical debt and structural erosion." http://www.nejug.org/events/show/170 |
| 02:32 |
|
pdurbin |
sounds uplifting |
| 02:42 |
|
sivoais |
:-) |
| 02:44 |
|
pdurbin |
"OpenSSL is written by scientific people" http://techblog.bozho.net/the-astonishingly-low-quality-of-scientific-code/ |
| 02:46 |
|
* sivoais |
knows "The Low Quality of Scientific Code" first hand... |
| 02:46 |
|
pdurbin |
heh |
| 02:46 |
|
pdurbin |
but is it really a problem, I wonder. that post seems pretty rant-y |
| 02:47 |
|
sivoais |
#swcarpentry exists for a reason. :-P |
| 02:47 |
|
sivoais |
Oh, and I work in a CS research lab... |
| 02:48 |
|
pdurbin |
yeah |
| 02:49 |
|
sivoais |
It's more on the science side of things, but I know that the engineering side of CS research isn't much better. I know a person that works in HPC and compilers. He's always venting about the state of the code. |
| 02:50 |
|
pdurbin |
ok, so it's a problem if you're a scientist |
| 02:50 |
|
sivoais |
writing good code as a scientist is thankless since few people read your code |
| 02:51 |
|
sivoais |
they just care about the pretty graphs at the very end |
| 02:52 |
|
pdurbin |
yeah. and it sounds like you just cite the software you used. it doesn't really matter |
| 02:53 |
|
sivoais |
Yep. And not all of that software is openly available. Or has proprietary deps. And data... oh, I could go on and on... |
| 02:53 |
|
pdurbin |
$1000 for a license for JMP, I hear |
| 02:54 |
|
sivoais |
that's really cheap relative to some others |
| 02:56 |
|
sivoais |
I don't remember the cost of ANSYS Fluent (CFD sim software), but the academic license was somewhere around hundred K $ for the engineering school for a version that was probably a decade old. |
| 02:57 |
|
pdurbin |
yikes. must be good stuff |
| 02:59 |
|
sivoais |
It's used heavily in industry. The version we had only ran on Linux, so everyone had to learn to use X11 forwarding. :-) |
| 03:00 |
|
sivoais |
because the software was only on certain remote computers and there was a limit to the number of concurrent licenses |
| 03:00 |
|
sivoais |
Oh, and the GUI for making meshes used the Motif toolkit, iirc |
| 03:03 |
|
sivoais |
OK, if one looked at a scientist working alone, I would have no problem with them writing code however they want... if it works for them, great! |
| 03:03 |
|
sivoais |
but scientists don't work alone ... it takes too much work to replicate every tiny detail |
| 03:05 |
|
pdurbin |
that's what http://www.runmycode.org is for, I guess |
| 03:08 |
|
sivoais |
hmm, I've seen that before, but for some reason I assumed they give you a VM to run your code on... |
| 03:09 |
|
sivoais |
but that's not the case... it just lets you upload your code. Which is a start. |
| 03:20 |
|
pdurbin |
you could ask skay about it: http://irclog.perlgeek.de/crimsonfu/2014-02-27#i_8357091 |
| 03:23 |
|
sivoais |
cool :-) |
| 05:35 |
|
|
aditsu joined #sourcefu |
| 06:08 |
|
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aditsu joined #sourcefu |
| 12:27 |
|
pdurbin |
sivoais: ah, nice, you pinged her and she replied: http://irclog.perlgeek.de/crimsonfu/2015-03-05 |
| 12:27 |
|
pdurbin |
so what's next for you? almost done with your CS masters? |
| 12:39 |
|
sivoais |
almost. Just need to finish my thesis. Then hopefully I ace my med school interview in a few months... then on to med school :-) |
| 12:44 |
|
pdurbin |
oh right, I think you mentioned this. good luck! |
| 12:45 |
|
pdurbin |
I have a doctor friend who's getting into bioinformatics. learning linux, compiling software |
| 12:48 |
|
sivoais |
thanks! hehe, awesome! |
| 12:49 |
|
pdurbin |
last I checked he was doing it all in a VM (virtualbox) on his PC laptop |
| 12:52 |
|
sivoais |
are they learning bioinformatics through Coursera? Or Rosalind? |
| 12:54 |
|
pdurbin |
hmm. dunno. a lot of just hacking around, I'm sure |
| 12:55 |
|
pdurbin |
maybe taking a course too |
| 12:56 |
|
pdurbin |
didn't ask |
| 12:57 |
|
pdurbin |
sivoais: should I get him to join this channel and ask you questions? :) |
| 12:58 |
|
pdurbin |
sivoais: here's an example of data he's looking at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34962 |
| 12:59 |
|
sivoais |
maybe... I'm not in bioinformatics though! I'm interested in learning it, but right now I'm doing biomedical imaging |
| 12:59 |
|
sivoais |
that's a nice big tar file... :-) |
| 13:00 |
|
pdurbin |
yeah |
| 13:00 |
|
sivoais |
oooh! One thing I liked about #dataverse was that it has MD5s of the files! I don't want to download gigs of bad data (though it would be corrupted anyway) |
| 13:01 |
|
pdurbin |
sivoais: yep! I even expose the md5 from the Search API |
| 13:01 |
|
pdurbin |
we also have a parallel concept of UNF for tabular data |
| 13:03 |
|
sivoais |
*something* normal form ? |
| 13:03 |
|
pdurbin |
searchbot: lucky unf fingerprint |
| 13:03 |
|
searchbot |
pdurbin: http://www.unf.edu/coehs/field-experiences/Fingerprinting.aspx |
| 13:03 |
|
pdurbin |
d'oh! |
| 13:03 |
|
pdurbin |
searchbot: lucky unf fingerprint dataverse |
| 13:03 |
|
searchbot |
pdurbin: http://thedata.org/ |
| 13:03 |
|
pdurbin |
sigh |
| 13:03 |
|
sivoais |
hahah |
| 13:03 |
|
sivoais |
Universal Numerical Fingerprint |
| 13:04 |
|
sivoais |
<http://dataverse.readthedocs.org/en/latest/Data_Citation/unf.html> |
| 13:04 |
|
pdurbin |
Universal Numerical Fingerprint (UNF) — Dataverse.org - http://guides.dataverse.org/en/latest/developers/unf/ |
| 13:05 |
|
pdurbin |
huh. those readthedocs files are stale |
| 13:07 |
|
sivoais |
isn't it supposed to build on push? |
| 13:08 |
|
sivoais |
slightly related, I've wondered about using a webhook to build ikiwiki pages on a GitHub gh-pages branch |
| 13:08 |
|
pdurbin |
no idea who set that up |
| 13:09 |
|
pdurbin |
sivoais: I have ikiwiki doing a build every time I push |
| 13:10 |
|
sivoais |
but does it do that on GitHub? :-) I'm trying to see if that would work as alternative to hosting it myself. |
| 13:10 |
|
sivoais |
and allowing others to edit |
| 13:11 |
|
pdurbin |
https://github.com/pdurbin/greptilian-vagrant/blob/master/modules/server1/files/usr/local/greptilian/bin/wiki-setup |
| 13:11 |
|
sivoais |
And get the benefit of making it easier to contribute, more visibility |
| 13:12 |
|
pdurbin |
my setup doesn't involve github |
| 13:14 |
|
pdurbin |
there's a git hook in https://github.com/pdurbin/wiki/blob/master/wiki.setup |
| 13:16 |
|
sivoais |
hehe, it seems you use your wiki like I use my vimoutliner files. Just put all your notes in it. :-) |
| 13:21 |
|
pdurbin |
it's pretty... random |
| 13:21 |
|
pdurbin |
but I like ikiwiki |
| 13:21 |
|
pdurbin |
it lets me put stuff into folders |
| 13:23 |
|
sivoais |
My workflow is: first, use vimoutliner for things that I haven't yet understood fully, then move those to a private ikiwiki to write out the ideas in longer form |
| 13:23 |
|
pdurbin |
ah |
| 13:24 |
|
pdurbin |
this channel is where I put things I haven't yet understood (obviously) :) |
| 13:24 |
|
sivoais |
hahah, yeah, IRC is good for that too! :-D |
| 13:25 |
|
pdurbin |
sivoais: see also http://irclog.greptilian.com/pdurbin/2012-11-28 |
| 13:28 |
|
sivoais |
oh, I saw this before... it inspired me to create my own, but turns out that I used it more for venting about bad code than actual notes. Kind of like Twitter... |
| 13:28 |
|
sivoais |
:-P |
| 13:30 |
|
sivoais |
ooh, O'Reilly has a "Learning iPython Notebook" course |
| 13:34 |
|
sivoais |
I've been using IPython notebook to write up ideas now. ikiwiki integration for that would be wonderful... |
| 13:56 |
|
pdurbin |
sivoais: I stopped using and logging #pdurbin a few months later. failed experiment |
| 21:57 |
|
sivoais |
this is interesting: <https://notablemind.org/>, <https://app.notablemind.org/tutorial/> |
| 21:57 |
|
sivoais |
via the IPython-dev mailing list |
| 21:57 |
|
sivoais |
<http://mail.scipy.org/pipermail/ipython-dev/2015-March/016056.html> |
