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05:11:51 <pingou> morning :)
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06:41:53 <faceface> moaning
06:53:26 <pingou> hi guys
06:53:50 <pingou> has anyone of you ever made a php client for biomobdy web services
06:54:23 <pingou> ?
06:56:00 <faceface> not me
06:56:03 <pingou> :)
06:56:21 <faceface> I used perl for the MSD webservice once... that is as close as I goty
06:56:22 <faceface> got
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07:48:50 <Lynx_> Hi all!
07:49:51 <Lynx_> Would anyone know how to read Roche 454 sff files? Googling turns up a program called sffinfo, but I can't find it anywhere, maybe it is also from Roche and not free.
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09:49:48 <faceface> Lynx_, perhaps something in emboss?
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09:52:10 <pingou> anyone using primer3 in command line here ?
09:52:20 <Tom``> Im starting my bsc in bioinformatics in a couple of months and im trying to be productive and learn some useful stuff before I do. What do you think would be the most useful to read/study?
09:52:57 <pingou> what do you know about programming and biology ?
09:53:17 <Tom``> ive done a little bit in programming, making hello world scripts etc
09:53:35 <Tom``> and ive finished A level biology and probally got the highest grade
09:53:51 <pingou> congrats :)
09:54:10 <Tom``> thanks :) But I dont think its going to help at uni, seems much much harder
09:54:44 <pingou> not necessarily since you have learned how to work :)
09:54:45 <Tom``> Im going to head to the library today to do some studying and theres quite a few bio books there
09:55:11 <Tom``> what aspect of biology would be the most important to read into do you think pingou?
09:55:15 <pingou> basically try to enforce yrou worse side :)
09:55:34 <pingou> Tom``: that *mainly* depends on what *you* like :)
09:56:13 <Tom``> hah, I like everything I've seen so far!
09:56:16 <pingou> genetics, proteomics, metabolomics, integrative network, system biology, neurology, biophysics, genetic mapping...
09:56:26 <pingou> that's all yours ;)
09:56:30 <Tom``> oh dear
09:56:41 <pingou> ^^
09:56:47 <Tom``> Its going to be a fun next few years!
09:57:07 <pingou> no you'll see some of this, depends on what you choose
09:57:14 <faceface> Also, Lynx_ that is, see http://seqanswers.com/
09:57:24 <pingou> animal vs plants vs bacteria
09:57:26 <pingou> ...
09:57:31 <Tom``> bacteria!!!
09:57:40 <Lynx_> pingou: i use primer3 cmd
09:57:59 <Tom``> whats the most used scripting language in the bioinformatics community? Perl?
09:57:59 <Lynx_> faceface: thanks, i'll check both of these
09:58:11 <pingou> Lynx_: could you  give me a hand ?
09:58:26 <pingou> Tom``: perl is widely used, but python, java and ruby can be to
09:58:32 <faceface> Tom``, perl, python, java
09:58:37 <Lynx_> pingou: i can try, but only als long as you don't want to call it from perl without writing a file in windows, i gave up on that ;)
09:58:46 <faceface> C++ .. fortran ... etc
09:58:52 <pingou> Lynx_: I need to test the RPMs I have made, do you have a file where you have the results that we can compare ?
09:58:55 <faceface> Tom``, study protein  / DNA sequence
09:59:07 <faceface> the most important concept in bioinf to begin with is sequence
09:59:12 <faceface> make it sequence sequence sequence
09:59:16 <pingou> DNA :D
09:59:22 * pingou loves DNA \o/
09:59:33 <Lynx_> pingou: i'll try to find one
10:00:09 <pingou> Lynx_: have a look at the microarrays and the arrays technology in general if you like genetics
10:00:13 <pingou> Lynx_: thanks :)
10:00:23 <Tom``> is it just the base sequence providing the amino acid sequence stuff? or is there much more to it
10:00:41 <faceface> Tom``, gene structure
10:00:42 <Tom``> I've sorta heard of genes switching on and off? never read about it though in text books
10:01:02 <pingou> yeah gene regulation is interesting
10:01:04 <faceface> Tom``, yup.. genetic regulatory control - another good topic... its part of gene structure really
10:01:11 <faceface> gene regulation
10:01:11 <pingou> look at QTL analysis that's also great
10:01:17 <faceface> pingou, lies ;-)
10:01:20 <pingou> :D
10:01:28 <pingou> faceface: protein structure is great too !
10:01:40 <faceface> yay! ... although I am doing genomics ...
10:01:46 <pingou> how the structure influence the interaction of the protein with its environment...
10:01:48 <faceface> QTL stuff like that ;-)
10:01:50 <Tom``> do most of you guys study bioinformatics or work in the field?
10:02:04 <faceface> wait... there is a field now?
10:02:09 <pingou> faceface is old, he is already working :p
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10:02:19 <pingou> faceface: look through the windows ;)
10:02:20 * faceface is always chatting
10:02:30 <Tom``> :)
10:02:33 <pingou> faceface: just turn your head ;)
10:02:47 <pingou> no the other side :)
10:03:10 <faceface> I can't see with these blinkers on
10:04:04 <Lynx_> pingou: how do you want the files? DCC won't work...
10:04:30 <pingou> Lynx_: http://rafb.net/paste ?
10:04:47 <Lynx_> right
10:05:21 <pingou> faceface: http://maps.google.fr/?ie=UTF8&ll=54.683322,-1.777532&spn=0.005135,0.018797&t=h&z=16 there is the field ;)
10:05:28 <pingou> right in the middle :)
10:05:30 <Lynx_> http://rafb.net/p/71WBiN35.html
10:05:50 <Lynx_> http://rafb.net/p/0n1XJw78.html
10:05:55 <Lynx_> in and outfile
10:05:58 <faceface> hmm.... I don't like the look of it
10:06:05 <Lynx_> primer3 1.1.4 windows version
10:06:20 <Lynx_> but should give the same result as linux binary
10:07:45 <pingou> look like he gaves me the same output thanks Lynx_  :)
10:08:00 <Tom``> Thanks for the help guys, going to head out and find some books to read on genetics :)
10:08:03 <Lynx_> pingou: cool
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10:08:15 <faceface> Tom``, genetics + sequence
10:08:16 <faceface> dang
10:08:18 <pingou> lol
10:08:22 <faceface> ;-)
10:08:24 <pingou> + protein + structure :)
10:08:30 <faceface> yeah
10:09:02 <pingou> ok if anyonw of you is interested by the primer3 RPM help yourself: http://pingou.fedorapeople.org/RPMs/
10:09:41 <pingou> the dev just mail me back \o/ That's gonna be in Fedora repo \o/ !
10:09:47 <pingou> faceface: shall I put it in EPEL ?
10:11:11 <Lynx_> hmm, the staden package seems to have support for the 454 sff files, but there seems to be only source for the io lib required. looks like work getting that to run.
10:11:24 <Lynx_> also, their webpage is outdated in all parts, a little annoying
10:21:29 <faceface> pingou, cool
10:21:44 <faceface> epel.. lemmy read the link you sent me last week...
10:23:20 <pingou> ^^
10:23:45 <pingou> EPEL =  repo RHEL developed by Fedora Community and therefore compatible with CentOS
10:24:59 <faceface> pingou, yup... but you sent me a link to an email...
10:25:09 * faceface scrolls up
10:25:45 * faceface changes his settings
10:27:07 <faceface> pingou, do you know if I can include your private (publlic) repo in CentOS?
10:27:52 <pingou> faceface: normally there should be no problem
10:28:05 <faceface> I guess not ... f != ce...
10:28:09 <faceface> I'll try...
10:28:49 <pingou> it should
10:28:54 <pingou> yum works in the same vein
10:29:04 <pingou> and the RPMs should be compatible
10:31:15 <faceface> got GPG?
10:33:27 <faceface> hmm.... what should I install first :D
10:33:49 <pingou> yum install R-\* :p
10:34:05 <faceface> http://pastebin.com/m4b31eeab
10:34:14 <pingou> faceface: no there is no gpg since the gpg is normally made by the official repo I did not sign my packages
10:34:34 <faceface> yum search bioc :p
10:35:07 <faceface> what the freak is this? Chaine de caractère représentant des séquences biologique? Some kind of alien hacker language?
10:35:42 <pingou> lol
10:35:52 <pingou> for the first packages I used to add the french translation
10:35:58 <pingou> I changed stop after ^^
10:36:10 <faceface> hehe... no support for 118n?
10:36:24 <pingou> not any more ^^
10:36:33 <pingou> my english has gone too good :D
10:37:17 <pingou> btw faceface did you have a look at https://fedoraproject.org/wiki/Features/Bioconductor
10:37:20 <pingou> ?
10:37:29 <faceface> yup, how can I help?
10:37:57 <pingou> https://fedoraproject.org/wiki/Features/Bioconductor#Planning suiting the 1st point ? :D
10:38:15 <faceface> OK, I'm here :D
10:38:47 <faceface> Package R-hgu95av2probe-1.16.3-2.fc8.noarch.rpm is not signed
10:38:52 <pingou> faceface: install a fedora somewhere create RPM submit them become fedora packager and let's move bioconductor into fedora & EPEL :)
10:39:06 <pingou> simple isn't it :)
10:39:12 <faceface> OK
10:39:20 <faceface> I got a 9 disk at home with my name on it
10:39:26 <faceface> (no really, its mine)
10:39:39 <faceface> OK, I needed to explicitly say gpgcheck=0
10:39:43 <pingou> faceface: none of my R-* are signed it will probably complain most of the time
10:39:46 <pingou> yes
10:39:56 <faceface> I just commented out the gpgcheck=1
10:40:01 <faceface> cool
10:40:06 <pingou> 0 should work
10:40:14 <faceface> yup 
10:40:24 <pingou> faceface: you will be interested by http://fedoraproject.org/wiki/PackageMaintainers/Join :)
10:40:25 <faceface> so... where is a list of bioinf related repos?
10:40:37 <pingou> there is a fedora-r-devel-list
10:40:51 <faceface> yiminy!
10:40:54 <faceface> so may sections
10:40:58 <faceface> and sub sections...
10:41:00 <pingou> https://www.redhat.com/archives/fedora-r-devel-list/2008-July/thread.html
10:41:16 <faceface> cool
10:41:29 <pingou> else there is https://fedoraproject.org/wiki/Category:SciTech_SIG
10:45:29 <pingou> PyPop - Python for Population Genomics 
10:45:31 <pingou> hm sounds nice
10:46:43 <Lynx_> hmm, there seems to be a debian package for ncbi-epcr. how would i get the source for that, or extract it from the .deb for compiling on windows/cygwin?
10:46:59 <pingou> link ?
10:47:10 <Lynx_> http://packages.ubuntu.com/hardy/science/ncbi-epcr
10:47:12 <Lynx_> for example
10:47:24 <Lynx_> i couldn't find that on the ncbi page, which would of course be best
10:48:17 <faceface> else there is http://biodatabase.org/index.php/List_of_RPM_repositories_for_biologists
10:48:21 <faceface> _dan, ?
10:48:36 <Lynx_> duh, i found it on the ncbi ftp server
10:49:15 <Lynx_> there's even a win32 binary :)
10:49:20 <pingou> :)
10:49:58 <faceface> well... thanks for help... I should work now.
10:50:09 <pingou> no pb :)
10:56:12 <Lynx_> what's an STS database? or STS sequence? i talks about those in the (very brief) e-prc manpage
10:56:22 <Lynx_> s/prc/pcr/
10:57:05 <Lynx_> ah, sequence tagged sites. whatever that may be.
10:57:20 <pingou> http://www.biology-online.org/biology-forum/about1652.html
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11:00:44 <pingou> faceface: I think I am going to package R2spec, that's a quite handy script
11:01:16 <Lynx_> ah, thanks.
11:01:28 <pingou> np
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13:23:30 * pingou goes gome ++
13:31:24 <CowbertDH> eww gnome
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17:04:05 <Alkw> hello, I am a student and I'm really interested about bioinformatics, but I have some doubts about this new area and I'd like to know if someone is free for a chat since I don't know how busy you may be
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17:22:33 <flu> wow, he waited for a whole 12 minutes :-/
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20:26:07 <wonklab> Guess he wasn't too interested.
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21:06:05 <CowbertDH> lol
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