00:11:10 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 00:20:36 *** synthasee has quit (Connection timed out) 00:49:08 *** ybit has quit (Remote closed the connection) 00:49:19 *** ybit (n=h@unaffiliated/ybit) has joined #bioinformatics 01:09:30 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 01:15:58 *** lafille (n=lafille@ANantes-257-1-8-146.w90-31.abo.wanadoo.fr) has joined #bioinformatics 01:17:46 *** lafille has quit (Client Quit) 01:44:40 *** jm has quit (Read error: 113 (No route to host)) 02:37:33 what's the difference between evodevo and comparative genomics 03:18:11 *** Biopunk (n=p@h169n1c1o261.bredband.skanova.com) has joined #bioinformatics 03:29:45 *** Splicer has quit (Read error: 110 (Connection timed out)) 04:25:42 *** slaydragon (n=roop@59.92.140.97) has joined #bioinformatics 04:34:16 *** slaydragon has quit ("Ex-Chat") 04:34:35 *** slaydragon_ (n=roop@59.92.140.97) has joined #bioinformatics 05:10:26 *** h2i (n=h@unaffiliated/ybit) has joined #bioinformatics 05:11:14 *** ybit has quit (Connection reset by peer) 05:13:30 *** pingou (n=pingou@AMontsouris-158-1-62-206.w92-128.abo.wanadoo.fr) has joined #bioinformatics 05:29:00 *** Splicer (n=p@h116n2c1o261.bredband.skanova.com) has joined #bioinformatics 05:44:25 *** Biopunk has quit (Read error: 110 (Connection timed out)) 05:54:07 *** Splicer has quit (Read error: 60 (Operation timed out)) 06:17:45 *** slaydragon_ has quit (Remote closed the connection) 06:18:10 *** slaydragon_ (n=roop@59.92.140.97) has joined #bioinformatics 06:18:30 *** slaydragon_ has parted #bioinformatics ("Kotta Ko") 06:27:50 *** slaydragon__ (n=roop@59.92.140.97) has joined #bioinformatics 06:32:42 *** slaydragon__ has quit (Remote closed the connection) 07:53:59 *** toru_ (n=gioby@137.204.142.219) has joined #bioinformatics 08:04:00 *** synthase has quit (Read error: 110 (Connection timed out)) 08:17:47 *** slaydragon_ (n=roop@59.92.151.145) has joined #bioinformatics 08:24:59 *** clarezoe has quit (Read error: 104 (Connection reset by peer)) 08:31:05 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 08:35:14 *** slaydragon_ is now known as slaydragon 08:37:20 *** slaydragon is now known as Guest14247 08:40:06 *** Guest14247 is now known as slaydragon 09:09:31 *** slaydragon has quit (Read error: 110 (Connection timed out)) 09:24:06 *** blarney (n=blarney@ip72-208-108-93.ph.ph.cox.net) has joined #bioinformatics 09:25:27 hey there, any folks who know some enzyme kinetics out there? 09:26:05 hi blarney :) 09:26:35 the regular Michaelis-Menten equation is normally written in terms of substrate concentration, S, i.e. v=Vmax*s/(Km+s) 09:26:39 pingou: hi there 09:27:42 I can derive this using the standard techniques, but I what I would like is to have the velocity (i.e. dP/dt) in terms of the enzyme concentration, E, it's not obvious how to do it 09:28:34 i.e. I want v=f(E) 09:29:59 http://en.wikipedia.org/wiki/Michaelis-Menten_kinetics#Equation number 4 ? 09:30:04 the normal assumption is that the total enzyme concentration stays roughly constant during the reaction 09:31:09 pingou: that is [ES]=[E][S]/Km right 09:31:20 *** slaydragon (n=roop@59.92.176.41) has joined #bioinformatics 09:31:35 pingou: but I need it in terms of [E] only, with no [ES] or [S] terms 09:32:23 v=K2[ES] and [ES]=[E][S]/Km can't you combine the two equations ? 09:32:35 arf no [S] term, ok 09:32:42 pingou: exactly 09:33:37 hm can't we express [S]=f([E]) ? 09:34:06 ok, it might be possible to assume that the substrate [S] is constant (this is the quasi-equilibrium assumption that d[ES]/dt=0) 09:35:38 pingou: you'd think so, but it's tricky, you can't just substitute in terms because there are various assumptions about each equation that might not be valid in a different context 09:36:04 pingou: so I'm trying to go back to the full system of differential equations and work my way up 09:36:18 make sense sure :) 09:37:06 the higher [E] the higher V right ? (for [S] >> [E]) 09:37:39 pingou: right, so that [E] sets the Vmax value 09:38:43 isn't Vmax specific to an enzyme ? 09:39:59 yes 09:40:29 as far as I understand wikipedia there, v is more a function of [S] than [E] 09:41:29 right, I think v is actually a linear function of [E] as v=k2[ES]=k2[E][S]/Km would imply 09:41:41 for a fixed amount of substrate 09:41:43 [S] 09:43:18 I am writing a django application to manage blood samples in a laboratory 09:43:24 do you want to take a look at it? 09:43:52 http://github.com/dalloliogm/samples-database/tree/master 09:49:46 If [S] is large compared to Km, [S]/(Km + [S]) approaches 1. Therefore, the rate of product formation is equal to k2[E0] in this case. 09:50:23 so if [S] >> Km V=k2[E0] 09:50:41 so if [S] >> Km V=k2[E0] V=Vmax 09:52:46 actually v=k2[ES]=k2([E0]-[E]) 09:53:26 because [E0]=[E]+[ES] is the initial concentration of the enzyme which must remain constant 09:54:13 nice :) 09:54:43 so in terms of the free enzyme [E] that's the answer, I think 09:54:55 not what I wanted, but there you go... ;) 09:55:26 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 09:55:41 there *you* go ;) 09:58:58 *** highvoltz has quit () 10:06:58 *** kushalsejwal (n=prashant@59.180.70.218) has joined #bioinformatics 10:07:17 guys anybody there?? 10:07:47 kushalsejwal: yep 10:07:47 nope 10:07:56 :) 10:08:13 * blarney checks and finds out that he's actually not here either 10:08:15 hello everyone, man I am so happy to find a channel for bioinformatics 10:08:28 I just tried #bioinformtics :D 10:08:29 well congrats ! 10:08:51 Please tell me more about this channel 10:08:58 and you guys 10:09:25 the topic will already give you some informations ;) 10:10:11 topic? 10:10:32 "We are slow moving pathogens... so hang around if you want to be infected... 10:10:53 hehehehe, I am a pathogen like you guys :D 10:10:55 kushalsejwal: type "/topic" if you can't see it at the moment 10:11:49 okay I got it 10:12:12 So guys are you all Bioinformaticians? 10:12:56 we are working on it 10:13:12 Is this channel related to bioinformtics.org ? Since i am also a member of bioinformatics.org 10:13:19 okay 10:13:36 let's say partly but not directly 10:13:46 I just finished my graduation in Life Science this year and planning to go for Master in Bioinformtics 10:14:21 This subject really attracts and interest me a lot :) 10:19:40 *** kushalsejwal has parted #bioinformatics () 10:20:28 <_dan> animated gif of the day: http://i256.photobucket.com/albums/hh164/wfmuhotrod1/Cicada_molting_animated.gif 10:20:48 blarney: do you have 5" ? 10:22:59 pingou: 5' or 3' antisense or sense? 10:23:44 I have been wordering recently whether it would make sense to package the big bioinformatics project 10:23:51 such as NCBI or EMBOSS 10:24:27 would any sysadmin update there software using those... 10:24:49 would it make sense to have them on EPEL so that people having server on RHEL could access to it ? 10:25:27 pingou: ncbi toolkit, sure 10:25:53 pingou: I think I put it on the bioinformatics wishlist at some point on the fedora wiki 10:26:10 pingou: is bioconductor complete? 10:26:15 blarney: I think I saw it there yes 10:26:30 pingou: you should make a wiki page for it, actually it could be a "Feature" 10:26:45 pingou: if it's complete enough like Fedora Electronic Lab 10:27:11 pingou: I saw you were switching from bioconductor 2.1 to 2.2 is 2.2 stable now? 10:27:17 blarney: I have two python scripts that allows to make the spec really really easily and to update them also really easily 10:27:21 yes 2.2 is stable 10:27:32 I have actually been late on the update 10:27:34 pingou: is it complete? 10:28:11 pingou: i.e. do we have all the base bioconductor packages now in Fedora? do they (the bioconductor project) define a "base" set? 10:28:52 we have some, and more that could be, but not up to Affy which is for me one of the basis package 10:29:05 I have them ready since I used affy 10:29:30 but for example i have not take the time to do the update to 2.2 for them 10:30:36 pingou: we should create a feature page as a central clearinghouse for this: https://fedoraproject.org/wiki/Features/Policy 10:31:09 pingou: i.e. it would just be a "proposal" initially: https://fedoraproject.org/wiki/Features/Policy/Proposals 10:31:37 pingou: here's a template: 10:31:38 https://fedoraproject.org/wiki/Features/Template 10:32:18 pingou: I reckon bioconductor's big enough to warrant that, plus it gets coverage in marketing and release notes etc. 10:32:27 ok I'll try to set a draft page and I'll send it to the fedora-R-devel ML 10:32:40 pingou: I can help a bit here and there 10:32:59 pingou: link it from the SciTech page too 10:33:13 I believe that bioconductor could be "automatically" updated from version to version... would it make sense ? 10:33:55 my main problem with those update are the changes in the R and BR they do... :/ 10:34:01 i.e. from https://fedoraproject.org/wiki/SIGs/SciTech and maybe also https://fedoraproject.org/wiki/SIGs/SciTech/BioinformaticsWishList 10:34:02 updates* 10:35:22 pingou: if by automated, you mean "supervised by a human" (i.e. you), then it seems OK if you do .spec file update via a script, but make sure you check each one before doing a CVS checkin 10:35:26 blarney: http://pingou.fedorapeople.org/biocpackages.svg 10:36:21 this is the relation graph between the packages for bioconductor (generated by torbjorn ) 10:36:44 pingou: yikes, my browser doesn't like that too much, but I could see it 10:37:20 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 10:38:05 blarney: Inkscape displays it correctly 10:38:17 pingou: bioconductor/R packages have the same updating problem that Perl packages from CPAN have, an upstream with their own package system that doesn't always 100% align with the RPM/spec file way of doing things 10:38:48 pingou: sure, I realise that I could open it in inkscape, I just clicked on the link 10:39:08 sorry, I am uploading the png but the picture is hudge... 10:46:09 pingou: don't worry I'll look at it later, I got the general idea though 10:46:27 pingou: I'd create a scaled down picture, perhaps put it on the Feature page 10:48:18 there is the png http://pingou.fedorapeople.org/biocpackages.png but it's still a 1.3Mo pict 10:48:54 hm reduced :D 10:50:36 http://pingou.fedorapeople.org/biocpackages.png 10:50:43 http://pingou.fedorapeople.org/ 10:50:49 they are there 10:51:15 pingou: http://pingou.fedorapeople.org/biocpackages.png 404 10:51:29 I just removed that one sorry was too big 10:52:06 got it: http://pingou.fedorapeople.org/biocpackages2.png 10:52:27 is that all just BioC package, or does it include some R packages? 10:54:07 It's made from BioC only but checking for the Depends of the files DESCRIPTION so there is probably some other libraries from the CRNA 10:54:10 CRAN* 10:54:40 (and it only takes into account the Depends not the suggest libraries) 10:55:01 which mean that it probably miss a large part of the datapackage 11:13:39 http://extjs.com/deploy/dev/examples/desktop/desktop.html this is impressive... 11:14:31 *** clarezoe has quit (Remote closed the connection) 11:36:20 pingou: is it simulation of a particular desktop environment? 11:37:14 pingou: anyway gotta go to bed ;) group meeting today (thank god I'm not presenting) 11:37:57 *** blarney has quit ("Leaving.") 11:59:13 pingou: are you a fedora contributor? 12:04:16 *** toru_ has quit (Read error: 104 (Connection reset by peer)) 12:18:29 *** synthase has quit (Read error: 110 (Connection timed out)) 12:23:30 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 12:35:42 *** gotgenes (n=chris@hc6521f39.dhcp.vt.edu) has joined #bioinformatics 12:50:00 the answer to toru_ is yes 13:00:07 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 13:08:16 *** rogers (i=rogers@bling.bling.org) has joined #bioinformatics 13:10:51 *** highvoltz has quit (Remote closed the connection) 14:02:55 *** craigoz (n=craigo@202.63.56.72) has joined #bioinformatics 14:22:48 *** rogers has quit () 14:28:56 *** kanzure (i=bryan@66.112.232.74) has joined #bioinformatics 15:17:13 *** slaydragon has quit ("Kotta Ko") 15:40:51 *** h2i is now known as ybit 15:54:47 *** jm|earth (n=jm@p57B9FD80.dip.t-dialin.net) has joined #bioinformatics 16:02:43 *** clarezoe has quit (Remote closed the connection) 16:07:35 *** clarezoe (n=clarezoe@clarezoe.csbnet.se) has joined #bioinformatics 16:22:43 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 16:51:56 *** gotgenes has quit ("I am a meat popsicle.") 17:49:11 *** Splicer (n=p@h47n1c1o261.bredband.skanova.com) has joined #bioinformatics 18:14:59 *** mercutio22 has quit (Read error: 110 (Connection timed out)) 18:22:27 *** mercutio22 (n=htorres@c95181ec.virtua.com.br) has joined #bioinformatics 18:26:07 NSF biology grants have this form about the organisms you study. 18:27:04 But it's obviously not set up to handle broad based evolutionary analyses. 18:27:33 You get to choose four out of around 20 groups of organisms, but they don't list the three domains of life. 18:27:55 yeah 18:27:56 And there's no "all organisms" choice. 18:28:01 you don't get to do that unless your name is Craig Venter 18:28:36 So we put down that we're studying prokaryotes, protists, fungi, and animals. 18:29:00 failnome :-P 18:31:12 *** synthasee (n=synthase@68.63.20.12) has joined #bioinformatics 18:41:01 *** synthase has quit (Connection timed out) 18:50:34 Heh. failnome. :-) I like it. 18:50:52 "Hell, you don't even have a genome. What we have here, sir, is a FAILnome." 19:00:57 I was reading a Venter paper the other day. 19:02:34 The M. jannaschii genome paper. 19:04:55 *** kushalsejwal (n=prashant@59.180.24.217) has joined #bioinformatics 19:05:14 Hi #bioinformatics :) 19:05:35 hi pingou 19:06:18 any body there? 19:06:44 Genome papers are pretty cool. 19:07:15 hi wonklab 19:08:28 *** kushalsejwal has parted #bioinformatics () 19:09:50 *** vivkrish has quit ("Leaving") 19:10:11 uh 19:11:00 Do people expect us to just sit here all day staring at IRC? 19:22:01 *** highvoltz (i=rogers@bling.bling.org) has joined #bioinformatics 19:28:57 Ha, I found a mistake in the M. jann. paper. 19:29:37 They refer to the "reductive trichloroacetic acid cycle" in a bit about carbon fixation. 19:30:01 I wonder how that got past everyone. 19:30:21 There's like 50 million authors. 19:30:28 And the paper was in Science. 20:07:59 *** synthasee has quit (No route to host) 20:24:55 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 20:58:06 *** synthasee (n=synthase@68.63.20.12) has joined #bioinformatics 21:07:38 *** synthase has quit (Connection timed out) 21:10:46 *** mercutio22 has quit () 21:53:28 *** craigoz has quit ("Leaving.") 22:03:46 *** synthase (n=synthase@68.63.20.12) has joined #bioinformatics 22:13:18 *** synthasee has quit (Success)