tag:blogger.com,1999:blog-8341686541622227200.post8171258249483721344..comments2024-02-08T12:10:38.282+00:00Comments on Life of a Lab Rat: MetabolomicsLab Rathttp://www.blogger.com/profile/07962574174521597312noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-8341686541622227200.post-18493245584903032462010-02-27T02:44:09.046+00:002010-02-27T02:44:09.046+00:00I always loved studying those complicated little d...I always loved studying those complicated little diagram flow-chart maps of hell. It's oh-so-satisfying to be able to finally understand what it means in the end. Like with jigsaw puzzle, once it fits together I get a brain happy. :)Captain Skelletthttp://www.aschoonerofscience.comnoreply@blogger.comtag:blogger.com,1999:blog-8341686541622227200.post-29237831123781430762010-02-26T08:45:24.682+00:002010-02-26T08:45:24.682+00:00@BiochemGirl: Loved the link! And I'm glad thi...@BiochemGirl: Loved the link! And I'm glad this was helpful too you. There's a good review here: http://mic.sgmjournals.org/cgi/content/short/156/2/287?rss=1 about integrating different 'omics' approaches if that's useful for you.<br /><br />@Herina: glad you enjoyed reading it :) Thanks for the comment.Lab Rathttps://www.blogger.com/profile/07962574174521597312noreply@blogger.comtag:blogger.com,1999:blog-8341686541622227200.post-83152832526351999522010-02-24T23:42:45.597+00:002010-02-24T23:42:45.597+00:00Haha, I think you just did my assignment for me! ...Haha, I think you just did my assignment for me! I was given a short essay on metabolomics literally 2 days ago (don't worry, I won't steal any :P). Your post led me to a <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449876/" rel="nofollow">"rant against neologisms</a> which was quite interesting.BiochemGirlhttps://www.blogger.com/profile/06276621104727993741noreply@blogger.comtag:blogger.com,1999:blog-8341686541622227200.post-10001252004664813472010-02-23T09:39:28.037+00:002010-02-23T09:39:28.037+00:00@Lucas: Thanks for the links! I got the metabolic ...@Lucas: Thanks for the links! I got the metabolic network from a SYSFYS page, so thought I'd better link back there. And computational flux analysis is fascinating, but I don't *completely* understand it, so I stayed away from trying to go through it in this post!<br /><br />@Xristoforos: I suspect the reason it looks a lot like an electronic circuit (and a tube map) is because humans more easily *understand* things that look like that. Dots connected to lines are fairly easy for the brain to process. I don't know if anyone's tried modelling this with hardware, I suspect not as it would be very complex to put together, and also very few biologists understand hardware (although as I said this is not an area I'm very into, so it's possible someone, somewhere has given it a go).<br /><br />@Charles: The most amazing thing future generations could have would be a full 3D model of this, with the fluxes in the third dimension and the pathways/intermediates in the 2D. Different colours depending on parameters, different sizes depending on concentrations; you could stand right in the middle and pull different bits towards you to change the parameters and then watch the full effect all around.<br /><br />That would be amazing. But completely science fiction atm unfortunately.<br /><br />Thanks for all the comments!Lab Rathttps://www.blogger.com/profile/07962574174521597312noreply@blogger.comtag:blogger.com,1999:blog-8341686541622227200.post-57325148486460113562010-02-23T05:06:36.738+00:002010-02-23T05:06:36.738+00:00The Pathway chart is as at least important as the ...The Pathway chart is as at least important as the periodic table. If anything it's just extremely far out. I like the color coding of the reference schematic. Perhaps the next generation would be to have a program in which intrinsic and extrinsic parameters could be adjusted in a computational schematic model that would take into account thermodynamically favorable potential pathways,with fading in and out intermediates, etc. Hmm...<br />The microprocessor-likeness of the chart does disturb me for some reason.Charles Kennetthttp://twitter.com/Armchair_Darwinnoreply@blogger.comtag:blogger.com,1999:blog-8341686541622227200.post-76521255624353406522010-02-22T20:20:10.007+00:002010-02-22T20:20:10.007+00:00"it looks like the London Tube Map"
Ano..."it looks like the London Tube Map"<br /><br />Another thing it looks like a lot, is an electronic circuit. I have been wondering for a while how useful it might be to model complex systems using analog circuits. At the time I was thinking of the possible applications in AI, but this diagram makes me wonder if anyone has thought of trying creating a simulation using just transistors, capacitors etc. Different points in the circuit could correspond to levels of particular molecules. I can go into greater detail as to how it might work, but I'm wondering if you've heard of anyone having tried it.Xristoforoshttps://www.blogger.com/profile/01352832106825352078noreply@blogger.comtag:blogger.com,1999:blog-8341686541622227200.post-46612359228721609982010-02-22T20:13:53.179+00:002010-02-22T20:13:53.179+00:00Nice overview of a cool and dynamic field!
As some...Nice overview of a cool and dynamic field!<br />As someone who likes computers (a lot), I'd like to point out the value of computational analyses of metabolic networks, like <a href="http://www.pnas.org/content/107/3/1082.abstract" rel="nofollow">in this paper</a>. By modeling metabolic fluxes, it becomes possible to identify those reactions that are absolutely necessary for the organism. These then are nice potential targets for new antimicrobials.<br /><br />(The metabolic network is not by SYSFYS btw, but by KEGG: http://www.genome.jp/kegg/pathway/map/map01100.html<br />For a cool interactive version of this map, see <a href="http://pathways.embl.de/" rel="nofollow">http://pathways.embl.de/</a>)Lucas Brouwershttps://www.blogger.com/profile/15192035237302508309noreply@blogger.com