Talk:Metagenomics

message: I think the subject also need some comments the study of organisms acting as a community. An example being the flow of a metabolite through the different metabolisms. Any thoughts? Or Perhaps that comes under systems biology instead?
It does include an aspect of studying an entire community at a genetic level.
: I'd say yes and no to this.  Following a metabolite through different metabolisms would fall under something like systems biology and might not require any genomic information at all so metagenomics might not be the right label.  Such studies are also not the sole concern of metagenomics.  Diversity and evolution are also concerns in the field.  
: On the other hand, such a study is one of the really useful things that metagenomics can do and do well and probably  what a lot of people in the field are doing,  so it definitely deserves a prominent mention if not is own section.  It's just not what I'm doing in metagenomics, so I didn't think to put it in.
: Also, just because I started the page page, doesn't mean you can't add what you'd like to it.  If you have some knowledge or interest in this area, please contribute.  Jmeppley 21:05, 25 Jan 2005 (UTC)
replies: text: This should probably go into the microbiome article instead. Estevezj (talk) 06:24, 20 December 2011 (UTC)
thread_title:  

message: It's the first time I've seen the term "chip-based pyrosequencing" being used; the reason it's not used so much is that it could cause confusion with oligo-chips based resequencing, which is a totally different technology which is not used at all in metagenomics. The term is otherwise essentially used in one (solid) paper ("Bacterial flora-typing with targeted, chip-based Pyrosequencing" BMC Microbiology). How would others feel about changing the term "chip-based pyrosequencing" to "massively parallel pyrosequencing"?
--Pascal.hingamp (talk) 11:30, 16 April 2008 (UTC)
thread_title:  chip-based pyrosequencing 

message: Since CARMA3 has shown to outperform MEGAN and SOrt-ITEMS it should probably also be mentioned, reference here: http://dx.doi.org/10.1093/nar/gkr225 93.130.46.13 (talk) 19:47, 26 June 2011 (UTC)
thread_title:  Software 

message: I saw that this article has been tagged for a while so I went ahead and cleared out the further reading list. I'm going to work through those and use them to build on the framework that exists. This is my first major edit, so corrections, suggestions are welcome. Estevezj (talk) 05:09, 7 December 2011 (UTC)
replies: text: Hey there - I've fixed a broken link and also reorganised the External links section - now all the tools are together.  Sarahburge (talk) 15:59, 8 December 2011 (UTC)

text: I'm just going ahead with these edits. You can see what I have planned on my metagenomics sandbox. I also don't think the long list of binning software is necessary; these can be broken out into a separate page, with one or two examples of an algorithm or approach. Estevezj (talk) 06:24, 20 December 2011 (UTC)
thread_title:  Reorganization, F'11

message: Any objection to converting footnotes to list-defined (LDR) format? This many inline citations are getting awkward. Estevezj (talk) 11:07, 28 December 2011 (UTC)
replies: text: Done. Estevezj (talk) 23:46, 19 January 2012 (UTC)
thread_title:  Converting footnotes to list-defined (LDR) format 

message: I'm wondering what the consensus is regarding what the focus of the bioinformatics section should be. I've been operating under the supposition that the focus should be on the rationales and methods behind commonly used tools rather than a list of those tools (cf. how things used to be). I've taken the Koonin (2008) and Wooley (2010) review articles as my models in reorganizing and expanding this section, and the way they handle the balance between discussing approaches versus software would be my suggestion as to how we should proceed. Estevezj (talk) 05:38, 5 January 2012 (UTC)
thread_title:  Tools vs methods vs. "why" 

message: This article lacks the discussion on sampling techniques, which I believe is quite particular for environmental analysis. I'm thinking to add a section about it and put it together with the sequencing and bioinformatics sections into a "method" section or something similar. --sentausa (talk) 08:40, 27 February 2015 (UTC)
thread_title:  Sampling? 

message: Hello fellow Wikipedians,
I have just modified 2 external links on Metagenomics. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
*Added archive https://web.archive.org/web/20120404174757/http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=913954&q=Analyzing+natural+microbial+populations+by+rRNA+sequences&uid=790164755&setcookie=yes to http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=913954&q=Analyzing+natural+microbial+populations+by+rRNA+sequences&uid=790164755&setcookie=yes
*Added archive https://web.archive.org/web/20120331040553/http://www.microbemagazine.org/index.php/07-2011-home/3553-towards-tera-terra-terabase-sequencing-of-terrestrial-metagenomes to http://www.microbemagazine.org/index.php/07-2011-home/3553-towards-tera-terra-terabase-sequencing-of-terrestrial-metagenomes
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
Cheers.—InternetArchiveBot (Report bug) 12:17, 23 January 2018 (UTC)
thread_title:  External links modified (January 2018) 

message: I just came across a page from 2013 called Metagenomics: An Alternative Approach to Genomics. Is there anything salvagable from it to merge in here? Otherwise it can be deleted. T.Shafee(Evo&Evo)talk 10:44, 8 January 2020 (UTC)
replies: text: Klbrain (talk) 14:17, 23 February 2021 (UTC)
thread_title:  Anything salvageable from parallel draft?