Talk:Flux balance analysis

message: Hi.  Some equations under "Mathematical description" are not formatted correctly and do not appear.  How can this be fixed?.  Thanks!.  Omer.  — Preceding unsigned comment added by 132.76.50.5 (talk) 10:34, 9 February 2014 (UTC)
thread_title: Fix Equations

message: *Need to add historical notes, as well as some images.
:–Karthik.raman 09:56, 23 February 2006 (UTC)
thread_title:  Adds 

message: *Just completely rewrote the page. I hope it's okay but this is my first Wikipedia article. This is the subject of my PhD so I am reasonably well-qualified. I will try and update the Mathematical description over the next few months, it's not great at the moment.
:- Thomasf2811 (talk) 11:47, 15 March 2010 (UTC)
replies: text: - Tomsmedal (talk) 11:47, 15 March 2010 (UTC)
replies: text: Alas no. About a year ago my buddy who sat next to me for two years in the lab got a post-doc at UCSD. I checked out the IP address that 'Tomsmedal' was created at and sure enough it returned San Diego. Deleting his medal comment will only encourage his trolling further. Thomasf2811 (talk) 21:49, 13 November 2010 (UTC)
thread_title:  Rewrite 

message: *Thanks for checking out the maths there, I'll have a look myself over the next couple of days and make the corrections. If I get time I'll do a better example too. I'm also looking into clarifying the 'fluxomics' addition that's been made. It's quite a new word but to my understanding this is actual measurement of flux through a network, not prediction using FBA. Fluxomics doesn't even seem to have a wikipedia page, someone who knows more about it should maybe make one.
:- Thomasf2811 (talk) 00:39, 17 October 2010 (UTC)
replies: text: There was an article called Fluxomics. It had a 20-month old merge tag, was tagged as a neologism, and seemed to be the exact same thing as Flux balance analysis. I redirected it here. You could maybe pop into the history to see what it said. If I was wrong for redirecting that page, go ahead and restore it, but make the distinction between fluxomics and flux balance analysis clear. D O N D E groovily Talk to me 00:16, 17 October 2010 (UTC)
replies: text: Cool, thanks Dondegroovily. I'm a Wikipedia n00b so it's good to have someone with a lot of experience on the case. I will have a chat with some people I know who work on fluxomics and try and get them to write a proper page for it. 20 months ago the topic was very niche but it's now getting big and one of them should take a day to write an awesome page on it. In the meantime we can keep the link to this page and I'll add an explanatory sentence over the next few days just so it's correct. Thanks again. Thomasf2811 (talk) 23:53, 21 October 2010 (UTC)
thread_title:  Fluxomics 

message: There is no citation to choke point analysis. Since I am not familiar with this term, someone else therefore might be in a better position to include a suitable reference for this section.
Rhodydog (talk) 19:35, 24 September 2011 (UTC)
thread_title:  Reference Needed for Choke Point Analysis 

message: I'm not sure if the model preparation section really belongs on Wikipedia. It seems like something that belongs on a website with protocols or information, but the information should really be presented in a more encyclopaedic format like the mathematical section below in my opinion. Maybe instead add a properties section that talks about the structure of the underlying graph and how the reaction equations all line up? Any other opinions? Vramasub (talk) 18:38, 21 January 2012 (UTC)
thread_title:  Model Preparation Section Appropriate? 

message: This page was started in 2006 by Karthik.raman, who identifies himself as Indian, using what seems like UK English. The most considerable contribution since that time has been by me, Thomasf2811, in UK English. Recently I noticed that the language of the article has changed to US English with words such as "analyzing", "characterized", "optimization", "realizing" and "catalyzing" being added or replacing previous UK spellings. Where the word "utilization" appeared this has been corrected to the standard English "use" which is more correct and understandable. Piratemurray appears to have changed all US English spellings to UK English but this change was overturned by an anonymous contributor against the Wikipedia Guidelines. Clearly we need to come to an agreement on this issue.
I have no wish for an international dispute but it would seem in keeping with Wikipedia Guidelines that as the first contributor and the main contributor both chose to use UK English this should remain the language of the article and the US English spellings should be converted as per Piratemurray's edit.
Please speak up if you disagree.  — Preceding unsigned comment added by Thomasf2811 (talk • contribs) 19:15, 16 April 2012 (UTC)
thread_title:  Standardising localisation 

message: I think that there is inconsistent mass in the "simple example". Reaction 1 can be written as follows in terms of mass:
A + B = C
For Reaction 2:
A = C
Plugging back in, we get:
A + B = A
Thus: 
B = 0
A simple fix would be to put a coefficient of two on A in Reaction 2 (and the corresponding adjustments to the differential equations).
My apologies if I'm misunderstanding something.  — Preceding unsigned comment added by 75.101.96.251 (talk) 00:15, 22 October 2012 (UTC)
thread_title:  Inconsistent mass in "Simple Example" 

message: I noticed that the simple example under Mathematical Description has gone (edited out by Abhi asus). The explanation in the history page is: "(removed the example for FBA, I think it should be a separate page. Kind of takes the attention away". This was an extremely useful section for students when studying FBA, I used to use it for my classes. Without the example I think the entire page has become far too technical (particularly the math explanation) and it seems I am not alone in this opinion (see top of article page). I've seen this happen many times on Wikipedia. If the change is to remain we should have a separate student's guide to FBA. The current page is written for experts. Abhi asus suggests moving the example to a new page, has this been done, couldn't find a link on the main page.  Rhodydog (talk) 00:03, 19 March 2013 (UTC)
thread_title:  Simple Example Gone 

message: The canonical form given for FBA, while indeed often stated in this way in the primary literature, is unnecessarily restrictive. For some reason linear inequality constraints of the form Av <= b and equality constraints of the form Av = b are omitted, leaving only the flux bounds lb <= v <= ub. There is, however, no good reason for this omission, and I suspect actual implementations of FBA don't have this artificial limitation... 134.169.106.133 (talk) 09:33, 2 July 2014 (UTC)
thread_title:  Canonical form 

message: I somewhat disagree with the WP:Technical tag (I am passing by and found it mostly okay --I don't know the backstory). Why was it put there?
IIRC WP:Technical is relative to how narrow the topic in question is, e.g. an article on the hisA gene does not have to explain what enzymes and histidine are, which are assumed facts. In fact, too much background information makes an article painful to read (at the cost of structure and cohesion), plus a put-as-much-info-as-possible attitude isn't correct as an article/entry is a monographic account of a subtopic named in the title. I am bothering to ask, because I fear it was put there in fear that the article might baffle an arithmophobic biologist (there are many). I am pretty sure the article is still understandable when the maths is skipped and for someone who cares about it, the maths is simple. --Squidonius (talk) 16:28, 20 July 2015 (UTC)
thread_title:  WP:Technical 

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thread_title:  External links modified