Talk:Flux balance analysis

Fix Equations

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)

Adds

• Need to add historical notes, as well as some images.

–Karthik.raman 09:56, 23 February 2006 (UTC)

Rewrite

• 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)

• have a medal.

- Tomsmedal (talk) 11:47, 15 March 2010 (UTC)

• Did you create a sockpuppet account just to give yourself a medal? D O N D E groovily Talk to me 23:04, 21 October 2010 (UTC)

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) —Preceding unsigned comment added by 129.11.76.215 (talk)

Matrix Error

• In the example for the stoichiometrix matrix, there is a matrix multiplication mistake (the second and third entry of the product should be swapped, it should be [-v_1 + v_2, v1, v_2 - v_1]); however, the example is somewhat ill-chosen as it implies v_1 = 0, v_2 =0, v_3 = 0 and hence carries not much information ... —Preceding unsigned comment added by 134.76.74.121 (talk) 10:05, 8 October 2010 (UTC)

Completely agree, as below. This has now been fixed but perhaps I should choose a better example that is equally simple but has more than just the null solution.

- Thomasf2811 (talk) 22:03, 28 March 2011 (UTC)

Fluxomics

• 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)

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)

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)

Choke Points

The phrase choke point is used near the start of the article, what is a choke point? It should be defined, preferably operationally rather than in some hand-waving way. Rhodydog (talk) 01:12, 11 January 2011 (UTC)

Agreed. Choke-points are usually defined as reactions where metabolites can flow only either in or out but not both. I will add this small change now but I personally dislike the technique and have seen varying applications of it.

- Thomasf2811 (talk) 22:05 28/03/2011 (UTC)

I see, thanks for the clarification. The phrase choke-points seems to be the poor term for this idea. A chock-point implies a small opening or something that restricts. An enzyme catalyzed reaction going one way could however have lots of capacity and therefore not be very limiting. I guess I should read the original articles. Rhodydog (talk) 22:49, 13 April 2011 (UTC)

Move Comparison Section

I hope no one minds but I've moved the comparison with other methods towards the bottom of the page after FBA has been fully described. The reason I did this is that people (eg students) who are new to the field will know very little about FBA and almost immediately come across a comparison with other methods when they haven't yet absorbed what FBA is. Rhodydog (talk) 16:23, 26 January 2011 (UTC)

Completely agree with this move, makes things much neater.

- Thomasf2811 (talk) 22:07, 28 March 2011 (UTC)

Switched Constraints ando objective function

I changed the order in which constraints and objective function are described. I translated this page to spanish. We could use a better description of what the objective function is, I found it a little bit ambiguous (I'm not familiar with this topic). In the section Optimisation (the objective/biomass function) the line In the more general case any reaction be defined and added defined as a biomass function with either the condition[...] must be corrected but I can't figure out the proper meaning of that sentence. Please help. --Vloody (talk) 05:49, 19 April 2011 (UTC)Vloody

Wow, awesome translation. I may do a French version too. Agreed with objective/biomass function problem and will update this as soon as possible. At the time of writing I wasn't too clear on this but now I think I've got it sorted.

- Thomasf2811 (talk) 19:30, 19 April 2011 (UTC) —Preceding unsigned comment added by 129.11.77.198 (talk)

Reference Needed for Choke Point Analysis

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)

Added Brief Section on FBA

I've added a brief section on the early history of FBA, if any one has any problems with this, please edit and comment as appropriate. Rhodydog (talk) 19:53, 24 September 2011 (UTC)

I really like this, thank you. Always good to see how the newest science is built upon prior work.

- Thomasf2811 (talk) 15:30, 19 October 2011 (UTC)

Model Preparation Section Appropriate?

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)

Standardising localisation

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)

I edited the page along the exact guidelines described here http://en.wikipedia.org/wiki/Wikipedia:ENGVAR#National_varie ties_of_English. I believe it should be written in British English. piratemurray 07:51, 17 April 2012 (UTC) — Preceding unsigned comment added by Piratemurray (talk • contribs)

Inconsistent mass in "Simple Example"

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)

You're right, well spotted. The network does not conserve mass. I think a simple change could be to make the reaction C -> A, UniBi, i.e C -> A + D. The diagram itself is also drawn in a unconventional way, see similar diagrams in biochemistry textbooks to see what I mean.Rhodydog (talk) 17:54, 26 December 2012 (UTC)

Simple Example Gone

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)

Canonical form

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)

WP:Technical

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)

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