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Accounting traditionally is presented as describing efficiently flux (what comes in, and goes out) and stock (what is held, at a given time), and as debit and credit. It is also about matching the terms of an exchange.
How can we move the model beyond the basic number-based description, into more data-rich (including metadata, descriptors, etc) frameworks, while benefiting from the deep and long experience of accounting over human history?
With Matrices of sets [1], a first endeavour was made to describe objects rather than numbers attached to them (price, quantity, measurements and features).
With Matrices of L-sets [2] we are going one step further, distinguishing actual assets (as classical sets) and wish lists, orders, needs, requirements which are not yet owned or available. We show how an operational and computable framework can be obtained with such objects.
References:
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Hi! Some people say that blockchain will change the traditional accounting model. Some more information in my latest paper published. Please, see attached.
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I am studying this pathway in yeast whose job is to transport some proteins from the cytoplasm into the mitochondria. I am thinking of using flux balance analysis as a computational tool to understand the essentiality of some key genes in this pathway. However, since none of these genes are not directly involved in any metabolic process (but their substrates do), I don't know if FBA can be used in this case.
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You can try complex models to study that, see wether your interested genes are included in proteme-constrained models such as yETFL or pcYeast or whole-cell model. You can used FBA to analyze in pcYeast, but TFA in yETFL. It is a little bit difficult for whole-cell model, since it is time dependent, but they already studied the essential genes in their paper. It is worth to check first.
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Hello!
I am looking for methods to estimate the uncertainty associated with spatial upscaling of biogenic CO2 fluxes measured in geographical locations point sources (the aggregation error of the point emission upscaling into urban scale). Estimation of the spatial uncertainty should assume combined uncertainties for CO2 flux rate and emission aggregation error on the gridded map. Uncertainties for measured flux rate is available, the issue is how to estimate the uncertainty for the second item based on the distance between the results generated with the aggregated data set within each grid cell and the original sampling points data set? Thank you!
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Maybe some work of Joanna Kamińska will be helpful?
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I would like to calculate the neutron flux from a 1Ci activity neutron source.
Please suggest some methods to do it.
I would like to know the energy of the neutron from the Am-Be Source having Dose of 22mREM/hr.
I will be very much thankful to you for the reply to above questions.
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Neutron spectra is complex with average 4-5Mev; neat spikes at 4.7, 6.5 & 8 Mev.
Neutron flux can be calculated from the known yield of 80n/10exp6 Bq .
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Dear all, I am working on a knockout strain of e coli for mixed acid production and have so far got a bit of understanding of Flux Balance Analysis. Now, for my next part of the project, I have to experimentally verify the results obtained from flux balance analysis. I haven't got much literature on where the people have done experimental verification of flux balance analysis. For that, I have devised the following experimental design-
  • Batch Reactor(1.5 L working Volume)- Data to be taken only for the exponential phase.
  • M9 minimal media with xylose as the carbon source(No other carbon source and no use of yeast extract, even though it enhances growth)
  • Controlled pH of 6.8
  • Oxygen supply and agitation speed- optimized values for mixed acid production. However, the Dissolved Oxygen probe shows the value to zero after a few hours of experiment, which means whatever oxygen is provided is consumed readily
  • Calculating oxygen uptake rate- Not sure, need help
I request to look at the experimental procedure and provide your suggestions, answers, and comments. 
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Hi Prashant
I have a question, when you simulated your model in minimal medium, what are the constrained you used. what was your model.medium lower_bound and upper_bound?
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Dear researchers, I do not work directly on Flux Balance Analysis, but I studied the theory behind and I appreciate well done papers about the issue. I think that when made in the right way, this approach can provide useful hints. However, recently I found a number of papers where models are reconstructed for non-model organisms and it is never indicated the degree of overlapping with models available for model species.My feeling is that in most cases these new models are simply E. coli or yeast models, (slightly) adapted to the new species. This simply because there is not yet enough functional information for reactions not present in model organisms. Indeed TCA, pentose phosphate, glycolysis, amino acid biosynthesis and so on are more or less always present, but I wonder how much novel and species-specific reactions are included in such models beside the core Carbon metabolism that we can also model in yeast or E. coli. Given the absence of parameters in such models (except for minimum and maximum flux that are always set to a quite large range because we don't know the true range), if there are no specific reactions of a certain novel organism (or only periferic specific reactions, often with zero flux), one would obtain the same results with an E. coli model (eventually removing things not present in the novel organism). A similar issue arises concerning the objective function, which is more or less always similar also among very different organisms.
Anyone studied this overlapping and novelty issue more in detail?
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Hi Matteo.
I feel the answer to your first question is "always". The way draft models are generated (mainly using sequence similarity relationships) by automated tools usually generates  coli-like reconstructions (at least in bacteria). So I would not be surprised to find that many (if not most) of the microbial models out there are just small modifications of the E. coli famous reconstruction.
The amount of novelty introduced in a new model is proportional to the effort put in manual curation after initial automatic reconstruction  and to the available experimental data for that organism (see Thiele and Palsson bible on this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/). It is hard sometimes to find (or generate) such information for non model bugs but  it is essential to produce something that brings some novelty to the community. Antibiotics production routes or fermentation processes are rarely accounted for by automated tools, for example. It is crucial to use papers and past information to refine the reconstruction and to render it bug-specific. By the way, this is often a great chance for bringing to new life papers that are dated back to the 70s, in which one can find accurate biochemical assays.
The very same concepts hold for biomass assembly reactions. A nice paper on this topic: http://link.springer.com/article/10.1007/s11306-015-0819-2 
Unfortunately, the importance of reconstructions from non-model organisms is rarely recognised during the reviewing process (and no, I did not have a rejected paper on this issue recently!) but is arguably higher than flux predictions made on an ecoli-like model from a non e-coli like organism.
ciao,
m.
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Lets see an example. The reaction R00344 is mentioned as irrversible in KEGG
</reaction>
<reaction id="44" name="rn:R00344" type="irreversible">
<substrate id="58" name="cpd:C00022"/>
<product id="60" name="cpd:C00036"/>
</reaction>
Although, in TCA this reaction should be in reverse direction. I mean it should produce ATP by ADP not should consume ATP as KEGG said.
How can we refine such kind of inconsistency?
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Ashmit,
Reaction directionalities  are not "usually" correct in KEGG. You can check the correct reaction directionality in BiGG knowledge base, since the metabolic reconstructions provided in BiGG are manually curated and their directionalities can be "trusted" much more than those provided in KEGG.
Nevertheless, in case of your KEGG reaction, you can check the manually curated equivalent reaction abbreviation in BiGG database (refer to attached image). As you may see, the irreversible reaction of PC produces one phosphate by converting ATP into ADP.  You may find other corresponding reactions in MetaNetX repository (here).
Good luck.
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Fractional Metabolite concentrations in the form of relative intensities are measured from metabolomics experiments. Can I use these fractional concentrations as coefficients of the biomass objective function in Flux balance Analysis?
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Dear Abhishek,
I thought you might have something like this in mind. True, if you had an idea of the total pool of free metabolites in a cell (there is some literature on that), you could suspect that by summing over relative intensities of all metabolites at a given time point you could get an estimate of their relative concentrations at that time point and even convert that to an absolute value using the total metabolite concentration estimate.
However, for this you implicitly assume that, say, 1mM of ATP in your sample gives you the same relative intensity than 1mM of pyruvate. Unfortunately, this is not true in most metabolomics measurement methods (e,g, LC-MS, GC-MS) as signal intensity varies significantly with chemical nature of the metabolite (not to speak of matrix effects).
But if you could get an idea of the intensity to concentration relations of the most predominant metabolites in your sample, you can maybe get an approximate estimate of the relative content of the remaining metabolites.
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In many papers they have used GAMS(commercial S/w) for FBA. Is there any s/w similar to GAMS that is freely available? 
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there is also surreyFBA (http://sysbio3.fhms.surrey.ac.uk/sfba/index.html) (you go graphical with their JyMet package), FlexFlux for java users(http://lipm-bioinfo.toulouse.inra.fr/flexflux/documentation.html) and cobrapy for python users (http://cobrapy.readthedocs.org/en/latest/).
What is the best tool? I think that would depend on you too. Do you prefer Matalab or python or java or a gui?
Personally I use cobrapy. Although COBRA lacks a gui, its very flexible, update quite often and has an active google group for discussions. I chose cobraPY, since Matlab is not free. There are some drawbacks such as functions that identify exchange reactions only if it has an "EX" tag, etc but I think you can work around it if  you need to. So for me, cobrapy feels like the best
There are more obviously. I came across this recently, which you might find interesting
Look for the column with headers ODE, Opensource, Academic
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I am using Recon2 model for analysis. But the BIGG database does not have the map file for Recon2 model. Also, Escher provides the visualization only for selected metabolic pathways in human. Kindly suggested other tools which are helpful in visualizing the fluxes in the Recon2 model.
Thanks in advance.
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Thanks again Mario for replying.
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Metabolic engineering
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Thank you for all of your answers. 
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Is there an online or standalone tool for analyzing flux balance analysis of E.coli gene knockouts which also considers the regulatory controls ex. RFBA, SRFBA, PROM etc.?
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Take a look the a the link below.It may come handy. You must first choose the metabolic network you want for example E.coli in your case. Then you can perform FBAonline, But I think Matlab Cobra toolbox is a better choice although it's not online 
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  1. I tried to expand the ecoli-core model attached below.I wanted to change it in a way that the organism consumes Co2 as carbon source and sulfate as energy source.To achieve this goal I removed the ATP producing reactions from the model ( there were 2 reactions) and replace a reaction which produces ATP from sulfate and and Calvin cycle to produce glucose from CO2.When I performed FBA By CobraToolbox,Calvin cycle's reactions worked properly but the flux of ATP production from Sulfate was zero.To solve this I make the reactions which could reversibly produce ATP irreversible so that they can not produce ATP anymore.But even in this case it shows growth,Is it possible to have growth without ATP?I wanted to relate Sulfur metabolism to central meabolism by the help of ATP producing reaction,But If this models continues to grow without ATP there is no way to attach these two parts of metabolism.
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Dear Alexandra
Thanks for your answer.As you said I use the E.coli core from gcrg.ucsd.edu/Downloads/EcoliCore,I actually make these for reactions irreversible and replace my favorable reaction which produce ATP from a sulfur compound in this case the added reactions have non zero flux but growth yield is zero I think making those 4 reactions irreversible prevent the network from producing needed precursors and that is why there is no growth.But I don't know how to solve it
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I am about to reconstruct a metabolic network for a chemelithiautotroph thiobacillus. It uses Co2 as the carbon source and Thiosulfate as the energy source. I have setted a central metabolsim for this micro organism inculding Calvin cycle (The dark part), TCA cycle, Glycolysis and other common pathway but when in comes to sulfur metabolsim in which Thiosulfate is consumed and terationathe is produced then terathionate oxidizes and so on. When I add sulfur metabolsim network become infeasible and there is no link between central metabolsim and sulfur. I'd be very thankful if anyone could help me.
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Hello Jack
Thanks a lot for answering my question,I used the following reaction to create a link between sulfur metabolism and central metabolism but it did not work
Na2S2O3+2O2+H2O+4ADP+4Pi=>Na2So4+H2SO4+4ATP
the p/o ration for this organism is 1.12.
Due to the infeasibility I can not expand the network now it just includes central metabolism and 4 reaction of sulfur metabolism one for thiosulfate exchange,2 for thiosulfate oxidation and one for tetrathionate conversion to sulfate and sulfur
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I could not find any articles about this topic!
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Thank you John unfortunately my project is about Chemolithoautotrphic metabolsim in fact I had no reference to make sure that if the fluxes I've obtained are right or not
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We have always used N2 purging to dry up the samples. However, since we do not have an automated instrument for the N2 purging, we do it manually, one sample at a time and this is becoming very laborious and time consuming as we have several samples to analyse at a time. Hence, I was thinking of changing my drying procedure and use a SpeedVac Evaporator for the same. Our SpeedVac can be operated at ambient temperatures and I have run some dummy samples and found that the temperature of my sample is actually lower than the ambient temperature because of the vacuum pressure that is generated in the chamber. Hence, I do not think there is a problem of sample heating. My run time was about 1 hour for drying up 1ml sample. I would like to know if this procedure is safe and will it create any problems if I use these samples for GC-MS or LC-MS analysis.
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Dear Deepti,
Hello, I recommend you lyophilisation, lyophilization, or cryodesiccation which is a safe method for drying. But if you encounter with non-volatile and heat stable analytes, your method can be used with confidence. I have an experiment with (some piece of silicon hose, some syringe needle (gauge 19), some glass test tube and a Nitrogen capsule) for drying a set of liquid samples. It as very easy, fast and cheap.
best
mehdi