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There are a number of factors that make the direct conversion of a cobra model into a stoichiometric matrix for Bayesian MCA challenging.
1. Bayesian MCA does not handle zero flux reactions well.
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### Description of the issue:
Richelle et al., in a recent [research article](https://www.sciencedirect.com/science/article/pii/S2667237521000850#!) suggested an approach for interpretation of omics …
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Currently, for metabolic flux analysis, MFAPipe models the independent fluxes of the reaction network as the independent variables of the regression. Hence, the values of the independent fluxes are fi…
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Hi Francisco,
Thanks so much for taking the time to develop these great tutorials.
In my project I am comparing two groups of species (Entero co-colonizers vs co-excluders) and have identified a…
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## Target functionality
tINIT is an (umbrella name for an) algorithm that obtains a subset of a genome-scale metabolic model based on the gene expression (typically in healthy/diseased bulk tissue …
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Hello :)
Very nice paper, congratulations.
I've just one question, in the manuscript you stated that you used gapseq to "facilitate the taxonomic and functional identification of core and rare spec…
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Hi everyone,
Here is a question for me, as the author performed cube root transformation on TCGA LUAD flux output to preserve the sign(direction) of fluxes. If it possible to use the absolute value o…
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Need to update. Current text from 2012:
There will be four key output from the EMP:
1. Gene Atlas (GA) is a centralized repository and database for all information acquired during this study. This re…
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Hello FluxML dev team,
I read the specifications for FluxML and I have a very naive question: why didn't you choose to make an [SBML package](http://sbml.org/Documents/Specifications#SBML_Level_3_P…
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Dear Dr.Damiani,
I was really impressed by your ideas and methods. However, I notice that the time consumed (113 cells / 10h, 1048cells / 82h) is much longer than the time you mentioned in your pap…