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Hi
I'm not able to genereat/retrieve models in PATRICK using mackinac. Any help would be appreciated.
This is what I've done:
-installed mackinac 0.8.4 in a virtual environment with python 3.5.0…
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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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The unit in the model is fine (every thing is `DM`) if we don't have `respiration`.
However, the unit of carbon cycle is not clear when `ConversionEfficiency` and `MaintenanceRespiration` are not…
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Following curation of PMID:24790093 I think this could be a good paper to try to automate the generation of a Noctua model. We can discuss. See the image below (maybe you even mentioned this paper for…
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when I study the "Compass Analysis" notebook about analyzing the results of the compass algorithm and replicates figures 2E and 2C from the paper, I found some prior knowledge called "labeled_reaction…
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This thread to serve as a request for a presentation at the next Data Stewards / DCPPC call on Alliance for Genome Resources (AGR) Supplement Aims. Specific Aim 2: "Development of interactive and prog…
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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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#### Rather than specific only to the biomass reaction as the objective function extend tests to include any set objective.
Some models may not have a biomass objective function, but rather altern…
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load wikipathways
load recon3d
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Thank you for developing smetana!
I just have a general question. I'm currently building models with carveme by using the default command (`carve genome.faa`) without
specifying any media via `--gap…