Haris Zafeiropoulos
Haris Zafeiropoulos
It would be super useful to return the pema main output (otu/asv table) in a 7-level taxonomy format, meaning all taxonomy assignments are as: ``` d__Bacteria; p__Abyssubacteria; c__SURF-5; o__SURF-5; f__SURF-5; ...
New version of the CREST algorithm is also available [now](https://github.com/xapple/crest4). In this version, the latest Silva version and the PR2 database are included. Thus, by integrating this CREST algorithm, then...
Hi all. I am trying to reproduce the [Cytoscape ladder](https://github.com/cytoscape/cytoscape/wiki/Setup-Cytoscape-App-Development) using the Intellij IDE. When I [Expand Lifecycle and run install by double-click (or right-click-select)](https://github.com/cytoscape/cytoscape/wiki/Build-a-SampleApp-from-Intellij), I keep getting the following...
Hi! I tried to run the `tutorial_atomicallyResolveReconstruction.mlx` tutorial on MATLAB online and I got the following error: ``` Error using readtable (line 498) Unable to open file '/MATLAB Drive/COBRA/fork-cobratoolbox/tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx as...
Aim of this PR is: 1. to provide an easier way to get flux values from fba and fva and flux distributions from samples, based on reaction ids. 2. to...
Should we rename [this](https://github.com/GeomScale/dingo/blob/aaae4ae63f432da45eb0f4363a92767ba537a074/dingo/MetabolicNetwork.py#L146) to `objective function` ? This way when we are not using the biomass function as objective we will not have misunderstandings.
Thermodynamics constraints are rather important in metabolic modeling. If not considered, they would lead to thermodynamically infeasible/implausible flux loops within flux sample. *Loopless* space though is a non-convex one. Approaches...
To avoid installation issues among operating issues, consider coming up with a Docker image for `dingo`. There is a [Docker Image of gurobi](https://hub.docker.com/r/gurobi/python) that could probably be used as the...
Up to now, `dingo` supports sampling using the uniform, the multivariate exponential and the multivariate Gaussian distributions. A quite interesting addition from the biologist-point-of-view would be to enable sampling using...
```python model = dingo.MetabolicNetwork.from_json("ext_data/e_coli_core.json") model.set_opt_percentage(90) sampler = dingo.PolytopeSampler(model) sampler.generate_steady_states() model.set_opt_percentage(20) sampler = dingo.PolytopeSampler(model) sampler.generate_steady_states() ``` would return: ```bash phase 1: number of correlated samples = 500, effective sample size =...