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### Background
VCell (http://vcell.org) is an open source software platform that can model and simulate reaction-diffusion systems in geometries derived from 3D experimental microscopy images; it can…
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Original Author: @shelby3
Original URL: https://github.com/keean/zenscript/issues/35#issue-243345358
Original Date: July 17, 2017
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- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
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Hello Everyone!
I'm Daniel, a PhD student at [saezlab](https://saezlab.org/). I'm opening this GitHub issue motivated by our recent comparison of cell-cell communication methods[1] as well as disc…
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So I'll use this issue to kick off the discussion on EFMs and MCSs
The two methods I've had the most luck with in calculating EFMs and MCSs are [`efmtool`](http://www.csb.ethz.ch/tools/software/efmto…
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Dear mapequationistas,
I recently tried to use the significance clustering procedure to map changes in metabolic networks over time. The setup and everything worked fine. However, when running the al…
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*What is the feature or improvement you would like to see?*
It would be great to implement a [widest paths](https://en.wikipedia.org/wiki/Widest_path_problem) algorithm in igraph. The 'width' of a …
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Hi,
I read the paper "METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks" related to this tool, rece…
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In an unmodified installation of SKiMpy, every tutorial script exits with error when run in the way described in the Docker README, except for `python /skimpy/tutorials/basics/tutorial_import_cobra.py…
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Hi @ArnaudBelcour,
I have been having some issues running m2m_analysis powergraph. Using genome-scale metabolic models for almost 3300 gut microbes, I am trying to visualize the minimal communities…