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Commit 63e0da48 authored by Florian Centler's avatar Florian Centler

Updateing to v1.1.1

parent 3aa0879a
......@@ -76,7 +76,9 @@ The FBA models stem from *S. Magnúsdóttir et al., “Generation of genome-scal
### Simulation Output
Two files are generated at the end of the simulation with a date and time stamp in the filename indicating the start of the simulation. Both files hold Matlab data structures. The file `*_restartInit.mat` records the final state of the simulator and can be used as the initial conditions to continue the simulation in a subsequent run of µbialSim. The other file holds the simulated trajectory in the Matlab structure trajectory. The fields `time`, `compounds`, `biomass`, and `mu` hold the time, compound concentrations, biomass concentrations, and specific growth rates for each integration step. The field `FBA` stores data for each FBA model, including the temporal dynamics of all metabolic fluxes, and the mass balance for all exchange reactions. The field `limitingFluxes` stores over time those reactions, for which thecurrent flux is identical to its current flux boundary (upper or lower). These are typically the growth-limiting fluxes.
Additionally, once the simulation is finished, the trajectory is automatically visualized in three Matlab figures detailing the evolution of compound and biomass concentrations as well as exchange fluxes for all species.
Additionally, once the simulation is finished, the trajectory is automatically visualized in three Matlab figures detailing the evolution of compound and biomass concentrations as well as exchange fluxes for all species. To visualize only the most abundant microbial species or compounds, the function `plotTopBiomassCompounds()` can be used.
To inspect compound consumption and production rates at a given time, the function `getCmpndExchangeTable()` can be used, filtered (`filterCmpndExchangeTable()`), and saved to file as an adjacency matrix (`writeCmpndExchangeTableToFile()`) for subsequent visualization as a network.
## Built With
......@@ -94,8 +96,9 @@ We use [SemVer](http://semver.org/) for versioning. For the versions available,
## Version History
* v1.0.0 - July 2019 - initial version
* v1.1.1 - April 2020 - new plot routine for visualizing the most abundant microbial species and compounds only, new parameter for the numerical solver, minor bugfixes
* v1.1.0 - January 2020 - improved parallel performance, new function to estimate maximal uptake flux required to achieve given specific growth rate, new functions to collect, filter, and write compound exchange within the community at a given simulation time point, new feature to record growth-limiting compounds for each species during the simulation, bugfixes
* v1.0.0 - July 2019 - initial version
## Authors
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