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NEWS
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NEWS
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BacArena v.1.8 (Release data: 2019-02-15)
Changes:
- improved detection of limiting substances (shadow costs)
- shadow costs analysis now possible with cplex, too
- support for non-default objective functions
- fixed interaction finding in findfeeding3()
- occupied arena cells valid also for human cells (bug in emptyHood)
* github reference: https://github.com/euba/BacArena/releases/tag/v1.8
BacArena v.1.7 (Release date: 2018-05-09)
==============
Changes:
- fine-tuning on growth model
* several duplications per time step
* fixed no growth bug for very high accumulated biomass
- improved handling of non-biomass objectives
- better status printing
- more then one compound in chemotaxis
- wrong unit of diffusion constant
- several small updated in plotting methods
* github reference: https://github.com/euba/BacArena/releases/tag/v1.7
BacArena v.1.6 (Release date: 2017-03-21)
==============
Changes:
- redefined growth model
* max cell weight value is used as upper bound for biomass reaction to avoid biomass accumulation in case of overcrowding
* deathrate is now scaled according to time steps
- fixed several issues related to grid geometry (relevant for non-square grids)
- handling of alternative solutions with flux variability analysis
- diffusion and advection can be blocked for occupied cells
- corrected bugs related to continuing of simulations
- expanded tutorial
- renamed growth to biomass in arena@orgdat
- fast stiring
- vectorized addOrg
- new reactions
* plotReaActivity (plot reaction activity)
* findRxnFlux (find usage of metabolite in reactions)
* plotSubDist, plotSubDist2 (plot spatial distribution for substances)
* github reference: https://github.com/euba/BacArena/tree/v1.6
BacArena v1.5.1 (Release date: 2016-07-20)
===============
Changes:
* improved vignette
* gut community example data set
* improved plotting
* github reference: https://github.com/euba/BacArena/commit/67957d833e91d8ba4d118f69f5c3bbe8353ee548
BacArena v1.5 (Release date: 2016-07-13)
=============
Changes:
* parallel support
* methods for evaluation of replicates
* fixed numerical bugs
* fixed growth model
* findInArena(), getSubHist()
* advances plotting using ggplot2:
- plotSubCurve(), plotGrowthCurve(), plotPhenCurve()
- plotAbundances(), plotSpecActivity(), plotSubUsages()
* integration of shadow prices
* addDefaultMed() and addEssentialMed()
* imporved cross feeding detection
* alternative objectives integration
* lots of smaller bugfixes...
* github reference: https://github.com/euba/BacArena/commit/5416fb09d82cbe87bcd701cc7bf389c6116e57ee
BacArena v1.0.1 (Release date: 2016-01-06)
=============
Changes:
* new method statSpec()
* fixed bug in addSubs()
* new method findFeeding()
* fixed bug in addEval()
* new method openArena()
* corrected vignette
* github reference: https://github.com/euba/BacArena/tree/8ce106f1351af95d387cc70ed2bd1fd18669ed84
BacArena v1.0 (Release date: 2015-12-08)
=============
initial cran release
* github reference: https://github.com/euba/BacArena/tree/8bf7459530c4a8eda9040e8feb2fa416dea55ab2