BacArena version 1.8.1 release

• matlab import support
• fixed several issues when adding organisms
• corrected default diffusion constant in addSubs
• igraph is now only suggested
• complied with new R CRAN guidelines (matrix is of class matrix + array now)

BacArena version 1.8 release

• 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)

BacArena version 1.7 release

• 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

v1.6

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)

Cran release 1.5

Most important 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...

1.0.1

• new method statSpec()
• fixed bug in addSubs()
• new method findFeeding()
• fixed bug in addEval()
• new method openArena()
• corrected vignette

release candidate

Working simulation and evaluation functions, ready to use

BacArena initial

first R package