Version History

#------------------------------------------------#
version 0.1
* first public release

#-----------------------------------------------#
version 0.2
* Fixed bug in double knockout result processor.
* Fixed labeling error in graph generated from double knockout processing.
* Included case for blocked reactions in Perturbation Analysis the absence of which caused crashes when the function was run on blocked reactions.
* The return of the flux distribution matrix generated during Perturbation Analysis has been made optional.
* added argument in Perturbation Analysis to observe fluxes other than the default objective flux in the graph.
* the Exhaustive_single_deletion function has a new argument to pass a subset of reactions for deletion.
* the PDF graph output generated by Exhaustive_single_deletion has been made optional via function argument.
* FLUX_VARIABILITY_ANALYSIS can now be performed on a subset of reactions instead of the whole reaction set.(Speed-up fix for the impatient.)
* removed a redundant function designed to help detect abnormalities in flux distribution of wild-type and mutant
* Added Gene_del, a function implementing multiple-gene deletions by interpreting boolean relations encoded in GPR.
* Added Gene Annotations, GPR information to models included in package dataset.
* updated documentation. 
#------------------------------------------------#
version 0.3

* The FLD_matrix in Perturbation Analysis does NOT have the WT fluxes in the first column anymore, it is only the ramp fluxes.
* Phenotypic Phase plane analysis has been completely re-written and is quite improved compared to the previous version.
* A 2-D,3-D argument has been added to PHPP function. The 2-D plot uses (levelplot:lattice), 3-D is rgl as before. In a new feature added, the objective of the PHPP can be a different reaction than the default biomass flux (or model default objective function). Note that this does not mean that the objective function in the Linear Programming optimization has changed, it merely means that PHPP is now a 2-D version of PERTURBATION_analysis where you can look at how a particular reaction changes flux when two other reactions have co-varying fluxes.

* Optimal ranges are now automatically derived for the PHPP from the model, manual "forced" ranges can also be done by changing arguments.
* To enable easier navigation on the model, SEARCH_reaction/metabolite functions detect the input as numeric/character and change outputs accordingly.
* a new function, Flux_Ranger has been added to help PHPP and PERTURBATION_analysis detect the optimal fluxes for the combinatorial ramp.
* The Gene_del now can return either the whole FBA model or reaction numbers corresponding to the genes deleted via the argument return_reactions.
Gene_del is an upgraded new version of the Gene_del function in version 0.2. We've ironed out a bug in multiple-gene-deletion implementation. This version has some more informative error messages and a much improved evaluation of GPR not relying on hard-coded boolean evaluation R code like the previous version.

#------------------------------------------------#
version 0.4
* Rglpk has been upgraded and this broke abcdeFBA, due corrections have been made but abcdeFBA will only work with Rglpk 0.3.1
* Another bug (yet again) in Gene_del which caused a crash in similar locus names in the S_cerevisiae model has been fixed.
