Changes in version 1.6.0 (2013-03-12):

    o   BUG FIX
	
	  * readMIDAS: DV, DA and TR can now be in the specy name
	
	  * makeCNOlist: bug fixed when only one experiment was present
	
	  * plotModel: figures where in B and W due to issue in Rgraphviz
	    package
	
	  * gaBinaryT family: (1) fix bug when only one model found within
	    the tolerance. (2) a faster hash table used in the
	    optimisation.

    o   CHANGES
	
	  * writeSIF: can overwrite existing file with a parameter
	
	  * remove cutAndPlotResultsT2: use cutAndPlotResultsTN instead or
	    cutAndPlot
	
	  * plotOptimResultsPan: NA are now rendered in gray and species
	    are rectangle instead of ellipses. The black line connecting
	    measurements is printed.  The ylim for the y axis can be set
	    manually to overwrite the default behaviour.
	
	  * readSIF can now read relation "A 1 B C D E" as excepted in SIF
	    format.
	
	  * makeCNOlist/CNOlist: variances available in the structure

    o   NEW FEATURES
	
	  * CNOdata: a function to fetch data from www.cellnopt.org
	
	  * plotModel
	
	  * exhaustive function: a simple exhaustive function to perform
	    optimisation for small models
	
	  * cutCNOlist: cut a cnolist given a list of species
	
	  * CNOlist: 3 new methods: length, randomize and plot accepts
	    either one or 2 cnolist arguments.
	
	  * randomizeCNOlist: function to perform different randomization
	    of the data
	
	  * model2igraph function
	
	  * compatCNOlist to convert CNOlist back to old style; used by
	    CNORode

Changes in version 1.3.33 (2012-09-20):

    o   BUG FIX
	
	  * writeMIDAS uses the new CNOlist class as an input. For back
	    compatibility, the input can also be the data frame output by
	    makeCNOlist; this option was buggy, which is now fixed.

Changes in version 1.3.32 (2012-09-10):

    o   BUG FIX
	
	  * plotModel can handle CNOlist=NULL as it used to be the case

    o   CHANGES
	
	  * simulatorT1 and TN have additional check for AND gates with any
	    NA inputs.

Changes in version 1.3.31 (2012-09-06):

    o   BUG FIXES
	
	  * typo in checkSignals in warning message.
	
	  * fixing bug (typo) in cutAndPlotResultsT1

Changes in version 1.3 (2012-08-30):

    o   BUG FIXES
	
	  * fixed bug in writeDot function when only 1 stimuli present.
	
	  * cutNONC function recompte reacID on its own so that if
	    compresion and expansion are not performed, reacID are correct

    o   CHANGES AND UI SIMPLIFICATION
	
	  * major update that changes User Interface to uniformise the code
	    for users and developers (e.g., readSif function is now called
	    readSIF and prep4Sim is prep4sim).  Similarly many arguments
	    are not required anymore. For instance, indexList and simList
	    are not required anymore (for back compatibilty these 2
	    arguments are usually kept and set to NULL).
	
	  * improvment of plotModel function to have more graphviz options
	
	  * gaBinary default initBstring argument is set to ones.
	
	  * MAJOR refactoring to merge T1, T2, TN functions (cutAnPlot,
	    gaBinary, simulator).
	
	  * simulateTN combines simulateT1 and simulateTN so only one
	    function is required.
	
	  * gaBinaryT2 is deprecated. Use TN version instead.
	
	  * gaBinaryT1 and TN do no need the indexList and simList
	    parameters anymore
	
	  * preprocessing now returns only the model. indices are not
	    required anymore.  preprocessing can now handle model without
	    cnolist provided (e.g. for expansion only)
	
	  * add a cutAndPlot dispatcher that calls the proper
	    cutandPlotResultsTX function.
	
	  * cutSimList argument called bitString renamed bString
	    (developers)
	
	  * computeScoreT1, cutSimList had an argument called bitString. it
	    is now called bString and this convention is used throughout
	    the code (e.g., bStringT1 not bitStringT1) simlist and
	    indexlist are now optional are after the bString argument.
	
	  * show argument removed from cutAndPlot function family

    o   NEW FEATURES
	
	  * c Simulator implemented making the optimisation much faster.
	
	  * steady states extended from T1 and T2 to any time TN
	
	  * add a CNOlist class that is now used throughout the code (has a
	    plot method that replaces plotCNOlist calls)
	
	  * add plotParams parameter in cutAndPlot family.
	
	  * hash table in gaBinaryT1 (maxSizeHashTable as optional
	    argument)
	
	  * add cutModel function to make code more modular (for
	    developers)
	
	  * add mapBack function
	
	  * add computeScore functions to make the code modular.
	
	  * conversion functions sif2graph, model2sif, graph2sif added to
	    the package
	
	  * add writeMIDAS function
	
	  * add writeSIF function
	
	  * add prior knowledge bitstring in the GA algorithm (T1 and T2)
	
	  * add a test suite in tests directory