\title{NEWS}
\name{CellNOptR NEWS}

\section{CHANGES IN VERSION 1.25.0: (2018-01-10)}{
Changes since 1.10.0

First release after Bioconductor changed from SVN to Github.
\itemize{
    \item{BUG FIX}
        \itemize{
            \item{fix gray boxes in plotOptimResultsPan}
            \item{in plotOptimResultsPan when errors were greater than 99.9\% color were white (instead of red)}
            \item{c simulator bug fix: at time 0, node that are inhibited and measured were
      reset to 0 but inhibitors are off. Fix is simple: do not reset inhibitors
      where time is zero}
            \item{Fixing issue with time 0 not being simulated properly (see
      https://github.com/cellnopt/CellNOptR/issues/6)
      This fixes regression bug following fix made in release 1.11.3}
            \item{node name in the sif file containing the word AND (e.g. ligand) will not result in an AND-node anymore}
            \item{Fixing issues with matrix subsetting, when the subsetting converts the matrix to a vector}
            \item{plotOptimResultsPan: in the computation of root-mean-square error(for coloring the background), the NA data is not counted in the number of data points}

        }
    \item{CHANGES}
        \itemize{
            \item{Bioconductor's version of the package got merged with the Github's version leading to minor changes}
            \item{readSIF reads only the unique interactions/lines from the SIF file}
            \item{plotOptimResultsPan and plotCNOlist plots intermediate cue values (0,1) for CNORode add-on}
        }
    \item{NEW FEATURES}
        \itemize{
            \item{add readErrors and writeErrors functions in CNOlist: read/write measurement error/variance from/to MIDAS files}
            \item{toSBML() function writes the model to SBMLqual format}
            \item{makeCNOlist() can import MIDAS with multiple, continuous cue levels}
            \item{add new function called crossInhibitedData}
        }
}
}






\section{CHANGES IN VERSION 1.10.0: (2014-03-13)}{
Changes since 1.8.0

\itemize{
    \item{BUG FIX}
        \itemize{
            \item{typos leading to failure fixed in cutCNOlist}
            \item{typos leading to failure in CNOlist if variance were provided}
        }
    \item{CHANGES}
        \itemize{
            \item{Changed warning into errors in readMIDAS and checkSignals
functions}
        }
    \item{NEW FEATURES}
        \itemize{
            \item{self loop can be read from the SIF files}
            \item{readSBMLQual do not need to add dummy nodes anymore}
        }
}
}



\section{CHANGES IN VERSION 1.8.0: (2013-08-28)}{
Changes since 1.6.0
\itemize{
    \item{BUG FIX}
        \itemize{
            \item{readMIDAS: DV, DA and TR can now be in the specy name}
            \item{prep4sim can read self loop}
            \item{plotOptimResultsPan: fix special cases with one or no inhibitors/stimuli}
            \item{fix bug in cutNONC: notMat was not populated}
            \item{readSIF: can read and gates coded in big caps as well as small ones}
            \item{writeMIDAS: manages absence of inhibitors}
        }
    \item{CHANGES}
        \itemize{
            \item{CNOlist: subfield parameter has been removed. Subfield are
                automatically found from the header}
            \item{expandAndGates are not limited to 4 inputs anymore}
            \item{normaliseCNOlist: EC50 is set to 1 by default}


        }
    \item{NEW FEATURES}
        \itemize{
            \item{readSBMLQual: a function to read prior knowledge network in
                SBMLqual format. !! This is a prototype. use with care for now.}
            \item{cutCNOlist function can cut a MIDAS file over time}
        }
    }
}
    



\section{CHANGES IN VERSION 1.6.0: (2013-03-12)}{
Changes since 1.4.0
\itemize{
    \item{BUG FIX}
        \itemize{
            \item{readMIDAS: DV, DA and TR can now be in the specy name}
            \item{makeCNOlist: bug fixed when only one experiment was present}
            \item{plotModel: figures where in B and W due to issue in Rgraphviz package}
            \item{gaBinaryT family: (1) fix bug when only one model found within
            the tolerance. (2) a faster hash table used in the optimisation. }
        }


    \item{CHANGES}
        \itemize{
            \item{writeSIF: can overwrite existing file with a parameter}
            \item{remove cutAndPlotResultsT2: use cutAndPlotResultsTN instead or
                cutAndPlot}
            \item{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.        }
          \item{ readSIF can now read relation "A 1 B C D E" as excepted in SIF
            format.}
          \item{makeCNOlist/CNOlist: variances available in the structure}
}
    
    \item{NEW FEATURES}
        \itemize{
            \item{CNOdata: a function to fetch data from www.cellnopt.org}
            \item{plotModel}
            \item{exhaustive function: a simple exhaustive function to perform optimisation for small models}
            \item{cutCNOlist: cut a cnolist given a list of species}
            \item{CNOlist: 3 new methods: length, randomize and plot accepts either one or 2 cnolist arguments.}
            \item{randomizeCNOlist: function to perform different randomization of the data}
            \item{model2igraph function}
            \item{compatCNOlist to convert CNOlist back to old style; used by CNORode}
        }
    }
}




\section{CHANGES IN VERSION 1.3.33: (2012-09-20)}{
    \itemize{
        \item{BUG FIX}
            \itemize{
                \item{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.}
            }
    }
}


\section{CHANGES IN VERSION 1.3.32: (2012-09-10)}{
    \itemize{
        \item{BUG FIX}
            \itemize{
                \item{plotModel can handle CNOlist=NULL as it used to be the case}
            }
        \item{CHANGES}
            \itemize{
                \item{simulatorT1 and TN have additional check for AND gates with any NA inputs.}
            }
    }
}

\section{CHANGES IN VERSION 1.3.31: (2012-09-06)}{
    \itemize{
        \item{BUG FIXES}
            \itemize{
                \item{typo in checkSignals in warning message.}
                \item{fixing bug (typo) in cutAndPlotResultsT1}
            }
   }
}

\section{CHANGES IN VERSION 1.3 to 1.3.30: (2012-08-30)}{
    \itemize{
        \item{BUG FIXES}
           \itemize{
                \item{fixed bug in writeDot function when only 1 stimuli present.}
                \item{cutNONC function recompte reacID on its own so that if compresion and
                  expansion are not performed, reacID are correct}
            }
        \item{CHANGES AND UI SIMPLIFICATION}
         \itemize{
            \item{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).}
            \item{improvment of  plotModel function to have more graphviz options}
            \item{gaBinary default initBstring argument is set to ones.}
            \item{MAJOR refactoring to merge T1, T2, TN functions (cutAnPlot, gaBinary,  simulator).}
            \item{simulateTN  combines simulateT1 and simulateTN so only one function is required.}
            \item{gaBinaryT2 is deprecated. Use TN version instead.}
            \item{gaBinaryT1 and TN do no need the indexList and simList parameters anymore}
             \item{preprocessing now returns only the model. indices are not required anymore.
                      preprocessing can now handle model without cnolist provided (e.g. for expansion only)}
            \item{add a cutAndPlot dispatcher that calls the proper cutandPlotResultsTX function.}
             \item{cutSimList argument called bitString renamed bString (developers)}
            \item{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.}
            \item{ show argument removed from cutAndPlot function family}
         }

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






