Changes in version 1.26.0 (2018-11-08)
o BUG FIX
• TO BE ADDED
o CHANGES
• TO BE ADDED
o NEW FEATURES
• readBND and readBNET reads MaBoSS style boolean network
definition files and converts them to CellNOpt network
models - credits for Luis Tobalina
Changes in version 1.25.0 (2018-01-10)
o BUG FIX
• fix gray boxes in plotOptimResultsPan
• in plotOptimResultsPan when errors were greater than 99.9%
color were white (instead of red)
• 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
• 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
• node name in the sif file containing the word AND (e.g.
ligand) will not result in an AND-node anymore
• Fixing issues with matrix subsetting, when the subsetting
converts the matrix to a vector
• 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
o CHANGES
• Bioconductor's version of the package got merged with the
Github's version leading to minor changes
• readSIF reads only the unique interactions/lines from the
SIF file
• plotOptimResultsPan and plotCNOlist plots intermediate cue
values (0,1) for CNORode add-on
o NEW FEATURES
• add readErrors and writeErrors functions in CNOlist:
read/write measurement error/variance from/to MIDAS files
• toSBML() function writes the model to SBMLqual format
• makeCNOlist() can import MIDAS with multiple, continuous
cue levels
• add new function called crossInhibitedData
Changes in version 1.10.0 (2014-03-13)
o BUG FIX
• typos leading to failure fixed in cutCNOlist
• typos leading to failure in CNOlist if variance were
provided
o CHANGES
• Changed warning into errors in readMIDAS and checkSignals
functions
o NEW FEATURES
• self loop can be read from the SIF files
• readSBMLQual do not need to add dummy nodes anymore
Changes in version 1.8.0 (2013-08-28)
o BUG FIX
• readMIDAS: DV, DA and TR can now be in the specy name
• prep4sim can read self loop
• plotOptimResultsPan: fix special cases with one or no
inhibitors/stimuli
• fix bug in cutNONC: notMat was not populated
• readSIF: can read and gates coded in big caps as well as
small ones
• writeMIDAS: manages absence of inhibitors
o CHANGES
• CNOlist: subfield parameter has been removed. Subfield are
automatically found from the header
• expandAndGates are not limited to 4 inputs anymore
• normaliseCNOlist: EC50 is set to 1 by default
o NEW FEATURES
• readSBMLQual: a function to read prior knowledge network in
SBMLqual format. !! This is a prototype. use with care for
now.
• cutCNOlist function can cut a MIDAS file over time
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