Learn R Programming
sybilSBML (version 1.1.15)

NEWS: sybilSBML News

Arguments

encoding

UTF-8

newcommand

{http://CRAN.R-project.org/package=#1{#1}}
Changes in version 1.1.15 2012-10-15
{
  • updated package vignette
  • slotrhsof classmodelorgis not set
}
Changes in version 1.1.14 2012-04-20
{
  • fileNEWSis now ininst/NEWS.Rd
  • removed argumentsverboseMode,loglevel,logfileandlogfileEncfrom functionreadSBMLmod; use functionsinkinstead
  • fixed a bug in.uglyHack: tries no longer to fix SBMLWarnings, which is not necessary
  • .uglyHackusestempfile()to generate corrected SBML files
  • fixed a bug inreadSBMLmod(): slotsubSyswas not of correct data type in rare cases
  • better SBML id formatting inreadSBMLmod()
}
Changes in version 1.1.13 2012-03-16
{
  • compatible withsybilversion 0.5.12: replacedSparseMwithMatrix
  • some additions to.uglyHack()
  • fixed a small bug inreadSBMLmod(), when parsing sub systems
}
Changes in version 1.1.12 2011-12-12
{
  • fixed a small bug inreadSBMLmod()concerning the detection of gpr rules
  • fixed a bug inreadSBMLmod(): genes from reactions which are excluded from the model are not read
}
Changes in version 1.1.11 2011-12-09
{
  • very minor adjustments inreadSBMLmod()
  • readSBMLmod()will continue reading the model, ifrsbmlproduces warnings. Check warnings in the log file; argumentsloglevelandlogfileinreadSBMLmod()
}
Changes in version 1.1.10 2011-08-30
{
  • updated documentation
}
Changes in version 1.1.9 2011-08-30
{
  • added boolean argumentsremMet,contrMet,singletonMetanddeadEndmettoreadSBMLmod(), the two boolen argumentsremSingleMetandconstrSingleMetare removed, seehelp("readSBMLmod")for details
}
Changes in version 1.1.8 2011-08-15
{
  • some small changes according tocodetools
  • slotsmet_singleandreact_singleof classmodelorgare initialized withNA, notFALSE
}
Changes in version 1.1.7 2011-08-12
{
  • new arguments forreadSBMLmod():mergeMet,balanceReact,remUnusedMetReact,remSingleMet,constrSingleMetandtol. Seehelp("readSBMLmod")for details
}
Changes in version 1.1.6 2011-08-08
{
  • a warning is produced, if a metabolite is used only once in S
}
Changes in version 1.1.5 2011-08-08
{
  • readSBMLmod()removes unused metabolites and reactions (rows and lines without any non-zero entries)
  • readSBMLmod()merges and balances metabolites as inreadTSVmod()fromsybil
}
Changes in version 1.1.4 2011-08-05
{
  • fixed a bug inreadSBMLmod()concerning the number of metabolite names and metabolite compartments
}
Changes in version 1.1.3 2011-08-05
{
  • addedNAMESPACE
  • new boolean parameterbndCndinreadSBMLmod(): If set toTRUE, external metabolites are those, having the SBML tagboundaryConditionset toTRUE. If set toFALSE, external metabolites are recogized viaextMetFlag
  • usage of classsybilLoginreadSBMLmod()with four new parameters. Seehelp("readSBMLmod")for details.
}
Changes in version 1.1.2 2011-07-20
{
  • fixed a bug inreadSBMLmod(): if an external metabolite id is removed and it occcurs in a reaction, that particular reaction is read correctly.
}
Changes in version 1.1.1 2011-07-06
{
  • new boolean parameterignoreNoAninreadSBMLmod(): if set toTRUE, any notes and annotation fields in thelistOfReactionsin an SBML file are ignored (default:TRUE).
  • unused metabolites having no non-zero entry in S, are removed from S and the metabolites list in instances of classmodelorg
}
Changes in version 1.1.0 2011-05-17
{
  • updated documentation
}
Changes in version 1.0.3 2011-05-11
{
  • added compatibility tosybilversion$\geq$0.4.1: slotsubSysis now of classmatrix
  • fixed a bug inreadSBMLmod(): metablite id's differing only in the number of consecutive '_' are now recogized as different metabolite id's.
  • readSBMLmod()can now read the Yeast model in the fileSc_iND750_GlcMM.xmlfrom the Palsson group.
}
Changes in version 1.0.2 2011-03-02
{
  • If the SBML file contains reactions with metabolites used as reactands and products at the same time, the stoichiometric coefficient for those metabolites is the sum of reactand and product.
}
Changes in version 1.0.1 2011-03-01
{
  • fixed some regular expressions when parsing metabolite names and id's
  • added argumentextMetFlagwhich is used to identify external metabolites
  • reads subsystem information also from annotations
}
Changes in version 1.0.0 2011-01-25
{
  • initial public release
}