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Biodata toolbox

12 Nov 2008 (Updated 22 Aug 2009)

Database system coupled to chemometric algorithms that consequently stores spectra and related data

File Information
Description	The Biodata toolbox is a comprehensive database system that stores measurement signals and related data, such as sample labels, signal collection date, etc. in a single structure. The framework contains several mechanisms to prevent data corruption, e.g. when a sample is removed from the dataset, all related sample labels are removed as well. The database system is implemented as a matlab class and several chemometric preprocessing algorithms are coupled to the framework. The graphical addons GraphSel and GraphPlot enable the selection of subsets of the data and the generation of per sample label coloured plots. Biodata utilises several toolboxes for chemometrical processing (Tomcat, Discrim, EMSC toolbox, ...), and comes bundled with the toolboxes GSTools and Showpeaks. When using, please cite the paper Kris De Gussem, Joke De Gelder, Peter Vandenabeele, and Luc moens. The Biodata toolbox for MATLAB. Chemometrics and Intelligent Laboratory Systems, in press, doi 10.1016/j.chemolab.2008.08.0031 (http://dx.doi.org/10.1016/j.chemolab.2008.08.003)
MATLAB release	MATLAB 7.5 (R2007b)
Zip File Content
HTML Files	GSTools/history.html
Other Files	@Biodata/About.m, @Biodata/AdaptPlot.m, @Biodata/AddClassdes.m, @Biodata/AddEmptyClassdes.m, @Biodata/AddHistory.m, @Biodata/AddMapDescription.m, @Biodata/AddNrClass.m, @Biodata/AddOneSample.m, @Biodata/AddSample.m, @Biodata/AddSampleDescriptions.m, @Biodata/Auto.m, @Biodata/Biodata.m, @Biodata/BTree.m, @Biodata/CalculateMeans.m, @Biodata/CalculateMeans2.m, @Biodata/Clean.m, @Biodata/ClearAnalysisList.m, @Biodata/ClearTrees.m, @Biodata/Count.m, @Biodata/CountClass.m, @Biodata/Create2DReactionTables.m, @Biodata/CTreeBuild.m, @Biodata/CTreeEval.m, @Biodata/Cumtrapz.m, @Biodata/DeleteClassdes.m, @Biodata/DeleteMarkedSamples.m, @Biodata/DeleteSampleCombinations.m, @Biodata/DeleteSampleDescriptions.m, @Biodata/delsample.m, @Biodata/diff.m, @Biodata/display.m, @Biodata/DoAnalysis.m, @Biodata/DoAnalysisForIdentification.m, @Biodata/DoIdentification.m, @Biodata/DoIdentification2.m, @Biodata/EliminateOutliers.m, @Biodata/EliminateOutlyingSamplesInGroup.m, @Biodata/EliminateSmallGroups.m, @Biodata/EMSC.m, @Biodata/FFT2Dcor.m, @Biodata/FindIndexOfFreq.m, @Biodata/GetAnalysisList.m, @Biodata/GetBDinfo.m, @Biodata/GetClassComb.m, @Biodata/GetClassList.m, @Biodata/GetClassVal.m, @Biodata/GetLastAnalysis.m, @Biodata/GetLv.m, @Biodata/GetSamples.m, @Biodata/GetXRange.m, @Biodata/GetXRanges.m, @Biodata/Hilb2DCor.m, @Biodata/Hilb2DCorMW.m, @Biodata/Hilb2DCorNCI.m, @Biodata/Hilb2DCorSS.m, @Biodata/IsClassDes.m, @Biodata/join.m, @Biodata/lda.m, @Biodata/LOO.m, @Biodata/mean.m, @Biodata/mean_wo.m, @Biodata/mean_woK.m, @Biodata/median.m, @Biodata/mjoin.m, @Biodata/mncn.m, @Biodata/Mult.m, @Biodata/normaliz.m, @Biodata/normalize.m, @Biodata/pca.m, @Biodata/plot.m, @Biodata/plot2Dc.m, @Biodata/plot2Dfreq.m, @Biodata/plot2Dphase.m, @Biodata/plot2Dsimple.m, @Biodata/plotb.m, @Biodata/plotchar.m, @Biodata/plotdiff.m, @Biodata/plotloads.m, @Biodata/plotn.m, @Biodata/plotnfigs.m, @Biodata/PlotOneMap.m, @Biodata/plotpoint.m, @Biodata/pls.m, @Biodata/private/AdaptPlotReduced.m, @Biodata/private/AddAnalysis.m, @Biodata/private/CheckCoordinates.m, @Biodata/private/CheckIndices.m, @Biodata/private/CheckProductIn2DProductTable.m, @Biodata/private/Config.m, @Biodata/private/DirectEMSCAnalysis.m, @Biodata/private/DoplotSimpleLegend.m, @Biodata/private/GetAnalysisStructure.m, @Biodata/private/GetClassindex.m, @Biodata/private/GetDefaultPcaValues.m, @Biodata/private/GetSamplePos.m, @Biodata/private/IndicatorFunctionOfPCs.m, @Biodata/private/IsBTree.m, @Biodata/private/MakeEMSCZYDataFiles.m, @Biodata/private/MakeRepresentableStringFrom2DGroupAssignment.m, @Biodata/private/Obtain2DMWSequence.m, @Biodata/private/Obtain2DPeakGroups.m, @Biodata/private/PCAPlots.m, @Biodata/private/PCAPT.m, @Biodata/private/PCATC.m, @Biodata/private/PlotByClassColor.m, @Biodata/private/PlotEllipsoids.m, @Biodata/private/PlotLegend.m, @Biodata/private/PLSPT.m, @Biodata/private/PLSTC.m, @Biodata/private/QResiduals.m, @Biodata/private/SetXAxis.m, @Biodata/private/TsqOutliersCompare.m, @Biodata/RandomizeOrder.m, @Biodata/rAuto.m, @Biodata/rEliminateOutliers.m, @Biodata/rmncn.m, @Biodata/Rndcv.m, @Biodata/rPCA.m, @Biodata/rsnv.m, @Biodata/rTsqOutliers.m, @Biodata/SaveClassdes.m, @Biodata/savgol.m, @Biodata/SelectSampleCombinations.m, @Biodata/selectsamples.m, @Biodata/SetUpdating.m, @Biodata/ShowAnalysisList.m, @Biodata/ShowClassComb.m, @Biodata/ShowHistory.m, @Biodata/snv.m, @Biodata/StartEMSC.m, @Biodata/std.m, @Biodata/StopEMSC.m, @Biodata/subback.m, @Biodata/subbackmod.m, @Biodata/subsasgn.m, @Biodata/SubsClassDes.m, @Biodata/SubsClassDes2.m, @Biodata/subsref.m, @Biodata/Subtract.m, @Biodata/TransNorm.m, @Biodata/trimmean.m, @Biodata/TsqOutliers.m, @Biodata/Varsel.m, @Biodata/version.txt, @Biodata/viselim.m, @Biodata/WithHold.m, Additional/CellDisp.m, Additional/CellString2Double.m, Additional/FirstMax.m, Additional/FirstMin.m, Additional/GetComb.m, Additional/GetXRanges.m, Additional/INDFunc.m, Additional/IsToolboxPresent.m, Additional/LoadFile.m, Additional/mean_woK.m, Additional/mncn.m, Additional/NDIND.m, Additional/nmin.m, Additional/normaliz.m, Additional/printfigs.m, Additional/QResidualsLimit.m, Additional/ReplaceTabBySpaces.m, Additional/SaveCell.m, Additional/SaveFile.m, Additional/savgol.m, Additional/scale.m, Additional/sgsdf.m, Additional/ShowPeaks/GetPeakPos.m, Additional/ShowPeaks/GetPeakPos2.m, Additional/ShowPeaks/GetPeakPosFFT.m, Additional/ShowPeaks/PeakPosFFT.m, Additional/ShowPeaks/savgol.m, Additional/ShowPeaks/sgsdf.m, Additional/ShowPeaks/ShowPeakName.m, Additional/ShowPeaks/ShowPeakName2.m, Additional/ShowPeaks/ShowPeakNameBothSides.m, Additional/snv.m, Additional/SsqTable.m, Additional/subback.m, Additional/subbackmod.m, Additional/TLim.m, Additional/TransNorm.m, Bdtools/ControlSampleNr.m, Bdtools/ConvertInput2Num.m, Bdtools/GetBdVar.m, Bdtools/GetSelectedBd.m, Bdtools/graphmap.fig, Bdtools/graphmap.m, Bdtools/graphplot.fig, Bdtools/graphplot.m, Bdtools/graphsel.fig, Bdtools/graphsel.m, Bdtools/graphtools.fig, Bdtools/graphtools.m, Bdtools/InitializeGraphplot.m, Bdtools/InitializeGraphsel.m, Bdtools/InitializeGraphtools.m, Bdtools/LoadBdVar.m, Bdtools/SetAsSelectedBd.m, Bdtools/TransformClassdes.m, Biodata manual.pdf, Compatibility/isvector.m, Contents.m, gpl-3.0.pdf, GSTools/@BTree/About.m, GSTools/@BTree/Add.m, GSTools/@BTree/BTree.m, GSTools/@BTree/Count.m, GSTools/@BTree/display.m, GSTools/@BTree/getitem.m, GSTools/@BTree/GetItems.m, GSTools/@BTree/GetItemWithMostValues.m, GSTools/@BTree/GetSortedItemsList.m, GSTools/@BTree/history.txt, GSTools/@BTree/isitem.m, GSTools/@BTree/Plot.m, GSTools/@BTree/private/ConvertToBTree.m, GSTools/@BTree/private/DoCompare.m, GSTools/@BTree/private/GetThem.m, GSTools/@BTree/private/searchitem.m, GSTools/@BTree/subsasgn.m, GSTools/@BTree/subsref.m, GSTools/@BTree/version.txt, GSTools/@BTree/WriteContentsToFile.m, GSTools/Additional/CatBlank.m, GSTools/Additional/loadcell.m, GSTools/Additional/LocateItem.m, GSTools/Additional/MakeVector.m, GSTools/Additional/mystrcmp.m, GSTools/Additional/str.m, GSTools/Additional/str2.m, GSTools/Additional/trimleft.m, GSTools/Additional/trimright.m, GSTools/Additional/trimstr.m, GSTools/Contents.m, GSTools/DetermineClusters.m, GSTools/GetSPCAxisTypes.m, GSTools/GetTechniques.m, GSTools/gpl-3.0.pdf, GSTools/GSDendrogram.m, GSTools/GSImportspec.m, GSTools/GSSpcRead.m, GSTools/GSSpcReadStructure.m, GSTools/GSSpcWrite.m, GSTools/GSTools 0.4.3 manual.pdf, GSTools/GSToolsAbout.m, license.txt

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Updates
22 Aug 2009	Fixed important bug in 2D correlation analysis / dual licensed: added BSD license

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