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For more information on notebooks and Mathematica-compatible applications, contact Wolfram Research: web: http://www.wolfram.com email: info@wolfram.com phone: +1-217-398-0700 (U.S.) Notebook reader applications are available free of charge from Wolfram Research. *******************************************************************) (*CacheID: 232*) (*NotebookFileLineBreakTest NotebookFileLineBreakTest*) (*NotebookOptionsPosition[ 115053, 2820]*) (*NotebookOutlinePosition[ 157521, 4182]*) (* CellTagsIndexPosition[ 157477, 4178]*) (*WindowFrame->Normal*) Notebook[{ Cell[CellGroupData[{ Cell["SBML Model Visualization", "Subtitle"], Cell["\<\ This notebook provides an example of using \"visualizeSBMLModel\" \ to visualize an SBML model. \ \>", "Text"], Cell[CellGroupData[{ Cell[BoxData[ \(<< mathsbml.m\)], "Input"], Cell[BoxData[ \("MathSBML Version 2.6.0.6 (28-Oct-2006) using Mathematica Version 5.2 \ for Mac OS X x86 (32-bit) (February 24, 2006) reloaded 28-October-2006 \ 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"webMathematica"->FormBox[ RowBox[ {"web", AdjustmentBox[ StyleBox[ "Mathematica", FontSlant -> "Italic"], BoxMargins -> {{-0.17499999999999999, 0}, {0, 0}}]}], TextForm], Inherited}, CounterIncrements->"Subsection", CounterAssignments->{{"Subsubsection", 0}}, FontFamily->"Arial", FontSize->18, FontWeight->"Bold", FontColor->RGBColor[0.749996, 0, 0.749996], Background->RGBColor[0.749996, 1, 0.749996]], Cell[StyleData["Subsection", "Presentation"], CellMargins->{{56, 20}, {10, 28}}, FontSize->18], Cell[StyleData["Subsection", "Printout"]], Cell[StyleData["Subsection", "ColorPrintout"]] }, Open ]], Cell[CellGroupData[{ Cell[StyleData["Subsubsection"], CellFrame->{{0, 0}, {0, 0.5}}, CellDingbat->None, CellMargins->{{51, Inherited}, {Inherited, 12}}, CellGroupingRules->{"SectionGrouping", 50}, PageBreakBelow->False, CellFrameLabelMargins->6, InputAutoReplacements->{"TeX"->StyleBox[ RowBox[ {"T", AdjustmentBox[ "E", BoxMargins -> {{-0.074999999999999997, \ -0.085000000000000006}, {0, 0}}, 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"Mma"->"Mathematica", "MMA"->"Mathematica", "gridMathematica"->FormBox[ RowBox[ {"grid", AdjustmentBox[ StyleBox[ "Mathematica", FontSlant -> "Italic"], BoxMargins -> {{-0.175, 0}, {0, 0}}]}], TextForm], "webMathematica"->FormBox[ RowBox[ {"web", AdjustmentBox[ StyleBox[ "Mathematica", FontSlant -> "Italic"], BoxMargins -> {{-0.17499999999999999, 0}, {0, 0}}]}], TextForm], Inherited}, LineSpacing->{1, 6}, CounterIncrements->"Text"], Cell[StyleData["Text", "Presentation"], CellMargins->{{56, 20}, {8, 6}}, FontSize->18], Cell[StyleData["Text", "Printout"], Hyphenation->True, LineSpacing->{1, 5}, FontSize->10], Cell[StyleData["Text", "ColorPrintout"], Hyphenation->True, LineSpacing->{1, 5}, FontSize->10] }, Open ]], Cell[CellGroupData[{ Cell[StyleData["SmallText"], CellMargins->{{100, 38}, {4, 4}}, InputAutoReplacements->{"TeX"->StyleBox[ RowBox[ {"T", AdjustmentBox[ "E", BoxMargins -> {{-0.074999999999999997, \ -0.085000000000000006}, {0, 0}}, BoxBaselineShift -> 0.5], "X"}]], 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Cell[StyleData["SmallText", "ColorPrintout"], Hyphenation->True, FontSize->9] }, Closed]] }, Open ]], Cell[CellGroupData[{ Cell["Inline Formatting", "Section"], Cell["\<\ These styles are for modifying individual words or letters in a \ cell exclusive of the cell tag.\ \>", "Text"], Cell[StyleData["RM"], StyleMenuListing->None, FontWeight->"Plain", FontSlant->"Plain"], Cell[StyleData["BF"], StyleMenuListing->None, FontWeight->"Bold"], Cell[StyleData["IT"], StyleMenuListing->None, FontSlant->"Italic"], Cell[StyleData["TR"], StyleMenuListing->None, FontFamily->"Times", FontWeight->"Plain", FontSlant->"Plain"], Cell[StyleData["TI"], StyleMenuListing->None, FontFamily->"Times", FontWeight->"Plain", FontSlant->"Italic"], Cell[StyleData["TB"], StyleMenuListing->None, FontFamily->"Times", FontWeight->"Bold", FontSlant->"Plain"], Cell[StyleData["TBI"], StyleMenuListing->None, FontFamily->"Times", FontWeight->"Bold", FontSlant->"Italic"], Cell[StyleData["MR"], 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Cell[StyleData["SO"], StyleMenuListing->None, FontFamily->"Helvetica", FontWeight->"Plain", FontSlant->"Italic"], Cell[StyleData["SB"], StyleMenuListing->None, FontFamily->"Helvetica", FontWeight->"Bold", FontSlant->"Plain"], Cell[StyleData["SBO"], StyleMenuListing->None, FontFamily->"Helvetica", FontWeight->"Bold", FontSlant->"Italic"], Cell[CellGroupData[{ Cell[StyleData["SO10"], StyleMenuListing->None, FontFamily->"Helvetica", FontSize->10, FontWeight->"Plain", FontSlant->"Italic"], Cell[StyleData["SO10", "Printout"], StyleMenuListing->None, FontFamily->"Helvetica", FontSize->7, FontWeight->"Plain", FontSlant->"Italic"] }, Closed]], Cell[CellGroupData[{ Cell[StyleData["Inert"], StyleMenuListing->None, Background->RGBColor[0.870588, 0.905882, 0.972549]], Cell[StyleData["Inert", "Printout"], StyleMenuListing->None, Background->GrayLevel[1]] }, Closed]] }, Closed]], Cell[CellGroupData[{ Cell["Styles for Input/Output", "Section"], Cell["\<\ The cells in this section define styles used for input and output \ to the kernel. Be careful when modifying, renaming, or removing these \ styles, because the front end associates special meanings with these style \ names.\ \>", "Text"], Cell[CellGroupData[{ Cell[StyleData["Input"], CellFrame->True, CellMargins->{{36, 0}, {0, Inherited}}, Evaluatable->True, CellGroupingRules->"InputGrouping", CellHorizontalScrolling->True, PageBreakWithin->False, GroupPageBreakWithin->False, CellLabelMargins->{{3, Inherited}, {Inherited, Inherited}}, DefaultFormatType->DefaultInputFormatType, "TwoByteSyntaxCharacterAutoReplacement"->True, HyphenationOptions->{"HyphenationCharacter"->"\[Continuation]"}, LanguageCategory->"Formula", FormatType->InputForm, ShowStringCharacters->True, NumberMarks->True, LinebreakAdjustments->{0.85, 2, 10, 0, 1}, CounterIncrements->"Input", FontWeight->"Bold", FontColor->GrayLevel[0], Background->RGBColor[0.840558, 0.58323, 0.941176]], Cell[StyleData["Input", "Presentation"], CellMargins->{{56, 0}, {0, 8}}, CellFrameMargins->{{10, 10}, {12, 12}}, FontSize->18], Cell[StyleData["Input", "Printout"], LinebreakAdjustments->{0.85, 2, 10, 1, 1}, FontSize->10, Background->GrayLevel[0.900008]], Cell[StyleData["Input", "ColorPrintout"], LinebreakAdjustments->{0.85, 2, 10, 1, 1}, FontSize->10] }, Open ]], Cell[CellGroupData[{ Cell[StyleData["InlineInput"], Evaluatable->True, CellGroupingRules->"InputGrouping", CellHorizontalScrolling->True, PageBreakWithin->False, GroupPageBreakWithin->False, DefaultFormatType->DefaultInputFormatType, "TwoByteSyntaxCharacterAutoReplacement"->True, HyphenationOptions->{"HyphenationCharacter"->"\[Continuation]"}, AutoItalicWords->{}, FormatType->InputForm, ShowStringCharacters->True, NumberMarks->True, CounterIncrements->"Input", FontWeight->"Bold"], Cell[StyleData["InlineInput", "Presentation"], CellMargins->{{10, 4}, {6, 6}}, FontSize->18] }, Closed]], Cell[CellGroupData[{ Cell[StyleData["Output"], CellMargins->{{36, 0}, {Inherited, 0}}, CellEditDuplicate->True, CellGroupingRules->"OutputGrouping", CellHorizontalScrolling->True, PageBreakWithin->False, GroupPageBreakWithin->False, GeneratedCell->True, CellAutoOverwrite->True, CellLabelMargins->{{3, Inherited}, {Inherited, Inherited}}, DefaultFormatType->DefaultOutputFormatType, "TwoByteSyntaxCharacterAutoReplacement"->True, HyphenationOptions->{"HyphenationCharacter"->"\[Continuation]"}, LanguageCategory->"Formula", FormatType->InputForm, CounterIncrements->"Output", FontColor->GrayLevel[0], Background->RGBColor[0.711162, 0.834546, 1]], Cell[StyleData["Output", "Presentation"], CellMargins->{{56, 0}, {8, 0}}, CellFrameMargins->{{12, 10}, {12, 12}}, FontSize->18], Cell[StyleData["Output", "Printout"], FontSize->10, Background->GrayLevel[0.8]], Cell[StyleData["Output", "ColorPrintout"], FontSize->10] }, Closed]], Cell[CellGroupData[{ Cell[StyleData["Message"], CellDingbat->"\[LongDash]", CellMargins->{{64, Inherited}, {Inherited, Inherited}}, CellGroupingRules->"OutputGrouping", PageBreakWithin->False, GroupPageBreakWithin->False, GeneratedCell->True, CellAutoOverwrite->True, ShowCellLabel->False, CellLabelMargins->{{3, Inherited}, {Inherited, Inherited}}, DefaultFormatType->DefaultOutputFormatType, "TwoByteSyntaxCharacterAutoReplacement"->True, AutoStyleOptions->{"UnmatchedBracketStyle"->None}, HyphenationOptions->{"HyphenationCharacter"->"\[Continuation]"}, FormatType->InputForm, CounterIncrements->"Message", StyleMenuListing->None, FontFamily->"Helvetica", FontSize->10, FontSlant->"Oblique"], Cell[StyleData["Message", "Presentation"], CellMargins->{{96, 10}, {8, 6}}, FontSize->15], Cell[StyleData["Message", "Printout"], FontSize->8], Cell[StyleData["Message", "ColorPrintout"], FontSize->8] }, Closed]], Cell[CellGroupData[{ Cell[StyleData["Print"], CellMargins->{{36, 20}, {3, 3}}, CellGroupingRules->"OutputGrouping", CellHorizontalScrolling->True, PageBreakWithin->False, GroupPageBreakWithin->False, GeneratedCell->True, CellAutoOverwrite->True, ShowCellLabel->False, CellLabelMargins->{{3, Inherited}, 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Background->None], Cell[StyleData["Graphics", "Presentation"], CellMargins->{{56, 20}, {0, 2}}, CellFrameMargins->{{10, 10}, {12, 12}}, FontSize->18], Cell[StyleData["Graphics", "Printout"], FontSize->10, Background->GrayLevel[0.8]], Cell[StyleData["Graphics", "ColorPrintout"], FontSize->10] }, Closed]], Cell[CellGroupData[{ Cell[StyleData["CellLabel"], StyleMenuListing->None, FontFamily->"Helvetica", FontSize->9, FontColor->RGBColor[0.551492, 0.231144, 0.313466]], Cell[StyleData["CellLabel", "Presentation"], FontSize->14], Cell[StyleData["CellLabel", "Printout"], FontSize->8, FontColor->GrayLevel[0]], Cell[StyleData["CellLabel", "ColorPrintout"], FontSize->8] }, Closed]] }, Open ]], Cell[CellGroupData[{ Cell["Hyperlink Styles", "Section"], Cell["\<\ The cells below define styles useful for making hypertext \ ButtonBoxes. The \"Hyperlink\" style is for links within the same Notebook, \ or between Notebooks.\ \>", "Text"], Cell[CellGroupData[{ Cell[StyleData["Hyperlink"], StyleMenuListing->None, ButtonStyleMenuListing->Automatic, FontColor->RGBColor[0.269993, 0.308507, 0.6], ButtonBoxOptions->{ButtonFunction:>(FrontEndExecute[ { FrontEnd`NotebookLocate[ #2]}]&), Active->True, ButtonFrame->"None", ButtonNote->ButtonData}], Cell[StyleData["Hyperlink", "Presentation"], FontSize->16], Cell[StyleData["Hyperlink", "Condensed"], FontSize->11], Cell[StyleData["Hyperlink", "SlideShow"]], Cell[StyleData["Hyperlink", "Printout"], FontSize->10, FontColor->GrayLevel[0], FontVariations->{"Underline"->False}] }, Closed]], Cell["\<\ The following styles are for linking automatically to the on-line \ help system.\ \>", "Text"], Cell[CellGroupData[{ Cell[StyleData["MainBookLink"], StyleMenuListing->None, ButtonStyleMenuListing->Automatic, FontColor->RGBColor[0.269993, 0.308507, 0.6], 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