2013 lines
198 KiB
XML
2013 lines
198 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<office:document xmlns:officeooo="http://openoffice.org/2009/office" xmlns:css3t="http://www.w3.org/TR/css3-text/" xmlns:grddl="http://www.w3.org/2003/g/data-view#" xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:formx="urn:openoffice:names:experimental:ooxml-odf-interop:xmlns:form:1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rpt="http://openoffice.org/2005/report" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:config="urn:oasis:names:tc:opendocument:xmlns:config:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:ooo="http://openoffice.org/2004/office" xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:of="urn:oasis:names:tc:opendocument:xmlns:of:1.2" xmlns:calcext="urn:org:documentfoundation:names:experimental:calc:xmlns:calcext:1.0" xmlns:tableooo="http://openoffice.org/2009/table" xmlns:drawooo="http://openoffice.org/2010/draw" xmlns:loext="urn:org:documentfoundation:names:experimental:office:xmlns:loext:1.0" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:field="urn:openoffice:names:experimental:ooo-ms-interop:xmlns:field:1.0" xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns:form="urn:oasis:names:tc:opendocument:xmlns:form:1.0" xmlns:script="urn:oasis:names:tc:opendocument:xmlns:script:1.0" xmlns:xforms="http://www.w3.org/2002/xforms" office:version="1.3" office:mimetype="application/vnd.oasis.opendocument.text">
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<office:meta><meta:creation-date>2021-02-15T09:17:10.478673722</meta:creation-date><meta:editing-duration>PT4H50M41S</meta:editing-duration><meta:editing-cycles>52</meta:editing-cycles><meta:generator>LibreOffice/7.2.4.1$Linux_X86_64 LibreOffice_project/20$Build-1</meta:generator><dc:subject>Modèle et mini-guide</dc:subject><dc:title>Modèle Jres 2021</dc:title><dc:date>2022-01-07T01:28:07.900329662</dc:date><dc:creator>eda</dc:creator><meta:document-statistic meta:table-count="0" meta:image-count="1" meta:object-count="0" meta:page-count="7" meta:paragraph-count="96" meta:word-count="2331" meta:character-count="15893" meta:non-whitespace-character-count="13650"/></office:meta>
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<office:settings>
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<config:config-item config:name="ViewAreaHeight" config:type="long">14169</config:config-item>
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<config:config-item config:name="ShowRedlineChanges" config:type="boolean">false</config:config-item>
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<config:config-item config:name="InBrowseMode" config:type="boolean">false</config:config-item>
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<config:config-item-map-indexed config:name="Views">
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<config:config-item-map-entry>
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<config:config-item config:name="ViewId" config:type="string">view2</config:config-item>
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<config:config-item config:name="VisibleTop" config:type="long">131979</config:config-item>
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<config:config-item config:name="ViewLayoutBookMode" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ZoomFactor" config:type="short">110</config:config-item>
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<config:config-item config:name="IsSelectedFrame" config:type="boolean">false</config:config-item>
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<config:config-item config:name="KeepRatio" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AnchoredTextOverflowLegacy" config:type="boolean">false</config:config-item>
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</config:config-item-map-entry>
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</config:config-item-map-indexed>
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</config:config-item-set>
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<config:config-item-set config:name="ooo:configuration-settings">
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<config:config-item config:name="PrintProspect" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintReversed" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintSingleJobs" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintLeftPages" config:type="boolean">true</config:config-item>
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<config:config-item config:name="PrintTables" config:type="boolean">true</config:config-item>
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<config:config-item config:name="PrintControls" config:type="boolean">true</config:config-item>
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<config:config-item config:name="PrintPageBackground" config:type="boolean">true</config:config-item>
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<config:config-item config:name="PrintDrawings" config:type="boolean">true</config:config-item>
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<config:config-item config:name="PrintBlackFonts" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintAnnotationMode" config:type="short">0</config:config-item>
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<config:config-item config:name="PrintTextPlaceholder" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ProtectFields" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ProtectBookmarks" config:type="boolean">false</config:config-item>
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<config:config-item config:name="EmptyDbFieldHidesPara" config:type="boolean">true</config:config-item>
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<config:config-item config:name="DisableOffPagePositioning" config:type="boolean">false</config:config-item>
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<config:config-item config:name="SubtractFlysAnchoredAtFlys" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PropLineSpacingShrinksFirstLine" config:type="boolean">true</config:config-item>
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<config:config-item config:name="ApplyParagraphMarkFormatToNumbering" config:type="boolean">false</config:config-item>
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<config:config-item config:name="GutterAtTop" config:type="boolean">false</config:config-item>
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<config:config-item config:name="TreatSingleColumnBreakAsPageBreak" config:type="boolean">false</config:config-item>
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<config:config-item config:name="EmbedSystemFonts" config:type="boolean">false</config:config-item>
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<config:config-item config:name="EmbedComplexScriptFonts" config:type="boolean">false</config:config-item>
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<config:config-item config:name="EmbedAsianScriptFonts" config:type="boolean">false</config:config-item>
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<config:config-item config:name="EmbedLatinScriptFonts" config:type="boolean">true</config:config-item>
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<config:config-item config:name="EmbedOnlyUsedFonts" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ContinuousEndnotes" config:type="boolean">false</config:config-item>
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<config:config-item config:name="EmbedFonts" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ClippedPictures" config:type="boolean">false</config:config-item>
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<config:config-item config:name="FloattableNomargins" config:type="boolean">false</config:config-item>
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<config:config-item config:name="UnbreakableNumberings" config:type="boolean">false</config:config-item>
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<config:config-item config:name="HeaderSpacingBelowLastPara" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AllowPrintJobCancel" config:type="boolean">true</config:config-item>
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<config:config-item config:name="UseOldPrinterMetrics" config:type="boolean">false</config:config-item>
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<config:config-item config:name="TabOverMargin" config:type="boolean">false</config:config-item>
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<config:config-item config:name="TabsRelativeToIndent" config:type="boolean">true</config:config-item>
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<config:config-item config:name="UseOldNumbering" config:type="boolean">false</config:config-item>
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<config:config-item config:name="InvertBorderSpacing" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintPaperFromSetup" config:type="boolean">false</config:config-item>
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<config:config-item config:name="UpdateFromTemplate" config:type="boolean">true</config:config-item>
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<config:config-item config:name="CurrentDatabaseCommandType" config:type="int">0</config:config-item>
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<config:config-item config:name="LinkUpdateMode" config:type="short">1</config:config-item>
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<config:config-item config:name="AddParaSpacingToTableCells" config:type="boolean">true</config:config-item>
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<config:config-item config:name="FrameAutowidthWithMorePara" config:type="boolean">false</config:config-item>
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<config:config-item config:name="CurrentDatabaseCommand" config:type="string"/>
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<config:config-item config:name="PrinterIndependentLayout" config:type="string">high-resolution</config:config-item>
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<config:config-item config:name="ApplyUserData" config:type="boolean">true</config:config-item>
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<config:config-item config:name="PrintFaxName" config:type="string"/>
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<config:config-item config:name="CurrentDatabaseDataSource" config:type="string"/>
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<config:config-item config:name="ClipAsCharacterAnchoredWriterFlyFrames" config:type="boolean">false</config:config-item>
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<config:config-item config:name="IsKernAsianPunctuation" config:type="boolean">false</config:config-item>
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<config:config-item config:name="SaveThumbnail" config:type="boolean">true</config:config-item>
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<config:config-item config:name="UseFormerTextWrapping" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AddExternalLeading" config:type="boolean">true</config:config-item>
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<config:config-item config:name="AddParaTableSpacing" config:type="boolean">true</config:config-item>
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<config:config-item config:name="StylesNoDefault" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ChartAutoUpdate" config:type="boolean">true</config:config-item>
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<config:config-item-map-indexed config:name="ForbiddenCharacters">
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<config:config-item-map-entry>
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<config:config-item config:name="Language" config:type="string">fr</config:config-item>
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<config:config-item config:name="Country" config:type="string">FR</config:config-item>
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<config:config-item config:name="Variant" config:type="string"/>
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<config:config-item config:name="BeginLine" config:type="string"/>
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<config:config-item config:name="EndLine" config:type="string"/>
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</config:config-item-map-entry>
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</config:config-item-map-indexed>
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<config:config-item config:name="PrinterSetup" config:type="base64Binary"/>
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<config:config-item config:name="AddParaTableSpacingAtStart" config:type="boolean">true</config:config-item>
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<config:config-item config:name="Rsid" config:type="int">8293284</config:config-item>
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<config:config-item config:name="EmbeddedDatabaseName" config:type="string"/>
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<config:config-item config:name="FieldAutoUpdate" config:type="boolean">true</config:config-item>
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<config:config-item config:name="OutlineLevelYieldsNumbering" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AlignTabStopPosition" config:type="boolean">true</config:config-item>
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<config:config-item config:name="CharacterCompressionType" config:type="short">0</config:config-item>
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<config:config-item config:name="PrinterName" config:type="string"/>
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<config:config-item config:name="SaveGlobalDocumentLinks" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrinterPaperFromSetup" config:type="boolean">false</config:config-item>
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<config:config-item config:name="UseFormerLineSpacing" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AddParaLineSpacingToTableCells" config:type="boolean">false</config:config-item>
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<config:config-item config:name="UseFormerObjectPositioning" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintGraphics" config:type="boolean">true</config:config-item>
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<config:config-item config:name="SurroundTextWrapSmall" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ConsiderTextWrapOnObjPos" config:type="boolean">false</config:config-item>
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<config:config-item config:name="MsWordCompTrailingBlanks" config:type="boolean">false</config:config-item>
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<config:config-item config:name="TabAtLeftIndentForParagraphsInList" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintRightPages" config:type="boolean">true</config:config-item>
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<config:config-item config:name="TabOverSpacing" config:type="boolean">false</config:config-item>
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<config:config-item config:name="IgnoreFirstLineIndentInNumbering" config:type="boolean">false</config:config-item>
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<config:config-item config:name="RedlineProtectionKey" config:type="base64Binary"/>
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<config:config-item config:name="DoNotJustifyLinesWithManualBreak" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintProspectRTL" config:type="boolean">false</config:config-item>
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<config:config-item config:name="PrintEmptyPages" config:type="boolean">false</config:config-item>
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<config:config-item config:name="DoNotResetParaAttrsForNumFont" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AddFrameOffsets" config:type="boolean">false</config:config-item>
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<config:config-item config:name="IgnoreTabsAndBlanksForLineCalculation" config:type="boolean">false</config:config-item>
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<config:config-item config:name="LoadReadonly" config:type="boolean">false</config:config-item>
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<config:config-item config:name="DoNotCaptureDrawObjsOnPage" config:type="boolean">false</config:config-item>
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<config:config-item config:name="AddVerticalFrameOffsets" config:type="boolean">false</config:config-item>
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<config:config-item config:name="UnxForceZeroExtLeading" config:type="boolean">false</config:config-item>
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<config:config-item config:name="IsLabelDocument" config:type="boolean">false</config:config-item>
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<config:config-item config:name="TableRowKeep" config:type="boolean">false</config:config-item>
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<config:config-item config:name="RsidRoot" config:type="int">376182</config:config-item>
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<config:config-item config:name="PrintHiddenText" config:type="boolean">false</config:config-item>
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<config:config-item config:name="ProtectForm" config:type="boolean">false</config:config-item>
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<config:config-item config:name="MsWordCompMinLineHeightByFly" config:type="boolean">false</config:config-item>
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<config:config-item config:name="BackgroundParaOverDrawings" config:type="boolean">false</config:config-item>
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<config:config-item config:name="SaveVersionOnClose" config:type="boolean">false</config:config-item>
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<config:config-item config:name="MathBaselineAlignment" config:type="boolean">true</config:config-item>
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<config:config-item config:name="SmallCapsPercentage66" config:type="boolean">false</config:config-item>
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<config:config-item config:name="CollapseEmptyCellPara" config:type="boolean">true</config:config-item>
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<config:config-item config:name="TabOverflow" config:type="boolean">true</config:config-item>
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</config:config-item-set>
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</office:settings>
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<office:scripts>
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<office:script script:language="ooo:Basic">
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<ooo:libraries xmlns:ooo="http://openoffice.org/2004/office" xmlns:xlink="http://www.w3.org/1999/xlink">
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<ooo:library-embedded ooo:name="Standard"/>
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</ooo:libraries>
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</office:script>
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</office:scripts>
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<office:font-face-decls>
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<style:font-face style:name="Arial" svg:font-family="Arial" style:font-adornments="Gras Italique" style:font-family-generic="swiss" style:font-pitch="variable"/>
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<style:font-face style:name="Courier New" svg:font-family="'Courier New'" style:font-family-generic="modern" style:font-pitch="fixed"/>
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<style:font-face style:name="FreeSans" svg:font-family="FreeSans" style:font-family-generic="system" style:font-pitch="variable"/>
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<style:font-face style:name="FreeSans1" svg:font-family="FreeSans" style:font-family-generic="swiss"/>
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<style:font-face style:name="Liberation Mono" svg:font-family="'Liberation Mono'" style:font-adornments="Normal" style:font-family-generic="modern" style:font-pitch="fixed"/>
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<style:font-face style:name="Liberation Sans" svg:font-family="'Liberation Sans'" style:font-family-generic="swiss" style:font-pitch="variable"/>
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<style:font-face style:name="Liberation Serif" svg:font-family="'Liberation Serif'" style:font-family-generic="roman" style:font-pitch="variable"/>
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||
<style:font-face style:name="Noto Sans CJK SC" svg:font-family="'Noto Sans CJK SC'" style:font-family-generic="system" style:font-pitch="variable"/>
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||
<style:font-face style:name="Noto Serif CJK SC" svg:font-family="'Noto Serif CJK SC'" style:font-family-generic="system" style:font-pitch="variable"/>
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<style:font-face style:name="OpenSymbol" svg:font-family="OpenSymbol"/>
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</office:font-face-decls>
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<office:styles>
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<style:default-style style:family="graphic">
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<style:graphic-properties svg:stroke-color="#3465a4" draw:fill-color="#729fcf" fo:wrap-option="no-wrap" draw:shadow-offset-x="0.3cm" draw:shadow-offset-y="0.3cm" draw:start-line-spacing-horizontal="0.283cm" draw:start-line-spacing-vertical="0.283cm" draw:end-line-spacing-horizontal="0.283cm" draw:end-line-spacing-vertical="0.283cm" style:flow-with-text="false"/>
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||
<style:paragraph-properties style:text-autospace="ideograph-alpha" style:line-break="strict" style:font-independent-line-spacing="false">
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||
<style:tab-stops/>
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||
</style:paragraph-properties>
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||
<style:text-properties style:use-window-font-color="true" loext:opacity="0%" style:font-name="Liberation Serif" fo:font-size="12pt" fo:language="fr" fo:country="FR" style:letter-kerning="true" style:font-name-asian="Noto Serif CJK SC" style:font-size-asian="10.5pt" style:language-asian="zh" style:country-asian="CN" style:font-name-complex="FreeSans" style:font-size-complex="12pt" style:language-complex="hi" style:country-complex="IN"/>
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||
</style:default-style>
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||
<style:default-style style:family="paragraph">
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||
<style:paragraph-properties fo:orphans="2" fo:widows="2" fo:hyphenation-ladder-count="no-limit" style:text-autospace="ideograph-alpha" style:punctuation-wrap="hanging" style:line-break="strict" style:tab-stop-distance="1.251cm" style:writing-mode="page"/>
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||
<style:text-properties style:use-window-font-color="true" loext:opacity="0%" style:font-name="Liberation Serif" fo:font-size="12pt" fo:language="fr" fo:country="FR" style:letter-kerning="true" style:font-name-asian="Noto Serif CJK SC" style:font-size-asian="10.5pt" style:language-asian="zh" style:country-asian="CN" style:font-name-complex="FreeSans" style:font-size-complex="12pt" style:language-complex="hi" style:country-complex="IN" fo:hyphenate="false" fo:hyphenation-remain-char-count="2" fo:hyphenation-push-char-count="2" loext:hyphenation-no-caps="false"/>
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</style:default-style>
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||
<style:default-style style:family="table">
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||
<style:table-properties table:border-model="collapsing"/>
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||
</style:default-style>
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||
<style:default-style style:family="table-row">
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||
<style:table-row-properties fo:keep-together="auto"/>
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||
</style:default-style>
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||
<style:style style:name="Standard" style:family="paragraph" style:class="text">
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<style:paragraph-properties fo:margin-top="0.101cm" fo:margin-bottom="0.101cm" style:contextual-spacing="false" fo:text-align="justify" style:justify-single-word="false"/>
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||
</style:style>
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||
<style:style style:name="Heading" style:family="paragraph" style:parent-style-name="_2d__3e__20_JRES" style:next-style-name="Text_20_body" style:class="text">
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||
<style:paragraph-properties fo:margin-top="0.423cm" fo:margin-bottom="0.212cm" style:contextual-spacing="false" fo:keep-with-next="always"/>
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||
<style:text-properties fo:color="#00335f" loext:opacity="100%" style:font-name="Liberation Sans" fo:font-family="'Liberation Sans'" style:font-family-generic="swiss" style:font-pitch="variable" fo:font-size="10pt" style:font-name-asian="Noto Sans CJK SC" style:font-family-asian="'Noto Sans CJK SC'" style:font-family-generic-asian="system" style:font-pitch-asian="variable" style:font-size-asian="10pt" style:font-name-complex="FreeSans" style:font-family-complex="FreeSans" style:font-family-generic-complex="system" style:font-pitch-complex="variable" style:font-size-complex="10pt"/>
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</style:style>
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|
||
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||
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||
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||
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<text:list-level-style-number text:level="3" text:style-name="Numbering_20_Symbols" loext:num-list-format="%3%." style:num-suffix="." style:num-format="a" text:start-value="3">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="1.998cm" fo:text-indent="-1cm" fo:margin-left="1.998cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="4" text:style-name="Numbering_20_Symbols" loext:num-list-format="%4%." style:num-suffix="." style:num-format="a" text:start-value="4">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="3.249cm" fo:text-indent="-1.251cm" fo:margin-left="3.249cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="5" text:style-name="Numbering_20_Symbols" loext:num-list-format="%5%." style:num-suffix="." style:num-format="a" text:start-value="5">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="4.748cm" fo:text-indent="-1.499cm" fo:margin-left="4.748cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="6" text:style-name="Numbering_20_Symbols" loext:num-list-format="%6%." style:num-suffix="." style:num-format="a" text:start-value="6">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="6.549cm" fo:text-indent="-1.801cm" fo:margin-left="6.549cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="7" text:style-name="Numbering_20_Symbols" loext:num-list-format="%7%." style:num-suffix="." style:num-format="a" text:start-value="7">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="8.849cm" fo:text-indent="-2.3cm" fo:margin-left="8.849cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="8" text:style-name="Numbering_20_Symbols" loext:num-list-format="%8%." style:num-suffix="." style:num-format="a" text:start-value="8">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="11.449cm" fo:text-indent="-2.6cm" fo:margin-left="11.449cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="9" text:style-name="Numbering_20_Symbols" loext:num-list-format="%9%." style:num-suffix="." style:num-format="a" text:start-value="9">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="14.25cm" fo:text-indent="-2.801cm" fo:margin-left="14.25cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="10" text:style-name="Numbering_20_Symbols" loext:num-list-format="%10%." style:num-suffix="." style:num-format="a" text:start-value="10">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="17.351cm" fo:text-indent="-3.101cm" fo:margin-left="17.351cm"/>
|
||
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|
||
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|
||
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|
||
<text:list-style style:name="Numbering_20_3" style:display-name="Numbering 3">
|
||
<text:list-level-style-number text:level="1" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1% " style:num-prefix=" " style:num-suffix=" " style:num-format="1">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="3cm" fo:text-indent="-3cm" fo:margin-left="3cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="2" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="2" text:display-levels="2">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="6.001cm" fo:text-indent="-3cm" fo:margin-left="6.001cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="3" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="3" text:display-levels="3">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="9.001cm" fo:text-indent="-3cm" fo:margin-left="9.001cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="4" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="4" text:display-levels="4">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="12.002cm" fo:text-indent="-3cm" fo:margin-left="12.002cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="5" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4%.%5% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="5" text:display-levels="5">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
|
||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="15.002cm" fo:text-indent="-3cm" fo:margin-left="15.002cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="6" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4%.%5%.%6% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="6" text:display-levels="6">
|
||
<style:list-level-properties text:list-level-position-and-space-mode="label-alignment">
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="18.002cm" fo:text-indent="-3cm" fo:margin-left="18.002cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="7" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4%.%5%.%6%.%7% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="7" text:display-levels="7">
|
||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="21.003cm" fo:text-indent="-3cm" fo:margin-left="21.003cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="8" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4%.%5%.%6%.%7%.%8% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="8" text:display-levels="8">
|
||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="24.003cm" fo:text-indent="-3cm" fo:margin-left="24.003cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="9" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4%.%5%.%6%.%7%.%8%.%9% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="9" text:display-levels="9">
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||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="27.003cm" fo:text-indent="-3cm" fo:margin-left="27.003cm"/>
|
||
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|
||
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|
||
<text:list-level-style-number text:level="10" text:style-name="Numbering_20_Symbols" loext:num-list-format=" %1%.%2%.%3%.%4%.%5%.%6%.%7%.%8%.%9%.%10% " style:num-prefix=" " style:num-suffix=" " style:num-format="1" text:start-value="10" text:display-levels="10">
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||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="30.004cm" fo:text-indent="-3cm" fo:margin-left="30.004cm"/>
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||
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||
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|
||
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||
<text:list-style style:name="Numbering_20_4" style:display-name="Numbering 4">
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||
<text:list-level-style-number text:level="1" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%1%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" fo:text-indent="-0.6cm" fo:margin-left="0.7cm"/>
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||
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||
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||
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||
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<style:list-level-label-alignment text:label-followed-by="listtab" fo:text-indent="-0.6cm" fo:margin-left="0.7cm"/>
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||
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||
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||
<text:list-level-style-number text:level="3" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%3%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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<style:list-level-label-alignment text:label-followed-by="listtab" fo:text-indent="-0.6cm" fo:margin-left="0.7cm"/>
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||
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||
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||
<text:list-level-style-number text:level="4" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%4%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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<style:list-level-label-alignment text:label-followed-by="listtab" fo:text-indent="-0.6cm" fo:margin-left="0.7cm"/>
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||
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||
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||
<text:list-level-style-number text:level="5" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%5%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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<style:list-level-label-alignment text:label-followed-by="listtab" fo:text-indent="-0.6cm" fo:margin-left="0.7cm"/>
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||
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||
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||
<text:list-level-style-number text:level="6" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%6%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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||
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||
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||
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||
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||
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||
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||
<text:list-level-style-number text:level="8" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%8%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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||
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||
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||
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||
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||
<text:list-level-style-number text:level="10" text:style-name="Numbering_20_Symbols" loext:num-list-format="[%10%]" style:num-prefix="[" style:num-suffix="]" style:num-format="1">
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||
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<style:list-level-label-alignment text:label-followed-by="listtab" fo:text-indent="-0.6cm" fo:margin-left="0.7cm"/>
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||
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||
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||
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||
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||
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||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="0.4cm" fo:text-indent="-0.4cm" fo:margin-left="0.4cm"/>
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||
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||
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||
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||
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||
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||
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||
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||
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<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="3.186cm" fo:text-indent="-0.395cm" fo:margin-left="3.186cm"/>
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||
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||
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||
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||
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||
<style:list-level-label-alignment text:label-followed-by="listtab" text:list-tab-stop-position="3.976cm" fo:text-indent="-0.395cm" fo:margin-left="3.976cm"/>
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||
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||
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<text:list-level-style-bullet text:level="10" text:style-name="Numbering_20_Symbols" loext:num-list-format="%10%" text:bullet-char="•">
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<text:p text:style-name="P1">JRES 2021 – Marseille<text:tab/><text:tab/><text:page-number text:select-page="current">7</text:page-number>/<text:page-count>7</text:page-count></text:p>
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<text:p text:style-name="Title"><text:span text:style-name="T31">Modèle</text:span> de l’article JRES</text:p>
|
||
<text:p text:style-name="P65">Edlira Nano</text:p>
|
||
<text:p text:style-name="P88">Associations April, </text:p>
|
||
<text:p text:style-name="P88">La Quadrature Du Net, </text:p>
|
||
<text:p text:style-name="P88">informaticienne indépendante</text:p>
|
||
<text:p text:style-name="P88"><text:a xlink:type="simple" xlink:href="mailto:eda@mutu.net" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">eda@mutu.net</text:a> / eda@laquadrature.net</text:p>
|
||
<text:p text:style-name="P70">Olivier Langella</text:p>
|
||
<text:p text:style-name="P71">Plateforme PAPPSO</text:p>
|
||
<text:p text:style-name="P71">Laboratoire GQE-Le Moulon</text:p>
|
||
<text:p text:style-name="P71">Ferme du Moulon</text:p>
|
||
<text:p text:style-name="P71">91190 Gif-sur-Yvette</text:p>
|
||
<text:p text:style-name="P71">France</text:p>
|
||
<text:p text:style-name="P71">olivier.langella@universite-paris-saclay.fr</text:p>
|
||
<text:p text:style-name="P40"/>
|
||
<text:p text:style-name="P41"><text:span text:style-name="T23">Filippo</text:span><text:span text:style-name="T83"> </text:span><text:span text:style-name="T23">Rusconi</text:span></text:p>
|
||
<text:p text:style-name="P71">Plateforme PAPPSO</text:p>
|
||
<text:p text:style-name="P71">Laboratoire GQE-Le Moulon</text:p>
|
||
<text:p text:style-name="P71">Ferme du Moulon</text:p>
|
||
<text:p text:style-name="P71">91190 Gif-sur-Yvette</text:p>
|
||
<text:p text:style-name="P71">France</text:p>
|
||
<text:p text:style-name="P71">filippo.rusconi@universite-paris-saclay.fr</text:p>
|
||
<text:p text:style-name="Titre_20_résumé">Résumé</text:p>
|
||
<text:p text:style-name="P43"><text:change-start text:change-id="ct94407799201200"/>Ce document résume les instructions aux auteurs de la conférence JRES.</text:p>
|
||
<text:p text:style-name="P43"><text:change-end text:change-id="ct94407799201200"/>Le Logiciel libre et la recherche publique partagent un objectif : le bien commun, au service de tous. Cette présentation revient sur ce que sont le bien commun et la science ouverte pour essayer de les analyser à l'aide de l'exemple de la plateforme scientifique Analyses protéomiques de Paris Sud-Ouest(PAPPSO).</text:p>
|
||
<text:p text:style-name="P43"><text:line-break/>PAPPSO s'est dotée d'une infrastructure informatique complète basée exclusivement sur du Logiciel libre : réseau, serveurs, stockage, calcul et postes personnels. Elle développe plusieurs logiciels sous licence libre, dont ceux qui forment la chaîne de traitement des données de spectrométrie de masse. Ce choix naturel facilite la reproductibilité des traitements, apporte la maîtrise des logiciels et permet l'intégration de code source tiers.</text:p>
|
||
<text:p text:style-name="P43"><text:line-break/>L'apport majeur du Logiciel libre à la recherche publique permet l'utilisation des réseaux et systèmes informatiques. Scientifiquement, l'ouverture du code source et la liberté d'utilisation des logiciels garantissent l'échange des données, leur réutilisation et leur vérification par les pairs. Cet ensemble forme un bien commun protégé par des licences. De nombreux laboratoires y contribuent en utilisant ou en produisant des logiciels libres, comme en témoigne en partie la forge du code source du secteur public (<text:a xlink:type="simple" xlink:href="https://code.etalab.gouv.fr/" office:target-frame-name="_blank" xlink:show="new" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">https://code.etalab.gouv.fr</text:a>).</text:p>
|
||
<text:p text:style-name="P43"><text:line-break/>Comment contribuer efficacement ? Quelles sont les recommandations et obligations pour les <text:soft-page-break/>établissements publics ? Quelle licence choisir ? Comment une licence copyleft peut-elle aussi séduire les partenaires privés ? Nous apporterons des réponses et des éléments de réflexion pour corriger quelques fausses croyances et promouvoir la construction collective d'une culture libre, au service du bien commun.<text:change-start text:change-id="ct94407800321840"/>Le résumé doit faire de quinze à vingt lignes. <text:span text:style-name="T40">Comme le reste du document, i</text:span><text:span text:style-name="T34">l utilise la </text:span><text:span text:style-name="T35">feuille de style Jres ; ici, </text:span><text:span text:style-name="T34">définition de</text:span><text:span text:style-name="T12"> style « </text:span><text:span text:style-name="T33">Résumé » : </text:span>écrit<text:span text:style-name="T33">ure</text:span> en italique, police avec empattement en taille 12 points. Le titre <text:span text:style-name="T33">utilisant le style </text:span>« <text:span text:style-name="T33">Titre r</text:span>ésumé » (ainsi que le titre « Mots-clefs » ci-dessous) sont en 14 points, gras, sans empattement.<text:change-end text:change-id="ct94407800321840"/></text:p>
|
||
<text:p text:style-name="Titre_20_Mots-clés">Mots-clefs</text:p>
|
||
<text:p text:style-name="Mots-clefs"><text:change-start text:change-id="ct94407800399520"/><text:span text:style-name="T66">logiciel libre, </text:span><text:change-end text:change-id="ct94407800399520"/><text:change-start text:change-id="ct94407800399760"/><text:span text:style-name="T66">IPV6, PKI, CMS, </text:span><text:span text:style-name="T61">Calmar</text:span><text:span text:style-name="T66">…</text:span><text:change-end text:change-id="ct94407800399760"/><text:change-start text:change-id="ct94407800400000"/><text:span text:style-name="T66">licences</text:span><text:change-end text:change-id="ct94407800400000"/><text:change-start text:change-id="ct94407800400240"/><text:span text:style-name="T66">, </text:span><text:span text:style-name="T67">protéomique</text:span><text:change-end text:change-id="ct94407800400240"/></text:p>
|
||
<text:p text:style-name="Mots-clefs"/>
|
||
<text:p text:style-name="P89">% <text:span text:style-name="T94">Ajouter </text:span>Intro : Poser le contexte, présenter le sujet, et faire le lien entre nos parties <text:span text:style-name="T94">puis annoncer le plan.</text:span></text:p>
|
||
<text:h text:style-name="Heading_20_1" text:outline-level="1"><text:change-start text:change-id="ct94407799862176"/>Introduction<text:change-end text:change-id="ct94407799862176"/><text:change-start text:change-id="ct94407800312128"/><text:span text:style-name="T26">Plateforme d’analyses protéomique</text:span><text:change-end text:change-id="ct94407800312128"/><text:change-start text:change-id="ct94407800386752"/><text:span text:style-name="T26">s</text:span></text:h>
|
||
<text:p text:style-name="P37"><text:change-end text:change-id="ct94407800386752"/><text:span text:style-name="T66">La protéomique est l’étude de l’ensemble des protéines produites par une cellule, un organe ou un organisme dans des conditions particulières ou en réponse à un traitement. Elle permet de </text:span><text:span text:style-name="T67">répondre à de nombreuses questions biologiques, de comprendre la physiologie ou différentes pathologie</text:span><text:span text:style-name="T83">s</text:span><text:span text:style-name="T67"> dans de</text:span><text:span text:style-name="T83">s espèces distinctes</text:span><text:span text:style-name="T67"> ou </text:span><text:span text:style-name="T83">dans des </text:span><text:span text:style-name="T67">groupes d’espèces (métaprotéomique). On peut connaître les protéines impliquées dans un processus biologique, ainsi que leur quantité et en déduire les caractéristiques de certains génomes ou lignées, </text:span><text:span text:style-name="T83">ou encore </text:span><text:span text:style-name="T67">comprendre la réponse physiologique liée à un stress</text:span><text:span text:style-name="T83">,</text:span><text:span text:style-name="T67"> par exemple.</text:span></text:p>
|
||
<text:p text:style-name="P19">Depuis 1997, date d’apparition du terme « protéomique », les techniques utilisées n’ont cessé d’évoluer. <text:span text:style-name="T83">Il s'agit néanmoins toujours de mesurer la masse moléculaire des molécules qui pénètrent dans l'instrument: un spectromètre de masse. </text:span><text:span text:style-name="T68">Dans une expérience de protéomique, les échantillons biologiques sont préparés, les protéines extraites, séparées par chromatographie et analysées par spectrométrie de masse</text:span><text:span text:style-name="T83">.</text:span></text:p>
|
||
<text:p text:style-name="P22">Les analyses <text:span text:style-name="T83">par</text:span> spectrométrie de masse produisent de grande<text:span text:style-name="T83">s</text:span> quantité<text:span text:style-name="T83">s</text:span> de données, <text:span text:style-name="T83">directement en sortie de l'instrument. Chaque fabricant a son propre format de données, qui est le plus souvent propriétaire.</text:span> <text:span text:style-name="T83">Ordinairement, les données aux formats propriétaires sont traitées par les logiciels fournis avec l'instrument, eux aussi propriétaires. Comme souvent dans le domaine des formats de fichiers, c</text:span>es formats ne sont pas pérennes<text:span text:style-name="T83"> et les licences d'utilisation des logiciels propriétaires sont très coûteuses</text:span>. <text:span text:style-name="T83">Il y a donc ici un problème majeur d'interopérabilité.</text:span></text:p>
|
||
<text:p text:style-name="P37"><text:span text:style-name="T69">Depuis 2005, </text:span><text:span text:style-name="T83">l</text:span><text:span text:style-name="T69">a plateforme scientifique </text:span><text:span text:style-name="T83">"</text:span><text:span text:style-name="T69">Analyses protéomiques de Paris Sud-Ouest</text:span><text:span text:style-name="T83">"</text:span><text:span text:style-name="T69"> (PAPPSO) a fait le choix du </text:span><text:span text:style-name="T91">L</text:span><text:span text:style-name="T69">ogiciel libre pour garantir la pérennité de ses chaînes de traitement, la reproductibilité des expériences et </text:span><text:span text:style-name="T83">la </text:span><text:span text:style-name="T69">capitalisation de son savoir faire.</text:span><text:change-start text:change-id="ct94407800412240"/></text:p>
|
||
<text:p text:style-name="P23">Il est recommandé d’utiliser <text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">la dernière version stable de Libre Office (au moment de la rédaction, v</text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T65">7</text:span></text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">.</text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T65">0</text:span></text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">.</text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T65">4</text:span></text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">)</text:a>.</text:p>
|
||
<text:p text:style-name="P37"><text:span text:style-name="T13">L</text:span>e document sera <text:span text:style-name="T13">finalement </text:span>transformé en format « Portable Document Format » (.pdf) pour la phase finale de publication.<text:change-end text:change-id="ct94407800412240"/></text:p>
|
||
<text:h text:style-name="P39" text:outline-level="2"><text:change-start text:change-id="ct94407800429200"/>Taille des articles<text:change-end text:change-id="ct94407800429200"/><text:span text:style-name="T21">Transition d</text:span><text:span text:style-name="T22">es</text:span><text:span text:style-name="T21"> logiciel</text:span><text:span text:style-name="T22">s</text:span><text:span text:style-name="T21"> propriétaire</text:span><text:span text:style-name="T22">s</text:span><text:span text:style-name="T21"> au </text:span><text:span text:style-name="T22">L</text:span><text:span text:style-name="T21">ogiciel libre</text:span></text:h>
|
||
<text:p text:style-name="P37"><text:change-start text:change-id="ct94407800430096"/>L’article doit faire entre 5 et 10 pages.<text:change-end text:change-id="ct94407800430096"/><text:span text:style-name="T70">Le passage progressif au </text:span><text:span text:style-name="T83">L</text:span><text:span text:style-name="T70">ogiciel libre a permis une rationalisation de l’utilisation des ressources informatiques. Nous sommes passés de postes dédiés à licence unique</text:span><text:span text:style-name="T83"> pour usage</text:span><text:span text:style-name="T70"> unique </text:span><text:span text:style-name="T71">à une infrastructure collective combinant stockage, calcul et enchaînement des traitements depuis n’importe quel poste de travail.</text:span></text:p>
|
||
<text:p text:style-name="P37"><text:span text:style-name="T72">Durant la période 2005–2015, notre travail a été facilité par la définition de formats standards en protéomique, l’émergence de nombreux logiciels libres dans le domaine </text:span><text:span text:style-name="T72"><text:bookmark-ref text:reference-format="number" text:ref-name="__RefNumPara__4219_4199412181">[1]</text:bookmark-ref></text:span><text:span text:style-name="T72"><text:s/>et le développement en interne de nouvelles solutions </text:span><text:span text:style-name="T83">logicielles </text:span><text:span text:style-name="T73">(PROTICdb </text:span><text:span text:style-name="T73"><text:bookmark-ref text:reference-format="number" text:ref-name="__RefNumPara__4321_4199412181">[2]</text:bookmark-ref></text:span><text:span text:style-name="T73">, mineXpert2 </text:span><text:span text:style-name="T73"><text:bookmark-ref text:reference-format="number" text:ref-name="__RefNumPara__4323_4199412181">[3]</text:bookmark-ref></text:span><text:span text:style-name="T73">, X!TandemPipeline </text:span><text:span text:style-name="T73"><text:bookmark-ref text:reference-format="number" text:ref-name="__RefNumPara__4176_4199412181">[4]</text:bookmark-ref></text:span><text:span text:style-name="T73">, MassChroQ </text:span><text:span text:style-name="T73"><text:bookmark-ref text:reference-format="number" text:ref-name="__RefNumPara__4381_4199412181">[5]</text:bookmark-ref></text:span><text:span text:style-name="T73">)</text:span><text:span text:style-name="T72">.</text:span><text:change-start text:change-id="ct94407800423440"/></text:p>
|
||
<text:h text:style-name="P61" text:outline-level="2"><text:change-end text:change-id="ct94407800423440"/><text:soft-page-break/><text:span text:style-name="T83">Choix du s</text:span>ystème<text:span text:style-name="T83"> d'exploitation</text:span><text:change-start text:change-id="ct94407800445312"/></text:h>
|
||
<text:p text:style-name="P37"><text:change-end text:change-id="ct94407800445312"/><text:span text:style-name="T73">Le choix de PAPPSO s’est porté d’abord sur </text:span><text:span text:style-name="T83">la distribution GNU/Linux </text:span><text:span text:style-name="T73">Ubuntu</text:span><text:span text:style-name="T83">,</text:span><text:span text:style-name="T73"> puis sur Debian. </text:span><text:span text:style-name="T83">Un groupe de développeurs officiels Debian, dont un auteur de ce rapport, s'attache à fournir </text:span><text:span text:style-name="T84">dans la distribution </text:span><text:span text:style-name="T83">de </text:span><text:span text:style-name="T73">nombreux logiciels </text:span><text:span text:style-name="T83">pour la chimie, et en particulier pour la spectrométrie de masse ("team debichem")</text:span><text:span text:style-name="T73">. L</text:span><text:span text:style-name="T83">'intérêt principal de la </text:span><text:span text:style-name="T73">distribution Debian </text:span><text:span text:style-name="T83">est la richesse de son </text:span><text:span text:style-name="T73">offre </text:span><text:span text:style-name="T83">logicielle qui permet de disposer d'</text:span><text:span text:style-name="T73">un socle </text:span><text:span text:style-name="T83">de fonctionnalités robuste</text:span><text:span text:style-name="T73"> </text:span><text:span text:style-name="T83">couvrant les exigences "serveur" et les impératifs "</text:span><text:span text:style-name="T73">bureautique</text:span><text:span text:style-name="T83">"</text:span><text:span text:style-name="T73">. </text:span><text:span text:style-name="T83">Tous les logiciels développés par PAPPSO sont disponibles</text:span><text:span text:style-name="T74"> sous forme de paquets Debian dans </text:span><text:span text:style-name="T83">des</text:span><text:span text:style-name="T74"> dépôt</text:span><text:span text:style-name="T83">s</text:span><text:span text:style-name="T74"> publi</text:span><text:span text:style-name="T83">cs</text:span><text:span text:style-name="T74">. </text:span><text:span text:style-name="T83">Le déploiement des </text:span><text:span text:style-name="T84">logiciels </text:span><text:span text:style-name="T74">sur les serveurs et les postes de travail de l’équipe</text:span><text:span text:style-name="T84"> </text:span><text:span text:style-name="T83">est ainsi </text:span><text:span text:style-name="T84">totalement automatisé.</text:span><text:change-start text:change-id="ct94407800444576"/></text:p>
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<text:h text:style-name="P68" text:outline-level="2"><text:span text:style-name="T21">S</text:span><text:span text:style-name="T18">tockage</text:span></text:h>
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<text:p text:style-name="P28"><text:change-end text:change-id="ct94407800444576"/>Les besoins en stockage de la plateforme évoluent constamment en fonction des progrès techniques. <text:span text:style-name="T84"><text:s/>Chaque nouvelle génération d'instrument apporte des améliorations, en particulier sur la précision de mesure de masse, qui provoquent une augmentation significative du volume des données générées.</text:span> </text:p>
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<text:p text:style-name="P28">Le système de stockage <text:span text:style-name="T84">des données de spectrométrie de masse </text:span>doit permettre une adaptation en continu de l<text:span text:style-name="T84">a</text:span> volumétrie <text:span text:style-name="T84">d'espace disque </text:span>disponible ainsi que <text:span text:style-name="T84">l</text:span>es <text:span text:style-name="T84">meilleures </text:span>performances en lecture<text:span text:style-name="T84"> et </text:span>écriture. Les solutions classiques de type NAS ont été écartées pour éviter la dépendance matérielle et les problèmes liés au renouvellement des équipements.</text:p>
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<text:p text:style-name="P44">Dès 2011, nous avons été parmi les premiers à faire confiance à une solution nouvelle de stockage distribué: Ceph. La principale caractéristique de ce système de stockage est de ne requérir que des serveurs standard. La flexibilité et l'adaptabilité de ce système à des besoins perpétuellement en évolution en ont fait la solution la plus robuste que nous connaissions.</text:p>
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<text:p text:style-name="P37"><draw:frame draw:style-name="fr1" draw:name="Image1" text:anchor-type="char" svg:x="3.106cm" svg:y="0.18cm" svg:width="10.788cm" svg:height="6.396cm" draw:z-index="0"><draw:image xlink:href="deluge/deluge.png" xlink:type="simple" xlink:show="embed" xlink:actuate="onLoad" draw:mime-type="image/png"/>
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</draw:frame></text:p>
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<text:p text:style-name="P45"><text:span text:style-name="T47">Figure </text:span><text:span text:style-name="T47"><text:sequence text:ref-name="refFigure0" text:name="Figure" text:formula="ooow:Figure+1" style:num-format="1">1</text:sequence></text:span><text:span text:style-name="T47"><text:s/>– </text:span><text:span text:style-name="T86">Evolution des besoins de stockage de la plateforme en To/an, comparée à l’évolution des disques durs</text:span><text:change-start text:change-id="ct94407800482704"/></text:p>
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<text:h text:style-name="P59" text:outline-level="2">Calcul</text:h>
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<text:p text:style-name="P30"><text:change-end text:change-id="ct94407800482704"/>La plateforme PAPPSO est spécialisée dans les traitements en protéomique haut débit (nombreux échantillons<text:span text:style-name="T84"> à traiter dans les plus brefs délais</text:span>). Pour assurer la disponibilité de nos moyens de calcul à l’ensemble des utilisateurs, nous utilisons le gestionnaire de processus HTCondor.</text:p>
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<text:p text:style-name="P30"><text:soft-page-break/>Les besoins en calcul évoluent eux aussi en fonction des instruments utilisés. Avec l’évolution des techniques, de nouvelles possibilités sont apparues dans le traitement de données en protéomique exigeant elles aussi des capacités de calcul supplémentaires. Les machines dédiées au calcul doivent être ainsi renouvelées régulièrement et intégrées au fur et à mesure (comme pour le stockage).</text:p>
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<text:h text:style-name="P57" text:outline-level="1">Evolution sur 10 ans</text:h>
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<text:h text:style-name="P62" text:outline-level="2">Matériel</text:h>
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||
<text:p text:style-name="P32">L’<text:span text:style-name="T77">intégration de nouvelles machines de calcul ou de stockage s’est faite de manière transparente. Nous sommes passés d’une capacité de stockage initiale de 18To (3 serveurs R515, disques de 3To) en 2011 à une capacité de 917To (8 serveurs hétérogènes). Le réseau est passé du 1Gb cuivre au 10Gb SFP+. Il n’y a pas eu de transfert de données/migration, pas de modification de l’architecture logique pour les utilisateurs. Le système de fichier</text:span><text:span text:style-name="T84">s</text:span><text:span text:style-name="T77"> cephfs permet un accès direct aux données depuis chaque nœud de calcul</text:span><text:span text:style-name="T84">. Globalement</text:span><text:span text:style-name="T77">, les performances ont suivi les évolutions matérielles (augmentation du débit, augmentation des capacités de calcul). La résistance aux pannes a été mise à rude épreuve (panne électrique, disques ou erreurs humaines) et nous n’avons </text:span><text:span text:style-name="T84">jamais</text:span><text:span text:style-name="T77"> eu de perte de données.</text:span></text:p>
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<text:h text:style-name="P63" text:outline-level="2">Logiciel</text:h>
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<text:p text:style-name="P34">Les systèmes <text:span text:style-name="T84">pour les </text:span>serveurs et <text:span text:style-name="T84">pour les postes </text:span>utilisateur ont été migrés en 2013 de Ubuntu vers Debian. Nous y avons gagné en stabilité et en simplicité lors des mises à jour de version. <text:span text:style-name="T84">La stratégie consiste à maintenir le parc informatique sous Debian "stable" et effectuer le passage à la version successive dans les mois qui suivent sa publication officielle. </text:span>Le stockage centralisé est disponible pour tous les postes dans une arborescence commune,<text:span text:style-name="T84"> via un</text:span> montage automatique sur les nœud de calculs (cephfs via systemd sur les serveurs, sshfs sur les postes clients). Les logiciels sont les mêmes sur les serveurs et les postes utilisateurs. L’accès distant au cluster de calcul se fait avec x2go via <text:span text:style-name="T84">une </text:span>clé publique ssh.</text:p>
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<text:h text:style-name="P64" text:outline-level="2">Scientifique</text:h>
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<text:p text:style-name="P37"><text:span text:style-name="T78">Les analyses de la plateforme ont évolué pour passer de la technique des gels électrophorèses 2D vers les analyses shotgun en spectrométrie de masse. Le traitement d’images 2D était majoritairement effectué avec des logiciels propriétaires sous Windows</text:span><text:span text:style-name="T88">, sur des </text:span><text:span text:style-name="T78">postes dédiés, ce qui limitait les capacités de traitement. </text:span><text:span text:style-name="T88">Le passage progressif à des processus analytiques qui faisaient l'économie de l'étape d'électrophorèse a coincidé avec la révolution du Logiciel libre dans le domaine scientifique au milieu des années 2000. Nous avons alors pu effectuer la transition vers des </text:span><text:span text:style-name="T78">logiciels libres. </text:span><text:span text:style-name="T88">Cependant, les logiciels disponibles étaient principalement des librairies encore imparfaitement dotées des fonctionnalités requises. </text:span><text:span text:style-name="T78">Nous avons </text:span><text:span text:style-name="T88">alors entrepris le </text:span><text:span text:style-name="T78">développe</text:span><text:span text:style-name="T88">ment</text:span><text:span text:style-name="T78"> </text:span><text:span text:style-name="T88">de nos logiciels sur la base des besoins scientifiques particuliers à notre plateforme</text:span><text:span text:style-name="T79">. </text:span><text:span text:style-name="T87">Le logiciel </text:span><text:span text:style-name="T79"><text:s/>MassChroQ</text:span><text:span text:style-name="T87"> est né ainsi, de nos besoins en protéomique quantitative</text:span><text:span text:style-name="T79">. </text:span><text:span text:style-name="T87">Note </text:span><text:span text:style-name="T79">indépendance vis</text:span><text:span text:style-name="T87">-</text:span><text:span text:style-name="T79">à</text:span><text:span text:style-name="T87">-</text:span><text:span text:style-name="T79">vis des formats</text:span><text:span text:style-name="T87"> de données propriétaires </text:span><text:span text:style-name="T79">des fabricants nous a permis de produire un logiciel évolutif et pérenne dès le départ, évitant l’effet « boîte noire ». Ainsi, no</text:span><text:span text:style-name="T85">tre</text:span><text:span text:style-name="T79"> </text:span><text:span text:style-name="T87">offre logicielle a</text:span><text:span text:style-name="T79"> pu être adapté</text:span><text:span text:style-name="T87">e</text:span><text:span text:style-name="T79"> au fur et à mesure aux nouvelles techniques</text:span><text:span text:style-name="T87">, à des </text:span><text:span text:style-name="T79">instruments</text:span><text:span text:style-name="T87"> significativement différents de génération en génération</text:span><text:span text:style-name="T79">, absorbant </text:span><text:span text:style-name="T87">ainsi </text:span><text:span text:style-name="T79">les « chocs » technologiques : doublement des fréquences d’acquisition à chaque génération (3 ans), doublement d</text:span><text:span text:style-name="T87">u pouvoir</text:span><text:span text:style-name="T79"> résoluti</text:span><text:span text:style-name="T87">f</text:span><text:span text:style-name="T79"> (précision de</text:span><text:span text:style-name="T87">s</text:span><text:span text:style-name="T79"> mesure</text:span><text:span text:style-name="T87">s</text:span><text:span text:style-name="T79"> des masse).</text:span></text:p>
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<text:p text:style-name="P37"><text:span text:style-name="T79">La dernière « rupture technologique » </text:span><text:span text:style-name="T87">a été</text:span><text:span text:style-name="T79"> l’apparition du tim</text:span><text:span text:style-name="T84">s</text:span><text:span text:style-name="T79">TOF </text:span><text:span text:style-name="T87">P</text:span><text:span text:style-name="T79">ro du fabricant Bruker. Cet appareil dispose d’une fréquence d’acquisition 10 fois </text:span><text:span text:style-name="T87">supérieure à celle de</text:span><text:span text:style-name="T79"> la génération précédente </text:span><text:soft-page-break/><text:span text:style-name="T79">ainsi que d’une nouvelle dimension de séparation des peptides (mobilité ionique). Fait unique depuis les débuts de la protéomique, Bruker </text:span><text:span text:style-name="T87">nous </text:span><text:span text:style-name="T79">a </text:span><text:span text:style-name="T87">confié </text:span><text:span text:style-name="T79">les spécifications techniques de son </text:span><text:span text:style-name="T87">format de fichier de données</text:span><text:span text:style-name="T79">. Cela nous a permis d’adapter MassChroQ pour pouvoir utiliser </text:span><text:span text:style-name="T87">de manière native</text:span><text:span text:style-name="T79"> les données </text:span><text:span text:style-name="T87">obtenues sur cet instrument</text:span><text:span text:style-name="T79">. No</text:span><text:span text:style-name="T87">tre savoir faire en développment C++ nous a ainsi permis d'obtenir</text:span><text:span text:style-name="T79"> des gains de performances remarquables par rapport aux logiciels commerciaux, ainsi que de meilleurs </text:span><text:span text:style-name="T87">résultats scientifiques</text:span><text:span text:style-name="T79">.</text:span></text:p>
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<text:p text:style-name="P35"/>
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<text:h text:style-name="P58" text:outline-level="1">Bilan <text:span text:style-name="T92">(</text:span>%<text:span text:style-name="T92">eda :</text:span> <text:span text:style-name="T92">mettre ce paragraphe en 2.4 et garder le 3 pour ma partie?)</text:span></text:h>
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<text:p text:style-name="P37"><text:span text:style-name="T80">Le passage au </text:span><text:span text:style-name="T87">L</text:span><text:span text:style-name="T80">ogiciel libre pour </text:span><text:span text:style-name="T87">tous les besoins informatiques de </text:span><text:span text:style-name="T80">la plateforme PAPPSO a permis une maîtrise totale de ses outils, de</text:span><text:span text:style-name="T87">pui</text:span><text:span text:style-name="T85">s</text:span><text:span text:style-name="T80"> la production des données brutes </text:span><text:span text:style-name="T87">ju</text:span><text:span text:style-name="T85">s</text:span><text:span text:style-name="T87">qu’</text:span><text:span text:style-name="T80">à l’interprétation biologique. Les sommes importantes économisées en licences de logiciels propriétaires (20k€ par an) ont été transférées dans la maintenance des ressources de calcul et de stockage. Le savoir faire développé par PAPPSO dans l’analyse protéomique haut débit est reconnu au niveau international (129 articles citant MassChroQ depuis 2011, </text:span><text:span text:style-name="T81">publication d’un article de référence en métaprotéomique </text:span><text:span text:style-name="T81"><text:bookmark-ref text:reference-format="number" text:ref-name="__RefNumPara__4411_4199412181">[6]</text:bookmark-ref></text:span><text:span text:style-name="T85">)</text:span><text:span text:style-name="T81">. Toutes les analyses sont complètement vérifiables et reproductibles, les logiciels étant tous librement </text:span><text:span text:style-name="T87">téléchargeables, </text:span><text:span text:style-name="T81">sous licence GPLv3</text:span><text:span text:style-name="T87">, sans demande préalable</text:span><text:span text:style-name="T81">.</text:span></text:p>
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<text:p text:style-name="P37"/>
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<text:h text:style-name="P78" text:outline-level="1"><text:span text:style-name="T28">Importance et apports du libre dans la recherche scientifique</text:span></text:h>
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<text:h text:style-name="P86" text:outline-level="2"><text:span text:style-name="T28">Importance</text:span></text:h>
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<text:p text:style-name="P96">* <text:span text:style-name="T92">idéologique : </text:span><text:span text:style-name="T97">idée de contribution aux communs, revenir sur l’histoire et la fonction de la recherche publique, notion de liberté et d’éthique du travail public </text:span></text:p>
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<text:p text:style-name="P93">* <text:span text:style-name="T92">scientifique :</text:span><text:span text:style-name="T97">, parler de la campagne public money public code, // avec l’édition libre et culture libre en général</text:span></text:p>
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||
<text:p text:style-name="P93">* <text:span text:style-name="T92">pratico-pragmatique </text:span></text:p>
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<text:h text:style-name="P86" text:outline-level="2"><text:span text:style-name="T28">Apport</text:span><text:span text:style-name="T29">s</text:span></text:h>
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<text:p text:style-name="P94">* <text:span text:style-name="T92">scientifique </text:span><text:span text:style-name="T94">(PAPPSO ci dessus)</text:span></text:p>
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<text:p text:style-name="P94">* <text:span text:style-name="T95">informatique: sécurité, communauté, auditable etc ...</text:span></text:p>
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<text:p text:style-name="P99">* <text:span text:style-name="T94">pratico-pragm</text:span><text:span text:style-name="T95">a</text:span><text:span text:style-name="T94">tique </text:span><text:span text:style-name="T95">(travail communautaire, économies sur les licences et autres coûts?)</text:span></text:p>
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<text:p text:style-name="P99">* <text:span text:style-name="T95">longévité (citer le rapport cour des comptes sur les logiciels en milieu médical)</text:span></text:p>
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<text:p text:style-name="P99"><text:span text:style-name="T94">citer d’autres exemples que Pappso p</text:span><text:span text:style-name="T92">des </text:span>et <text:span text:style-name="T94">des </text:span>contrexemples <text:span text:style-name="T92">(inkscape, plantnet, Rijkmuseum, etc …)</text:span></text:p>
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<text:p text:style-name="P99"><text:tab/>* <text:span text:style-name="T94">parler de œuvre culturelle libre</text:span></text:p>
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<text:p text:style-name="Standard">* <text:span text:style-name="T94">avantages économiques ? </text:span><text:span text:style-name="T92">quelques mots sur les modèles économiques actuels du libre (au passage parler de la SAT)</text:span></text:p>
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<text:p text:style-name="P95">* <text:span text:style-name="T92">idéologique : </text:span><text:span text:style-name="T95">bien commun + lutter contre la marchandisation de la recherche publique</text:span></text:p>
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<text:h text:style-name="P87" text:outline-level="2"><text:soft-page-break/><text:span text:style-name="T28">Comment libérer ses logiciels / infrastructures en pratique ? </text:span></text:h>
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<text:h text:style-name="P87" text:outline-level="2" text:is-list-header="true"><text:span text:style-name="T28">Etat actuel des recommandations et obligations officielles versus difficultés rencontrées</text:span></text:h>
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<text:p text:style-name="Standard">* Recommandations et obligations publiques actuelles</text:p>
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<text:p text:style-name="P98"><text:tab/>* circulaire Eyraut</text:p>
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<text:p text:style-name="P98"><text:tab/>* <text:span text:style-name="T92">Bothorel</text:span></text:p>
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<text:p text:style-name="P98"><text:tab/>* <text:span text:style-name="T92">Etalab</text:span></text:p>
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<text:p text:style-name="P92"><text:tab/>* SILL</text:p>
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||
<text:p text:style-name="P101">versus</text:p>
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||
<text:p text:style-name="P98">* Freins concrets / <text:span text:style-name="T93">réalité</text:span></text:p>
|
||
<text:p text:style-name="P98"><text:tab/>* <text:span text:style-name="T93">marchés fermés</text:span></text:p>
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<text:p text:style-name="P98"><text:span text:style-name="T93">Et enfin </text:span>– comment les déjouer <text:span text:style-name="T93">et procéder en pratique ?</text:span></text:p>
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<text:p text:style-name="P98"><text:s/><text:tab/>* <text:span text:style-name="T96">code.gouv.fr</text:span></text:p>
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<text:p text:style-name="P98"><text:tab/>* https://communs.numerique.gouv.fr/</text:p>
|
||
<text:p text:style-name="P98"><text:tab/>* <text:span text:style-name="T96">Etalab, atelier</text:span><text:span text:style-name="T97">s </text:span><text:span text:style-name="T96"><text:s/>et gazette bluehats : https://communs.numerique.gouv.fr/bluehats/ateliers/</text:span></text:p>
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<text:p text:style-name="P100">(Idée % de conclusion : privacy by default, security by design → libre parce que public, ou alors public money, public interest & public code)</text:p>
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<text:p text:style-name="Standard"/>
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<text:p text:style-name="P102"><text:span text:style-name="T24"/></text:p>
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<text:p text:style-name="P36"/>
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<text:p text:style-name="P36"/>
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<text:p text:style-name="Titre_20_Bibliographie">Bibliographie</text:p>
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<text:list xml:id="list3837479098" text:style-name="Numbering_20_4">
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<text:list-item>
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<text:p text:style-name="P74"><text:bookmark-start text:name="__RefNumPara__4219_4199412181"/>Rusconi F. Free Open Source Software for Protein and Peptide Mass Spectrometry- based Science. Curr Protein Pept Sci, 2 (22) 134-147, 2021 ; https://doi.org/10.2174/1389203722666210118160946<text:bookmark-end text:name="__RefNumPara__4219_4199412181"/></text:p>
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</text:list-item>
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<text:list-item>
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<text:p text:style-name="P75"><text:bookmark-start text:name="__RefNumPara__4321_4199412181"/>Langella O. , Valot B., Jacob D., Balliau T., Flores R., Hoogland C., Joets J., Zivy M.. (2013) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. Proteomics, 9 (13) 1457-66<text:bookmark-end text:name="__RefNumPara__4321_4199412181"/></text:p>
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</text:list-item>
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<text:list-item>
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<text:p text:style-name="P74"><text:bookmark-start text:name="__RefNumPara__4323_4199412181"/>Langella O, Rusconi F. mineXpert2: Full-Depth Visualization and Exploration of MSn Mass Spectrometry Data. J. Am. Soc. Mass Spectrom., 4 (32) 1138-114, mars 2021 ; https://doi.org/10.1021/jasms.0c00402<text:bookmark-end text:name="__RefNumPara__4323_4199412181"/></text:p>
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