Conf-JRES-April-Pappso/article_jres_olivier_modifs_filippo.fodt
2022-01-06 10:22:14 +01:00

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<dc:creator>Olivier Langella</dc:creator>
<dc:date>2022-01-04T17:46:00</dc:date>
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<dc:creator>Olivier Langella</dc:creator>
<dc:date>2022-01-04T17:49:03</dc:date>
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<dc:creator>Olivier Langella</dc:creator>
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<dc:creator>Olivier Langella</dc:creator>
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<dc:creator>Olivier Langella</dc:creator>
<dc:date>2022-01-04T17:51:01</dc:date>
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<dc:creator>Olivier Langella</dc:creator>
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<dc:creator>Olivier Langella</dc:creator>
<dc:date>2022-01-04T17:53:08</dc:date>
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<dc:creator>Olivier Langella</dc:creator>
<dc:date>2022-01-04T17:54:23</dc:date>
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<dc:creator>Olivier Langella</dc:creator>
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<dc:creator>Olivier Langella</dc:creator>
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<dc:creator>Olivier Langella</dc:creator>
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<text:p text:style-name="Title"><text:span text:style-name="T27">Modèle</text:span> de larticle JRES</text:p>
<text:p text:style-name="P56">Edlira Nano</text:p>
<text:p text:style-name="Laboratoire">Laboratoire ou service</text:p>
<text:p text:style-name="Adresse"><text:span text:style-name="T54">38</text:span> rue de ladresse</text:p>
<text:p text:style-name="Adresse"><text:span text:style-name="T39">13 0</text:span><text:span text:style-name="T54">13</text:span> M<text:span text:style-name="T39">arseille</text:span></text:p>
<text:p text:style-name="P59">Olivier Langella</text:p>
<text:p text:style-name="P57">Plateforme PAPPSO</text:p>
<text:p text:style-name="P57">Laboratoire GQE-Le Moulon</text:p>
<text:p text:style-name="P57">Ferme du Moulon</text:p>
<text:p text:style-name="P57">91190 Gif-sur-Yvette</text:p>
<text:p text:style-name="P57">France</text:p>
<text:p text:style-name="P57">olivier.langella@universite-paris-saclay.fr</text:p>
<text:p text:style-name="Adresse"/>
<text:p text:style-name="P55"><text:span text:style-name="T23">Filippo</text:span><text:span text:style-name="T78"> </text:span><text:span text:style-name="T23">Rusconi</text:span></text:p>
<text:p text:style-name="P57">Plateforme PAPPSO</text:p>
<text:p text:style-name="P57">Laboratoire GQE-Le Moulon</text:p>
<text:p text:style-name="P57">Ferme du Moulon</text:p>
<text:p text:style-name="P57">91190 Gif-sur-Yvette</text:p>
<text:p text:style-name="P57">France</text:p>
<text:p text:style-name="P57">filippo.rusconi@universite-paris-saclay.fr</text:p>
<text:p text:style-name="Titre_20_résumé">Résumé</text:p>
<text:p text:style-name="P58"><text:change-start text:change-id="ct93877000659456"/>Ce document résume les instructions aux auteurs de la conférence JRES.</text:p>
<text:p text:style-name="P58"><text:change-end text:change-id="ct93877000659456"/><text:change-start text:change-id="ct93877000801824"/>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&apos;aide de l&apos;exemple de la plateforme scientifique Analyses protéomiques de Paris Sud-Ouest(PAPPSO).</text:p>
<text:p text:style-name="P58"><text:line-break/>PAPPSO s&apos;est dotée d&apos;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&apos;intégration de code source tiers.</text:p>
<text:p text:style-name="P58"><text:line-break/>L&apos;apport majeur du Logiciel libre à la recherche publique permet l&apos;utilisation des réseaux et systèmes informatiques. Scientifiquement, l&apos;ouverture du code source et la liberté d&apos;utilisation des logiciels garantissent l&apos;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="P58"><text:line-break/>Comment contribuer efficacement ? Quelles sont les recommandations et obligations pour les 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 <text:soft-page-break/>corriger quelques fausses croyances et promouvoir la construction collective d&apos;une culture libre, au service du bien commun.<text:change-end text:change-id="ct93877000801824"/><text:change-start text:change-id="ct93877000828176"/>Le résumé doit faire de quinze à vingt lignes. <text:span text:style-name="T35">Comme le reste du document, i</text:span><text:span text:style-name="T30">l utilise la </text:span><text:span text:style-name="T31">feuille de style Jres ; ici, </text:span><text:span text:style-name="T30">définition de</text:span><text:span text:style-name="T12"> style « </text:span><text:span text:style-name="T29">Résumé » : </text:span>écrit<text:span text:style-name="T29">ure</text:span> en italique, police avec empattement en taille 12 points. Le titre <text:span text:style-name="T29">utilisant le style </text:span>« <text:span text:style-name="T29">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="ct93877000828176"/></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="ct93877000843712"/><text:span text:style-name="T61">logiciel libre, </text:span><text:change-end text:change-id="ct93877000843712"/><text:change-start text:change-id="ct93877000843952"/><text:span text:style-name="T61">IPV6, PKI, CMS, </text:span><text:span text:style-name="T56">Calmar</text:span><text:span text:style-name="T61"></text:span><text:change-end text:change-id="ct93877000843952"/><text:change-start text:change-id="ct93877000844192"/><text:span text:style-name="T61">licences</text:span><text:change-end text:change-id="ct93877000844192"/><text:change-start text:change-id="ct93877000844432"/><text:span text:style-name="T61">, </text:span><text:span text:style-name="T62">protéomique</text:span><text:change-end text:change-id="ct93877000844432"/></text:p>
<text:h text:style-name="Heading_20_1" text:outline-level="1"><text:change-start text:change-id="ct93877000703088"/>Introduction<text:change-end text:change-id="ct93877000703088"/><text:change-start text:change-id="ct93877000845312"/><text:span text:style-name="T25">Plateforme danalyses protéomique</text:span><text:change-end text:change-id="ct93877000845312"/><text:change-start text:change-id="ct93877000835024"/><text:span text:style-name="T25">s</text:span></text:h>
<text:p text:style-name="P12"><text:span text:style-name="T61">La protéomique </text:span><text:change-end text:change-id="ct93877000835024"/><text:change-start text:change-id="ct93877000833088"/><text:span text:style-name="T61">est létude de lensemble 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="T62">répondre à de nombreuses questions biologiques</text:span><text:change-end text:change-id="ct93877000833088"/><text:change-start text:change-id="ct93877000831040"/><text:span text:style-name="T62">, </text:span><text:change-end text:change-id="ct93877000831040"/><text:change-start text:change-id="ct93877000857472"/><text:span text:style-name="T11">Conformément au </text:span>document « Instructions aux auteurs », <text:span text:style-name="T11">l</text:span>e format <text:span text:style-name="T11">natif de </text:span>LibreOffice <text:span text:style-name="T11">(.odt)</text:span> sera utilisé durant <text:span text:style-name="T12">toute </text:span>la phase de relecture avec le comité de programme.</text:p>
<text:p text:style-name="P12"><text:span text:style-name="T11">L</text:span>e <text:span text:style-name="T11">présent fichier tient lieu de </text:span>modèle <text:span text:style-name="T12">pour les </text:span><text:span text:style-name="T11">article</text:span><text:span text:style-name="T42">s</text:span><text:span text:style-name="T11"> destiné</text:span><text:span text:style-name="T12">s</text:span><text:span text:style-name="T11"> aux </text:span><text:span text:style-name="T12">JRES, </text:span><text:span text:style-name="T11">rédigé</text:span><text:span text:style-name="T12">s</text:span><text:span text:style-name="T11"> avec </text:span><text:span text:style-name="T12">LibreOffice</text:span>. <text:span text:style-name="T11">Il contient également </text:span><text:span text:style-name="T56">quelques</text:span><text:span text:style-name="T11"> </text:span>instructions <text:span text:style-name="T12">sur le cycle de vie de ce document et </text:span><text:span text:style-name="T56">d</text:span><text:span text:style-name="T12">es conseils</text:span> de <text:span text:style-name="T11">mise en page.</text:span><text:change-end text:change-id="ct93877000857472"/><text:change-start text:change-id="ct93877000870496"/><text:span text:style-name="T62">de comprendre la physiologie ou différentes pathologie</text:span><text:change-end text:change-id="ct93877000870496"/><text:span text:style-name="T78">s</text:span><text:change-start text:change-id="ct93877000873472"/><text:span text:style-name="T62"> dans de</text:span><text:change-end text:change-id="ct93877000873472"/><text:span text:style-name="T78">s espèces distinctes</text:span><text:change-start text:change-id="ct93877000876448"/><text:span text:style-name="T62"> ou </text:span><text:change-end text:change-id="ct93877000876448"/><text:span text:style-name="T78">dans des </text:span><text:change-start text:change-id="ct93877000879424"/><text:span text:style-name="T62">groupes d</text:span><text:change-end text:change-id="ct93877000879424"/><text:change-start text:change-id="ct93877000880864"/><text:span text:style-name="T62">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:change-end text:change-id="ct93877000880864"/><text:span text:style-name="T78">ou encore </text:span><text:change-start text:change-id="ct93877000883616"/><text:span text:style-name="T62">comprendre la réponse physiologique liée à un stress</text:span><text:change-end text:change-id="ct93877000883616"/><text:span text:style-name="T78">,</text:span><text:change-start text:change-id="ct93877000889008"/><text:span text:style-name="T62"> par exemple.</text:span></text:p>
<text:p text:style-name="P11"><text:change-end text:change-id="ct93877000889008"/><text:change-start text:change-id="ct93877000889248"/>Depuis 1997, date dapparition du terme « protéomique », les techniques utilisées nont cessé<text:change-end text:change-id="ct93877000889248"/><text:change-start text:change-id="ct93877000889728"/> dévoluer.<text:change-end text:change-id="ct93877000889728"/><text:change-start text:change-id="ct93877000889488"/> <text:change-end text:change-id="ct93877000889488"/><text:span text:style-name="T78">Il s&apos;agit néanmoins toujours de mesurer la masse moléculaire des molécules qui pénètrent dans l&apos;instrument: un spectromètre de masse. </text:span><text:change-start text:change-id="ct93877000889968"/><text:span text:style-name="T63">Dans une expérience de protéomique, les échantillons biolo</text:span><text:change-end text:change-id="ct93877000889968"/><text:change-start text:change-id="ct93877000890208"/><text:span text:style-name="T63">giques sont préparés, les protéines extraites, séparées par chromatographie et analysées par spectrométrie de </text:span><text:change-end text:change-id="ct93877000890208"/><text:change-start text:change-id="ct93877000890448"/><text:span text:style-name="T63">masse</text:span><text:change-end text:change-id="ct93877000890448"/><text:span text:style-name="T78">.</text:span><text:change-start text:change-id="ct93877000891040"/></text:p>
<text:p text:style-name="P13"><text:change-end text:change-id="ct93877000891040"/><text:change-start text:change-id="ct93877000891280"/>Les analyses <text:change-end text:change-id="ct93877000891280"/><text:span text:style-name="T78">par</text:span><text:change-start text:change-id="ct93877000891520"/> spectrométrie de masse produisent de grande<text:change-end text:change-id="ct93877000891520"/><text:span text:style-name="T78">s</text:span><text:change-start text:change-id="ct93877000891760"/> quantité<text:change-end text:change-id="ct93877000891760"/><text:span text:style-name="T78">s</text:span><text:change-start text:change-id="ct93877000892000"/> de données<text:change-end text:change-id="ct93877000892000"/><text:change-start text:change-id="ct93877000892240"/>, <text:change-end text:change-id="ct93877000892240"/><text:span text:style-name="T78">directement en sortie de l&apos;instrument. Chaque fabricant a son propre format de données, qui est le plus souvent propriétaire.</text:span><text:change-start text:change-id="ct93877000892752"/> <text:change-end text:change-id="ct93877000892752"/><text:span text:style-name="T78">Ordinairement, les données aux formats propriétaires sont traitées par les logiciels fournis avec l&apos;instrument, eux aussi propriétaires. Comme souvent dans le domaine des formats de fichiers, c</text:span><text:change-start text:change-id="ct93877000892992"/>es formats ne sont pas pérennes<text:change-end text:change-id="ct93877000892992"/><text:span text:style-name="T78"> et les licences d&apos;utilisation des logiciels propriétaires sont très coûteuses</text:span><text:change-start text:change-id="ct93877000832832"/>. <text:change-end text:change-id="ct93877000832832"/><text:span text:style-name="T78">Il y a donc ici un problème majeur d&apos;interopérabilité.</text:span><text:change-start text:change-id="ct93877000880320"/></text:p>
<text:p text:style-name="P15"><text:change-end text:change-id="ct93877000880320"/><text:change-start text:change-id="ct93877000881264"/><text:span text:style-name="T64">Depuis 2005, </text:span><text:change-end text:change-id="ct93877000881264"/><text:span text:style-name="T78">l</text:span><text:change-start text:change-id="ct93877000782528"/><text:span text:style-name="T64">a </text:span><text:change-end text:change-id="ct93877000782528"/><text:change-start text:change-id="ct93877000828992"/><text:span text:style-name="T64">plateforme scientifique </text:span><text:change-end text:change-id="ct93877000828992"/><text:span text:style-name="T78">&quot;</text:span><text:change-start text:change-id="ct93877000831648"/><text:span text:style-name="T64">Analyses protéomiques de Paris Sud-Ouest</text:span><text:change-end text:change-id="ct93877000831648"/><text:span text:style-name="T78">&quot;</text:span><text:change-start text:change-id="ct93877000739408"/><text:span text:style-name="T64"> (PAPPSO) a fait le choix du logiciel libre pour</text:span><text:change-end text:change-id="ct93877000739408"/><text:change-start text:change-id="ct93877000739040"/><text:span text:style-name="T64"> garantir la pérennité de ses chaînes de traitement, la reproductibilité des expérience</text:span><text:change-end text:change-id="ct93877000739040"/><text:change-start text:change-id="ct93877000740144"/><text:span text:style-name="T64">s et </text:span><text:change-end text:change-id="ct93877000740144"/><text:span text:style-name="T78">la </text:span><text:change-start text:change-id="ct93877000873904"/><text:span text:style-name="T64">capitalisation de son savoir faire.</text:span><text:change-end text:change-id="ct93877000873904"/><text:change-start text:change-id="ct93877000836416"/></text:p>
<text:p text:style-name="P14">Il est recommandé dutiliser <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="T60">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="T60">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="T60">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="P15"><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="ct93877000836416"/></text:p>
<text:h text:style-name="P43" text:outline-level="2"><text:change-start text:change-id="ct93877000860832"/>Taille des articles<text:change-end text:change-id="ct93877000860832"/><text:change-start text:change-id="ct93877000861072"/><text:span text:style-name="T21">Transition d</text:span><text:change-end text:change-id="ct93877000861072"/><text:span text:style-name="T22">es</text:span><text:change-start text:change-id="ct93877000869088"/><text:span text:style-name="T21"> logiciel</text:span><text:change-end text:change-id="ct93877000869088"/><text:span text:style-name="T22">s</text:span><text:change-start text:change-id="ct93877000869328"/><text:span text:style-name="T21"> propriétaire</text:span><text:change-end text:change-id="ct93877000869328"/><text:span text:style-name="T22">s</text:span><text:change-start text:change-id="ct93877000869568"/><text:span text:style-name="T21"> au </text:span><text:change-end text:change-id="ct93877000869568"/><text:span text:style-name="T22">L</text:span><text:change-start text:change-id="ct93877000869808"/><text:span text:style-name="T21">ogiciel libre</text:span><text:change-end text:change-id="ct93877000869808"/></text:h>
<text:p text:style-name="P16"><text:change-start text:change-id="ct93877000742352"/>Larticle doit faire entre 5 et 10 pages.<text:change-end text:change-id="ct93877000742352"/><text:change-start text:change-id="ct93877000745664"/><text:span text:style-name="T65">Le passage progressif au </text:span><text:change-end text:change-id="ct93877000745664"/><text:span text:style-name="T78">L</text:span><text:change-start text:change-id="ct93877000736096"/><text:span text:style-name="T65">ogiciel libre a permis une rationalisation de lutilisation des ressources in</text:span><text:change-end text:change-id="ct93877000736096"/><text:change-start text:change-id="ct93877000859088"/><text:span text:style-name="T65">formatiques. Nous sommes passés de postes dédiés à licence unique</text:span><text:change-end text:change-id="ct93877000859088"/><text:span text:style-name="T78"> pour usage</text:span><text:change-start text:change-id="ct93877000859328"/><text:span text:style-name="T65"> unique </text:span><text:change-end text:change-id="ct93877000859328"/><text:change-start text:change-id="ct93877000862688"/><text:span text:style-name="T66">à une infrastructure collective combinant stockage, calcul et enchaînement </text:span><text:change-end text:change-id="ct93877000862688"/><text:change-start text:change-id="ct93877000865472"/><text:span text:style-name="T66">des traitements depuis nimporte quel poste de travail.</text:span></text:p>
<text:p text:style-name="P24"><text:change-end text:change-id="ct93877000865472"/><text:change-start text:change-id="ct93877000865712"/><text:span text:style-name="T67">Durant la période 20052015, notre travail a été facilité par la définition de formats </text:span><text:change-end text:change-id="ct93877000865712"/><text:change-start text:change-id="ct93877000865952"/><text:span text:style-name="T67">standards en protéomique, l</text:span><text:change-end text:change-id="ct93877000865952"/><text:change-start text:change-id="ct93877000866192"/><text:span text:style-name="T67">émergence de nombreux logiciels libres dans le domaine </text:span><text:span text:style-name="T68">(cf http://dx.doi.org/10.2174/1389203722666210118160946)</text:span><text:span text:style-name="T67"> et le développement en interne de nouvelles solutions </text:span><text:change-end text:change-id="ct93877000866192"/><text:span text:style-name="T78">logicielles </text:span><text:change-start text:change-id="ct93877000866832"/><text:span text:style-name="T68">(PROTICdb</text:span><text:change-end text:change-id="ct93877000866832"/><text:span text:style-name="T68">, mineXpert2</text:span><text:change-start text:change-id="ct93877000867072"/><text:span text:style-name="T68">, X!TandemPipeline</text:span><text:change-end text:change-id="ct93877000867072"/><text:span text:style-name="T68">, MassChroQ</text:span><text:change-start text:change-id="ct93877000854048"/><text:span text:style-name="T68">)</text:span><text:change-end text:change-id="ct93877000854048"/><text:change-start text:change-id="ct93877000855376"/><text:span text:style-name="T67">.</text:span><text:change-end text:change-id="ct93877000855376"/><text:span text:style-name="T67"><office:annotation>
<dc:creator>Filippo Matteo Rusconi</dc:creator>
<dc:date>2022-01-05T16:28:02.339188808</dc:date>
<meta:creator-initials>FMR</meta:creator-initials>
<text:p text:style-name="P83"><text:span text:style-name="T82">Nous avions dit que nous traiterions les applis dans lordre logique : stockage, visualisation, xtpcpp et quanti.</text:span></text:p>
</office:annotation></text:span><text:change-start text:change-id="ct93877000855616"/></text:p>
<text:h text:style-name="P49" text:outline-level="2"><text:change-end text:change-id="ct93877000855616"/><text:span text:style-name="T78">Choix du s</text:span><text:change-start text:change-id="ct93877000956240"/>ystème<text:change-end text:change-id="ct93877000956240"/><text:span text:style-name="T78"> d&apos;exploitation</text:span><text:change-start text:change-id="ct93877000954016"/></text:h>
<text:p text:style-name="P25"><text:span text:style-name="T68">Le choix de PAPPSO</text:span><text:change-end text:change-id="ct93877000954016"/><text:change-start text:change-id="ct93877000921296"/><text:span text:style-name="T68"> sest porté dabord sur </text:span><text:change-end text:change-id="ct93877000921296"/><text:span text:style-name="T78">la distribution GNU/Linux </text:span><text:change-start text:change-id="ct93877000907680"/><text:span text:style-name="T68">Ubuntu</text:span><text:change-end text:change-id="ct93877000907680"/><text:span text:style-name="T78">,</text:span><text:change-start text:change-id="ct93877000920704"/><text:span text:style-name="T68"> puis sur Debian. </text:span><text:change-end text:change-id="ct93877000920704"/><text:span text:style-name="T78">Un groupe de développeurs officiels Debian, dont un auteur de ce rapport, s&apos;attache à fournir </text:span><text:span text:style-name="T79">dans la distribution </text:span><text:span text:style-name="T78">de </text:span><text:change-start text:change-id="ct93877000871248"/><text:span text:style-name="T68">nombreux logiciel</text:span><text:change-end text:change-id="ct93877000871248"/><text:change-start text:change-id="ct93877000854368"/><text:span text:style-name="T68">s </text:span><text:change-end text:change-id="ct93877000854368"/><text:span text:style-name="T78">pour la chimie, et en particulier pour la spectrométrie de masse (&quot;team debichem&quot;)</text:span><text:change-start text:change-id="ct93877000961104"/><text:span text:style-name="T68">. L</text:span><text:change-end text:change-id="ct93877000961104"/><text:span text:style-name="T78">&apos;intérêt principal de la </text:span><text:change-start text:change-id="ct93877000944416"/><text:span text:style-name="T68">distribution Debian </text:span><text:change-end text:change-id="ct93877000944416"/><text:span text:style-name="T78">est la richesse de son </text:span><text:change-start text:change-id="ct93877000967760"/><text:span text:style-name="T68">offre </text:span><text:change-end text:change-id="ct93877000967760"/><text:span text:style-name="T78">logicielle qui permet de disposer d&apos;</text:span><text:change-start text:change-id="ct93877000970320"/><text:span text:style-name="T68">un socle </text:span><text:change-end text:change-id="ct93877000970320"/><text:span text:style-name="T78">de fonctionnalités robuste</text:span><text:change-start text:change-id="ct93877000972880"/><text:span text:style-name="T68"> </text:span><text:change-end text:change-id="ct93877000972880"/><text:span text:style-name="T78">couvrant les exigences &quot;serveur&quot; et les </text:span><text:soft-page-break/><text:span text:style-name="T78">impératifs &quot;</text:span><text:change-start text:change-id="ct93877000976784"/><text:span text:style-name="T68">bureautique</text:span><text:change-end text:change-id="ct93877000976784"/><text:span text:style-name="T78">&quot;</text:span><text:change-start text:change-id="ct93877000979264"/><text:span text:style-name="T68">.</text:span><text:change-end text:change-id="ct93877000979264"/><text:change-start text:change-id="ct93877000980592"/><text:span text:style-name="T68"> </text:span><text:change-end text:change-id="ct93877000980592"/><text:span text:style-name="T78">Tous les logiciels développés par PAPPSO sont disponibles</text:span><text:change-start text:change-id="ct93877000983264"/><text:span text:style-name="T69"> sous forme de paque</text:span><text:change-end text:change-id="ct93877000983264"/><text:change-start text:change-id="ct93877000984768"/><text:span text:style-name="T69">ts Debian dans </text:span><text:change-end text:change-id="ct93877000984768"/><text:span text:style-name="T78">des</text:span><text:change-start text:change-id="ct93877000987568"/><text:span text:style-name="T69"> dépôt</text:span><text:change-end text:change-id="ct93877000987568"/><text:span text:style-name="T78">s</text:span><text:change-start text:change-id="ct93877000988800"/><text:span text:style-name="T69"> publi</text:span><text:change-end text:change-id="ct93877000988800"/><text:span text:style-name="T78">cs</text:span><text:change-start text:change-id="ct93877000992992"/><text:span text:style-name="T69">. </text:span><text:change-end text:change-id="ct93877000992992"/><text:span text:style-name="T78">Le déploiement des </text:span><text:span text:style-name="T79">logiciels </text:span><text:span text:style-name="T69">sur les serveurs et les postes de travail de léquipe</text:span><text:span text:style-name="T79"> </text:span><text:span text:style-name="T78">est ainsi </text:span><text:span text:style-name="T79">totalement automatisé.</text:span><text:change-start text:change-id="ct93877000837216"/></text:p>
<text:h text:style-name="P47" text:outline-level="2"><text:span text:style-name="T21">S</text:span><text:span text:style-name="T18">tockage</text:span></text:h>
<text:p text:style-name="P18"><text:change-end text:change-id="ct93877000837216"/><text:change-start text:change-id="ct93877000945120"/>Les besoins en <text:change-end text:change-id="ct93877000945120"/><text:change-start text:change-id="ct93877000836160"/>stockage de la plateforme évoluent constamment en fonction des progrès techniques. <text:change-end text:change-id="ct93877000836160"/><text:span text:style-name="T79"><text:s/>Chaque nouvelle génération d&apos;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:change-start text:change-id="ct93877000883936"/> <text:change-end text:change-id="ct93877000883936"/><text:change-start text:change-id="ct93877000875152"/></text:p>
<text:p text:style-name="P18">Le système de stockage <text:change-end text:change-id="ct93877000875152"/><text:span text:style-name="T79">des données de spectrométrie de masse </text:span><text:change-start text:change-id="ct93877000946192"/>doit permettre <text:change-end text:change-id="ct93877000946192"/><text:change-start text:change-id="ct93877000840032"/>une adaptation en continu de l<text:change-end text:change-id="ct93877000840032"/><text:span text:style-name="T79">a</text:span><text:change-start text:change-id="ct93877000754496"/> volumétrie <text:change-end text:change-id="ct93877000754496"/><text:span text:style-name="T79">d&apos;espace disque </text:span><text:change-start text:change-id="ct93877000835264"/>disponible ainsi que <text:change-end text:change-id="ct93877000835264"/><text:span text:style-name="T79">l</text:span><text:change-start text:change-id="ct93877000755232"/>es <text:change-end text:change-id="ct93877000755232"/><text:span text:style-name="T79">meilleures </text:span><text:change-start text:change-id="ct93877000755968"/>performances en lecture<text:change-end text:change-id="ct93877000755968"/><text:span text:style-name="T79"> et </text:span><text:change-start text:change-id="ct93877000853504"/>écriture. Les solutions <text:change-end text:change-id="ct93877000853504"/><text:change-start text:change-id="ct93877000738304"/>classiques de type NAS ont été écartées pour éviter la dépendance<text:change-end text:change-id="ct93877000738304"/><text:change-start text:change-id="ct93877000758912"/> matérielle et les problèmes liés au renouvellement des équipements.</text:p>
<text:p text:style-name="P75"><text:change-end text:change-id="ct93877000758912"/>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&apos;adaptabilité de ce système à des besoins perpétuellement en évolution en ont fait la solution la plus robuste que nous connaissions.<text:change-start text:change-id="ct93877001000880"/></text:p>
<text:h text:style-name="P48" text:outline-level="2">Calcul</text:h>
<text:p text:style-name="P19"><text:change-end text:change-id="ct93877001000880"/><text:change-start text:change-id="ct93877000882816"/>La plateforme PAPPSO est spécialisée dans les traitements en protéomique haut débit (nomb<text:change-end text:change-id="ct93877000882816"/><text:change-start text:change-id="ct93877000878224"/>reux échantillons<text:change-end text:change-id="ct93877000878224"/><text:span text:style-name="T79"> à traiter dans les plus brefs délais</text:span><text:change-start text:change-id="ct93877000998288"/>). Pour assurer la disponibilité de nos moyens de calcul à lensemble des utilisateurs<text:change-end text:change-id="ct93877000998288"/><text:change-start text:change-id="ct93877000757440"/>, <text:change-end text:change-id="ct93877000757440"/><text:change-start text:change-id="ct93877000757072"/>nous utilisons le gestionnaire <text:change-end text:change-id="ct93877000757072"/><text:change-start text:change-id="ct93877000997040"/>de processus HTCondor.</text:p>
<text:p text:style-name="P19">Les besoins en calcul évoluent eux aussi en fonction <text:change-end text:change-id="ct93877000997040"/><text:change-start text:change-id="ct93877000755600"/>des instruments utilisés. Avec lévolution des techniques, de nouvelles possibilités sont apparues dans le traitement <text:change-end text:change-id="ct93877000755600"/><text:change-start text:change-id="ct93877000904592"/>de données en protéomique exigeant elles aussi des capacités de calcul supplémentaires. Les machines dédiées au calcul doivent être ainsi renouvelées régu<text:change-end text:change-id="ct93877000904592"/><text:change-start text:change-id="ct93877000754128"/>lièrement et intégrées au fur et à mesure (comme pour le stockage).<text:change-end text:change-id="ct93877000754128"/></text:p>
<text:h text:style-name="P40" text:outline-level="1">Evolution sur 10 ans</text:h>
<text:h text:style-name="P50" text:outline-level="2">Matériel</text:h>
<text:p text:style-name="P20">L<text:span text:style-name="T72">intégration de nouvelles machines de calcul ou de stockage sest faite de manière transparente. Nous sommes passés dune 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 ny a pas eu de transfert de données/migration, pas de modification de larchitecture logique pour les utilisateurs. Le système de fichier</text:span><text:span text:style-name="T79">s</text:span><text:span text:style-name="T72"> cephfs permet un accès direct aux données depuis chaque nœud de calcul</text:span><text:span text:style-name="T79">. Globalement</text:span><text:span text:style-name="T72">, 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 navons </text:span><text:span text:style-name="T79">jamais</text:span><text:span text:style-name="T72"> eu de perte de données.</text:span></text:p>
<text:h text:style-name="P51" text:outline-level="2">Logiciel</text:h>
<text:p text:style-name="P21">Les systèmes <text:span text:style-name="T79">pour les </text:span>serveurs et <text:span text:style-name="T79">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="T79">La stratégie consiste à maintenir le parc informatique sous Debian &quot;stable&quot; 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="T79"> via un</text:span> montage automatique sur <text:soft-page-break/>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. Laccès distant au cluster de calcul se fait avec x2go via <text:span text:style-name="T79">une </text:span>clé publique ssh.</text:p>
<text:h text:style-name="P52" text:outline-level="2">Scientifique</text:h>
<text:p text:style-name="P7"><text:span text:style-name="T73">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 dimages 2D était majoritairement effectué avec des logiciels propriétaires sous Windows</text:span><text:span text:style-name="T80">, sur des </text:span><text:span text:style-name="T73">postes dédiés, ce qui limitait les capacités de traitement. </text:span><text:span text:style-name="T80">Le passage progressif à des processus analytiques qui faisaient l&apos;économie de l&apos;étape d&apos;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="T73">logiciels libres. </text:span><text:span text:style-name="T80">Cependant, les logiciels disponibles étaient principalement des librairies encore imparfaitement dotées des fonctionnalités requises. </text:span><text:span text:style-name="T73">Nous avons </text:span><text:span text:style-name="T80">alors entrepris le </text:span><text:span text:style-name="T73">développe</text:span><text:span text:style-name="T80">ment</text:span><text:span text:style-name="T73"> </text:span><text:span text:style-name="T80">de nos logiciels sur la base des besoins scientifiques particuliers à notre plateforme</text:span><text:span text:style-name="T74">. </text:span><text:span text:style-name="T81">Le logiciel </text:span><text:span text:style-name="T74"><text:s/>MassChroQ</text:span><text:span text:style-name="T81"> est né ainsi, de nos besoins en protéomique quantitative</text:span><text:span text:style-name="T74">. </text:span><text:span text:style-name="T81">Note </text:span><text:span text:style-name="T74">indépendance vis</text:span><text:span text:style-name="T81">-</text:span><text:span text:style-name="T74">à</text:span><text:span text:style-name="T81">-</text:span><text:span text:style-name="T74">vis des formats</text:span><text:span text:style-name="T81"> de données propriétaires </text:span><text:span text:style-name="T74">des fabricants nous a permis de produire un logiciel évolutif et pérenne dès le départ, évitant leffet « boîte noire ». Ainsi, nos </text:span><text:span text:style-name="T81">offre logicielle a</text:span><text:span text:style-name="T74"> pu être adapté</text:span><text:span text:style-name="T81">e</text:span><text:span text:style-name="T74"> au fur et à mesure aux nouvelles techniques</text:span><text:span text:style-name="T81">, à des </text:span><text:span text:style-name="T74">instruments</text:span><text:span text:style-name="T81"> significativement différents de génération en génération</text:span><text:span text:style-name="T74">, absorbant </text:span><text:span text:style-name="T81">ainsi </text:span><text:span text:style-name="T74">les « chocs » technologiques : doublement des fréquences dacquisition à chaque génération (3 ans), doublement d</text:span><text:span text:style-name="T81">u pouvoir</text:span><text:span text:style-name="T74"> résoluti</text:span><text:span text:style-name="T81">f</text:span><text:span text:style-name="T74"> (précision de</text:span><text:span text:style-name="T81">s</text:span><text:span text:style-name="T74"> mesure</text:span><text:span text:style-name="T81">s</text:span><text:span text:style-name="T74"> des masse).</text:span></text:p>
<text:p text:style-name="P22"><text:span text:style-name="T74">La dernière « rupture technologique » </text:span><text:span text:style-name="T81">a été</text:span><text:span text:style-name="T74"> lapparition du tim</text:span><text:span text:style-name="T79">s</text:span><text:span text:style-name="T74">TOF </text:span><text:span text:style-name="T81">P</text:span><text:span text:style-name="T74">ro du fabricant Bruker. Cet appareil dispose dune fréquence dacquisition 10 fois </text:span><text:span text:style-name="T81">supérieure à celle de</text:span><text:span text:style-name="T74"> la génération précédente ainsi que dune nouvelle dimension de séparation des peptides (mobilité ionique). Fait unique depuis les débuts de la protéomique, Bruker </text:span><text:span text:style-name="T81">nous </text:span><text:span text:style-name="T74">a </text:span><text:span text:style-name="T81">confié </text:span><text:span text:style-name="T74">les spécifications techniques de son </text:span><text:span text:style-name="T81">format de fichier de données</text:span><text:span text:style-name="T74">. Cela nous a permis dadapter MassChroQ pour pouvoir utiliser </text:span><text:span text:style-name="T81">de manière native</text:span><text:span text:style-name="T74"> les données </text:span><text:span text:style-name="T81">obtenues sur cet instrument</text:span><text:span text:style-name="T74">. No</text:span><text:span text:style-name="T81">tre savoir faire en développment C++ nous a ainsi permis d&apos;obtenir</text:span><text:span text:style-name="T74"> des gains de performances remarquables par rapport aux logiciels commerciaux, ainsi que de meilleurs </text:span><text:span text:style-name="T81">résultats scientifiques</text:span><text:span text:style-name="T74">.</text:span></text:p>
<text:p text:style-name="P22"/>
<text:h text:style-name="P41" text:outline-level="1">Bilan</text:h>
<text:p text:style-name="P23"><text:span text:style-name="T75">Le passage au </text:span><text:span text:style-name="T81">L</text:span><text:span text:style-name="T75">ogiciel libre pour </text:span><text:span text:style-name="T81">tous les besoins informatiques de </text:span><text:span text:style-name="T75">la plateforme PAPPSO a permis une maîtrise totale de ses outils, de</text:span><text:span text:style-name="T81">pui</text:span><text:span text:style-name="T75"> la production des données brutes </text:span><text:span text:style-name="T81">juques </text:span><text:span text:style-name="T75">à linterprétation 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 lanalyse protéomique haut débit est reconnu au niveau international (129 articles citant MassChroQ depuis 2011, </text:span><text:span text:style-name="T76">publication dun article de référence en métaprotéomique </text:span><text:span text:style-name="T32">N</text:span><text:span text:style-name="T33">ature communication</text:span><text:span text:style-name="T32">s</text:span><text:span text:style-name="T76"> </text:span><text:span text:style-name="T81">, </text:span><text:span text:style-name="T76">2021). Toutes les analyses sont complètement vérifiables et reproductibles, les logiciels étant tous librement </text:span><text:span text:style-name="T81">téléchargeables, </text:span><text:span text:style-name="T76">sous licence GPLv3</text:span><text:span text:style-name="T81">, sans demande préalable</text:span><text:span text:style-name="T76">.</text:span></text:p>
<text:p text:style-name="P23"/>
<text:h text:style-name="P39" text:outline-level="1"><text:span text:style-name="T24">P</text:span><text:span text:style-name="T59">résentation générale</text:span></text:h>
<text:p text:style-name="P8">Le style <text:span text:style-name="T14">fourni </text:span><text:span text:style-name="T40">et utilisé dans ce </text:span><text:span text:style-name="T57">document</text:span><text:span text:style-name="T40"> </text:span>est dérivé <text:span text:style-name="T40">de celui de base</text:span> <text:span text:style-name="T40">de</text:span> LibreOffice. </text:p>
<text:p text:style-name="P8"><text:soft-page-break/><text:span text:style-name="T40">Les quelques </text:span><text:span text:style-name="T41">modifica</text:span>tions <text:span text:style-name="T40">sont </text:span>regroupées dans l<text:span text:style-name="T14">a hiérarchie de</text:span> styles « → Jres », <text:span text:style-name="T14">sous le </text:span>style de paragraphe par défaut. Autant que possible, lauteur doit s<text:span text:style-name="T14">y</text:span> conformer. <text:span text:style-name="T14">Les fontes utilisées sont </text:span><text:span text:style-name="T40">celles </text:span><text:span text:style-name="T35">fournies </text:span><text:span text:style-name="T40">par</text:span><text:span text:style-name="T35"> LibreOffice et ainsi </text:span><text:span text:style-name="T14">disponibles </text:span><text:span text:style-name="T40">en standard </text:span><text:span text:style-name="T14">sur chaque plate-forme (Windows, Mac, Linux &amp; BSD).</text:span></text:p>
<text:h text:style-name="P45" text:outline-level="2"><text:span text:style-name="T19">Utiliser</text:span> les styles <text:span text:style-name="T42">définis</text:span></text:h>
<text:p text:style-name="P9"><text:span text:style-name="T7">C</text:span>haque <text:span text:style-name="T51">élément</text:span> qui compose le document doit être lié à un style bien précis : les titres, les figures, les bibliographies…</text:p>
<text:p text:style-name="P9">Pour appliquer le style (taille et police) qui correspond, il suffit de se positionner sur la ligne ou bien de sélectionner la chaîne de caractères et dans le bandeau en haut en gauche du menu de sélectionner le style correspondant. Ainsi, le style lui sera automatiquement appliqué. <text:span text:style-name="T7">Il est important de respecter le style fourni ; non seulement </text:span><text:span text:style-name="T39">lhomogénéité des</text:span> numérotation<text:span text:style-name="T42">s</text:span> de<text:span text:style-name="T39">s</text:span> titres, sous-titres, figures est respectée, <text:span text:style-name="T7">mais </text:span><text:span text:style-name="T53">cela</text:span><text:span text:style-name="T7"> garanti</text:span><text:span text:style-name="T53">t</text:span> <text:span text:style-name="T53">aussi </text:span>que <text:span text:style-name="T7">votre article soit homogène avec le reste de la conférence</text:span>.</text:p>
<text:p text:style-name="P9"><text:span text:style-name="T51">Le document</text:span><text:span text:style-name="T40"> ne devrait quasiment pas </text:span><text:span text:style-name="T51">faire usage </text:span><text:span text:style-name="T40">de formatage direct. </text:span><text:span text:style-name="T51">Loption</text:span><text:span text:style-name="T44"> « </text:span><text:span text:style-name="T40">Effacer le formatage direct » </text:span><text:span text:style-name="T44">permet de </text:span><text:span text:style-name="T51">sassurer que </text:span><text:span text:style-name="T44">les styles</text:span> <text:span text:style-name="T51">définis sont bien </text:span><text:span text:style-name="T53">appliqués sans modifications</text:span><text:span text:style-name="T44">.</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:span text:style-name="T20">P</text:span>olices</text:h>
<text:p text:style-name="_2d__3e__20_JRES">La police de base est de type Liberation Serif en 1<text:span text:style-name="T1">2</text:span> points.</text:p>
<text:p text:style-name="P6"><text:span text:style-name="T12">Les titres </text:span><text:span text:style-name="T14">utilisent, selon la section, des déclinaisons de </text:span><text:span text:style-name="T16">Liberation Sans </text:span><text:span text:style-name="T17">de 20, 14 et 12 points </text:span>avec numérotation arabe, rappel du numéro de section et séparation par un point. L<text:span text:style-name="T14">a </text:span>couleur <text:span text:style-name="T15">bleu sombre RGB (0,51,95), #00335F</text:span> <text:span text:style-name="T14">est utilisée</text:span>.</text:p>
<text:p text:style-name="Standard">Les titres de niveaux inférieurs <text:span text:style-name="T14">à 3 </text:span>sont à éviter, pour des raisons de lisibilité.</text:p>
<text:p text:style-name="P34">Le code source est Liberation Mono 8 points.</text:p>
<text:p text:style-name="P34">Lutilisation du style approprié ajoute le cadre et grise le fond.</text:p>
<text:p text:style-name="Standard">Les notes de bas de page sont en 8 points<text:note text:id="ftn1" text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body>
<text:p text:style-name="P30">Comme ceci</text:p></text:note-body></text:note>.</text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2">Typographie</text:h>
<text:p text:style-name="Standard">Les auteurs sattacheront, dans la mesure du possible, à respecter les règles typographiques françaises.</text:p>
<text:p text:style-name="P3">En particulier, ils veilleront à utiliser des espaces insécables avant les ponctuations hautes (; : ! ?) et des guillemets français (<text:span text:style-name="T3">«»</text:span>).</text:p>
<text:p text:style-name="Standard">Il est suggéré aux auteurs de lire les leçons de typographie <text:bookmark-ref text:reference-format="number-all-superior" text:ref-name="__RefNumPara__1586_302321950">[1]</text:bookmark-ref><text:s/>de Jacques André.</text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2">Bibliographie</text:h>
<text:p text:style-name="Standard">La bibliographie sera réalisée avec le style « Bibliographie Liste de références » avec des numéros et dans lordre dapparition dans le texte.</text:p>
<text:p text:style-name="Standard">Pour faire référence à un élément de cette liste, il faut insérer un « Renvoi » en sélectionnant dans la partie « Paragraphes numérotés » le numéro de la référence de cet élément, par exemple <text:bookmark-ref text:reference-format="number-all-superior" text:ref-name="__RefNumPara__1569_302321950">[2]</text:bookmark-ref>.</text:p>
<text:list xml:id="list4040878399" text:style-name="L1">
<text:list-item>
<text:p text:style-name="P76"><text:soft-page-break/>Pour les articles dune revue, on indiquera obligatoirement les auteurs, le titre de larticle, la revue, le numéro, le volume, lannée et le mois. Voir <text:bookmark-ref text:reference-format="number-all-superior" text:ref-name="__RefNumPara__1569_302321950">[2]</text:bookmark-ref>.</text:p>
</text:list-item>
<text:list-item>
<text:p text:style-name="P76">Pour les articles dans les actes dun congrès, on mentionnera obligatoirement les auteurs, le titre de larticle, le titre des actes, lannée. Voir <text:bookmark-ref text:reference-format="number-all-superior" text:ref-name="__RefNumPara__2647_302321950">[3]</text:bookmark-ref> : (le mois et le lieu sont facultatifs mais conseillés).</text:p>
</text:list-item>
<text:list-item>
<text:p text:style-name="P76">Pour les livres, on citera obligatoirement le ou les auteurs, le titre, léditeur et lannée (il est conseillé de rajouter le lieu dédition) <text:bookmark-ref text:reference-format="number-all-superior" text:ref-name="__RefNumPara__2649_302321950">[4]</text:bookmark-ref>.</text:p>
</text:list-item>
</text:list>
<text:h text:style-name="Heading_20_2" text:outline-level="2">Adresses électroniques</text:h>
<text:p text:style-name="Standard">Pour diminuer les risques de moissonnage, aucune adresse mail ne figurera dans larticle.</text:p>
<text:p text:style-name="Standard">Pour les références à des pages web, il conviendra dutiliser le menu « Insertion/Hyperlien » disponible dans le menu de LibreOffice, par exemple comme ceci : <text:a xlink:type="simple" xlink:href="http://www.jres.org/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">http://www.jres.org</text:a>.</text:p>
<text:h text:style-name="Heading_20_1" text:outline-level="1">Mise en page</text:h>
<text:p text:style-name="P33">Tout comme le respect des règles de typographie, la mise en page du document est parfois négligée. Un document soigné augmente le confort de lecture et permet de se concentrer sur le fond plutôt que la forme : <text:span text:style-name="T58">l</text:span>article nen sera que plus apprécié.</text:p>
<text:h text:style-name="P46" text:outline-level="2">Marques de formatage</text:h>
<text:p text:style-name="P5"><text:span text:style-name="T9">Pour sassurer dune bonne qualité de </text:span><text:span text:style-name="T35">composition</text:span><text:span text:style-name="T9"> </text:span><text:span text:style-name="T35">du document</text:span><text:span text:style-name="T9">, </text:span><text:span text:style-name="T36">il est conseillé d</text:span><text:span text:style-name="T41">utiliser</text:span><text:span text:style-name="T36"> </text:span>la<text:span text:style-name="T35">ffichage des marques de formatage</text:span><text:span text:style-name="T9">. </text:span><text:span text:style-name="T41">Son activation</text:span><text:span text:style-name="T9"> </text:span>permet de <text:span text:style-name="T41">mieux </text:span>détecter quelques erreurs <text:span text:style-name="T41">souvent </text:span><text:span text:style-name="T9">peu visibles (doubles espaces, </text:span><text:span text:style-name="T5">retours de lignes ou </text:span><text:span text:style-name="T9">caractères parasites).</text:span></text:p>
<text:p text:style-name="P28"><draw:frame draw:style-name="fr1" draw:name="Image8" text:anchor-type="char" svg:width="0.3335in" svg:height="0.5209in" draw:z-index="0"><draw:image draw:mime-type="image/png">
<office:binary-data>iVBORw0KGgoAAAANSUhEUgAAACAAAAAyCAYAAAA9ZNlkAAAACXBIWXMAAA7HAAAOwwFc/upy
AAABUUlEQVR4nGP5+/fvf4YBBCwDafmoA0YdMOqAUQeMOgDsgAuvB9gB4pwDVxe9/M44CKJg
1AGjDiBG0Z+//xiOX3vGcOb2S4bnb78x/PzzlyjDJ2TYMzAyMlLmgI/ffjLM2nKJ4cnbrwQt
FOLlYFCVEmBQlRZkUJHiJ2g5QQeAfI7PcpgPC2YcZPj//z9DXbQ5UZYS7QBQsBPjc0oAXgec
ufWSppYTdMCLD98H1gH0AHgdICHAyfDg1WfaOgCUenEBEzUJvA5A14vPLOz6CYSAhaYEw4kb
wJzwhnY5Aa8DWJiZGFK9dBlmb7tMM0cQTIT8XOwMhYFGDCeuv2A4DcyWz99/Zfj5m7iimCoO
AAFmYEhY60iBMQgUzjxEcnxT5ABaglEHjDpg1AFkOaA/3Q4vn+YOoCYYUAeAStORHQKDwwEv
vg2wA/RFBnSwfBBEwYh3AAAof3HPQZH9CQAAAABJRU5ErkJggg==
</office:binary-data>
</draw:image>
</draw:frame><text:span text:style-name="T42">Figure </text:span><text:span text:style-name="T42"><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="T42"><text:s/> Bouton du bandeau supérieur à activer</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2">Figures</text:h>
<text:p text:style-name="P4">Les figures sont de préférence insérées à proximité du texte qui y fait référence. Elles sont numérotées et suivies dune légende explicite, en italique, non gras, à laide du style « Légende <text:span text:style-name="T38">Figure</text:span> ». Le texte <text:span text:style-name="T58">peut alors y </text:span>fai<text:span text:style-name="T58">re</text:span> référence <text:span text:style-name="T58">ainsi</text:span> : <text:sequence-ref text:reference-format="category-and-value" text:ref-name="ref0">Error: Reference source not found</text:sequence-ref>. Il est déconseillé de créer des liens dobjets dynamiques. Il conviendra plutôt dutiliser le menu « Insertion/Image » disponible dans le menu de LibreOffice.</text:p>
<text:p text:style-name="P4">En cas dinsertion de figure contenant des couleurs, il est souhaitable den assurer la lisibilité sur une imprimante noir et blanc.</text:p>
<text:h text:style-name="P45" text:outline-level="2">Puces et listes numérotées</text:h>
<text:p text:style-name="P9">Si les styles « Puce 1 » et « Liste » <text:span text:style-name="T58">sont utilisés</text:span>, voici quelques exemples quil est utile de rappeler et de respecter.</text:p>
<text:p text:style-name="P9">Que ce soit pour les puces ou les listes numérotées, il est conseillé de nutiliser que deux niveaux.</text:p>
<text:list xml:id="list927400281" text:style-name="List_20_2">
<text:list-item>
<text:p text:style-name="P53">exemple de niveau 1 pour les puces (style « Liste à puces ») ;</text:p>
<text:list>
<text:list-item>
<text:p text:style-name="P53"><text:span text:style-name="T3">e</text:span>xemple de niveau 2 pour les puces (style « Liste à puces Niveau 2 ») ;</text:p>
</text:list-item>
</text:list>
</text:list-item>
<text:list-item>
<text:p text:style-name="P53">deuxième exemple de niveau 1 pour les puces.</text:p>
</text:list-item>
</text:list>
<text:list xml:id="list2662960029" text:style-name="L2">
<text:list-item>
<text:p text:style-name="P77"><text:soft-page-break/>exemple de niveau 1 pour les listes numérotées (style « Liste numérotée ») ;</text:p>
<text:list>
<text:list-item>
<text:p text:style-name="P77">exemple de niveau 2 pour les listes numérotées (style « Liste numérotée Niveau 2 ») ;</text:p>
</text:list-item>
<text:list-item>
<text:p text:style-name="P77">deuxième exemple de niveau 2 pour les listes numérotées ;</text:p>
</text:list-item>
</text:list>
</text:list-item>
<text:list-item>
<text:p text:style-name="P78">deuxième exemple de niveau 1 pour les listes numérotées.</text:p>
</text:list-item>
</text:list>
<text:p text:style-name="P32">Annexe</text:p>
<text:p text:style-name="Standard">Les auteurs ajoutent, si nécessaire, une annexe avec une section non numérotée.</text:p>
<text:p text:style-name="Titre_20_Bibliographie">Bibliographie</text:p>
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<text:p text:style-name="P60"><text:bookmark-start text:name="__RefNumPara__1586_302321950"/>André J.. Petites leçons de typographie, 1990 ; <text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">http//jacques-andr</text:a><text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T28">e</text:span></text:a><text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">.fr/faqtypo/lessons.pd</text:a><text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T2">f</text:span></text:a>.<text:bookmark-end text:name="__RefNumPara__1586_302321950"/></text:p>
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<text:p text:style-name="Bibliographie_20_-_20_Liste_20_de_20_références"><text:bookmark-start text:name="__RefNumPara__1569_302321950"/>Auteur1 et Auteur2. Un article dans une revue. Nom de la revue, 3(10) :133139, <text:span text:style-name="T42">j</text:span>anvier 2001.<text:bookmark-end text:name="__RefNumPara__1569_302321950"/></text:p>
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<text:p text:style-name="Bibliographie_20_-_20_Liste_20_de_20_références"><text:bookmark-start text:name="__RefNumPara__2647_302321950"/>Auteur3. Un exemple darticle dans les actes dune conférence. Dans Actes de la conférence JRES2013, pages 3749, Montpellier, décembre 2013.<text:bookmark-end text:name="__RefNumPara__2647_302321950"/></text:p>
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<text:p text:style-name="Bibliographie_20_-_20_Liste_20_de_20_références"><text:bookmark-start text:name="__RefNumPara__2649_302321950"/>Auteur4. Les réseaux hauts débits. Presse Académique, 2002.<text:bookmark-end text:name="__RefNumPara__2649_302321950"/></text:p>
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<text:p text:style-name="Bibliographie_20_-_20_Liste_20_de_20_références">Auteur5. Un autre exemple darticle dans les actes en ligne dune conférence. Dans Actes du congrès JRES20<text:span text:style-name="T39">1</text:span>7, <text:span text:style-name="T39">Nantes</text:span>, <text:span text:style-name="T42">n</text:span>ovembre 20<text:span text:style-name="T39">1</text:span>7 ; <text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">http://20</text:a><text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T39">1</text:span></text:a><text:a xlink:type="simple" xlink:href="http://2007.jres.org/articles/123.pdf" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">7.jres.org/articles/123.pdf</text:a>.</text:p>
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