Conf-JRES-April-Pappso/article_jres_olivier_amoi.fodt

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   <text:p text:style-name="Title"><text:span text:style-name="T24">Modèle</text:span> de l’article JRES</text:p>
   <text:p text:style-name="Auteurs">Prénom Nom de l’auteur 1</text:p>
   <text:p text:style-name="Laboratoire">Laboratoire ou service</text:p>
   <text:p text:style-name="Adresse"><text:span text:style-name="T50">38</text:span> rue de l’adresse</text:p>
   <text:p text:style-name="Adresse"><text:span text:style-name="T35">13 0</text:span><text:span text:style-name="T50">13</text:span> M<text:span text:style-name="T35">arseille</text:span></text:p>
   <text:p text:style-name="Auteurs">Prénom Nom de l’auteur 2</text:p>
   <text:p text:style-name="Laboratoire">Laboratoire ou service</text:p>
   <text:p text:style-name="Adresse"><text:span text:style-name="T50">11</text:span> <text:span text:style-name="T43">avenue</text:span> d<text:span text:style-name="T43">u</text:span> <text:span text:style-name="T43">comité</text:span></text:p>
   <text:p text:style-name="Adresse"><text:span text:style-name="T35">67 000</text:span> <text:span text:style-name="T35">Strasbourg</text:span></text:p>
   <text:p text:style-name="Titre_20_résumé">Résumé</text:p>
   <text:p text:style-name="Résumé"><text:change-start text:change-id="ct94691391234048"/>Ce document résume les instructions aux auteurs de la conférence JRES.</text:p>
   <text:p text:style-name="Résumé"><text:change-end text:change-id="ct94691391234048"/><text:change-start text:change-id="ct94691391347952"/>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: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: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: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 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="ct94691391347952"/><text:change-start text:change-id="ct94691391364592"/>Le résumé doit faire de quinze à vingt lignes. <text:span text:style-name="T31">Comme le reste du document, i</text:span><text:span text:style-name="T28">l utilise la </text:span><text:span text:style-name="T29">feuille de style Jres ; ici, </text:span><text:span text:style-name="T28">définition de</text:span><text:span text:style-name="T12"> style « </text:span><text:span text:style-name="T27">Résumé » : </text:span>écrit<text:span text:style-name="T27">ure</text:span> en italique, police avec empattement en taille 12 points. Le titre <text:span text:style-name="T27">utilisant le style </text:span>« <text:span text:style-name="T27">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="ct94691391364592"/></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="ct94691391368416"/><text:span text:style-name="T57">logiciel libre, </text:span><text:change-end text:change-id="ct94691391368416"/><text:change-start text:change-id="ct94691391368656"/><text:span text:style-name="T57">IPV6, PKI, CMS, </text:span><text:span text:style-name="T52">Calmar</text:span><text:span text:style-name="T57">…</text:span><text:change-end text:change-id="ct94691391368656"/><text:change-start text:change-id="ct94691391368896"/><text:span text:style-name="T57">licences</text:span><text:change-end text:change-id="ct94691391368896"/><text:change-start text:change-id="ct94691391369136"/><text:span text:style-name="T57">, </text:span><text:span text:style-name="T58">protéomique</text:span><text:change-end text:change-id="ct94691391369136"/></text:p>
   <text:h text:style-name="Heading_20_1" text:outline-level="1"><text:change-start text:change-id="ct94691391277728"/>Introduction<text:change-end text:change-id="ct94691391277728"/><text:change-start text:change-id="ct94691391197920"/><text:span text:style-name="T23">Plateforme d’analyses protéomique</text:span><text:change-end text:change-id="ct94691391197920"/><text:change-start text:change-id="ct94691391357456"/><text:span text:style-name="T23">s</text:span></text:h>
   <text:p text:style-name="P12"><text:span text:style-name="T57">La protéomique </text:span><text:change-end text:change-id="ct94691391357456"/><text:change-start text:change-id="ct94691391358528"/><text:span text:style-name="T57">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="T58">répondre à de nombreuses questions biologiques</text:span><text:change-end text:change-id="ct94691391358528"/><text:change-start text:change-id="ct94691391354496"/><text:span text:style-name="T58">, </text:span><text:change-end text:change-id="ct94691391354496"/><text:change-start text:change-id="ct94691391402848"/><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="T38">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="T52">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="T52">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="ct94691391402848"/><text:change-start text:change-id="ct94691391416144"/><text:span text:style-name="T58">de comprendre la physiologie ou différentes pathologie dans de nombreuses espèces ou groupes d’</text:span><text:change-end text:change-id="ct94691391416144"/><text:change-start text:change-id="ct94691391420272"/><text:span text:style-name="T58">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, comprendre la réponse physiologique liée à un stress par exemple.</text:span></text:p>
   <text:p text:style-name="P11"><text:change-end text:change-id="ct94691391420272"/><text:change-start text:change-id="ct94691391421232"/><text:soft-page-break/>Depuis 1997, date d’apparition du terme « protéomique », les techniques utilisées n’ont cessée<text:change-end text:change-id="ct94691391421232"/><text:change-start text:change-id="ct94691391421856"/> d’évoluer.<text:change-end text:change-id="ct94691391421856"/><text:change-start text:change-id="ct94691391422096"/> <text:span text:style-name="T59">Dans une expérience de protéomique, les échantillons biolo</text:span><text:change-end text:change-id="ct94691391422096"/><text:change-start text:change-id="ct94691391421568"/><text:span text:style-name="T59">giques sont préparés, les protéines extraites, séparées par chromatographie, et analysées par spectrométrie de </text:span><text:change-end text:change-id="ct94691391421568"/><text:change-start text:change-id="ct94691391423520"/><text:span text:style-name="T59">masse.</text:span></text:p>
   <text:p text:style-name="P13"><text:change-end text:change-id="ct94691391423520"/><text:change-start text:change-id="ct94691391423760"/>Les analyses en spectrométrie de masse produisent de grande quantité des données<text:change-end text:change-id="ct94691391423760"/><text:change-start text:change-id="ct94691391424000"/>, dans des formats propriétaires. <text:change-end text:change-id="ct94691391424000"/><text:change-start text:change-id="ct94691391424240"/>Ces données sont elles mêmes traitées le plus souvent par d’autres logiciels propriétaires. <text:change-end text:change-id="ct94691391424240"/><text:change-start text:change-id="ct94691391424480"/>Ces formats ne sont pas pérennes dans le temps<text:change-end text:change-id="ct94691391424480"/><text:change-start text:change-id="ct94691391424720"/>. Les licences sont <text:change-end text:change-id="ct94691391424720"/><text:change-start text:change-id="ct94691391426464"/>coûteuses, <text:span text:style-name="T60">l’interopérabilité entre logiciels est très limitée.</text:span></text:p>
   <text:p text:style-name="P15"><text:change-end text:change-id="ct94691391426464"/><text:change-start text:change-id="ct94691391426704"/><text:span text:style-name="T60">Depuis 2005, La </text:span><text:change-end text:change-id="ct94691391426704"/><text:change-start text:change-id="ct94691391427232"/><text:span text:style-name="T60">plateforme scientifique Analyses protéomiques de Paris Sud-Ouest (PAPPSO) a fait le choix du logiciel libre pour</text:span><text:change-end text:change-id="ct94691391427232"/><text:change-start text:change-id="ct94691391427520"/><text:span text:style-name="T60"> garantir la pérennité de ses chaînes de traitement, la reproductibilité des expérience</text:span><text:change-end text:change-id="ct94691391427520"/><text:change-start text:change-id="ct94691391428320"/><text:span text:style-name="T60">s et </text:span><text:change-end text:change-id="ct94691391428320"/><text:change-start text:change-id="ct94691391428560"/><text:span text:style-name="T60">capitalisation de son savoir faire.</text:span><text:change-end text:change-id="ct94691391428560"/><text:change-start text:change-id="ct94691391429792"/></text:p>
   <text:p text:style-name="P14">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="T56">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="T56">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="T56">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="ct94691391429792"/></text:p>
   <text:h text:style-name="P34" text:outline-level="2"><text:change-start text:change-id="ct94691391433664"/>Taille des articles<text:change-end text:change-id="ct94691391433664"/><text:change-start text:change-id="ct94691391433904"/><text:span text:style-name="T21">Transition du logiciel propriétaire au logiciel libre</text:span><text:change-end text:change-id="ct94691391433904"/></text:h>
   <text:p text:style-name="P16"><text:change-start text:change-id="ct94691391396112"/>L’article doit faire entre 5 et 10 pages.<text:change-end text:change-id="ct94691391396112"/><text:change-start text:change-id="ct94691391362832"/><text:span text:style-name="T61">Le passage progressif aux logiciels libres a permis une rationalisation de l’utilisation des ressources in</text:span><text:change-end text:change-id="ct94691391362832"/><text:change-start text:change-id="ct94691391355584"/><text:span text:style-name="T61">formatiques. Nous sommes passés de postes dédiés, à licences uniques, usage unique </text:span><text:span text:style-name="T62">pour un traitement particulier</text:span><text:change-end text:change-id="ct94691391355584"/><text:change-start text:change-id="ct94691391413536"/><text:span text:style-name="T62"> à une infrastructure collective combinant stockage, calcul et enchaînement </text:span><text:change-end text:change-id="ct94691391413536"/><text:change-start text:change-id="ct94691391309504"/><text:span text:style-name="T62">des traitements depuis n’importe quel poste de travail.</text:span></text:p>
   <text:p text:style-name="P17"><text:change-end text:change-id="ct94691391309504"/><text:change-start text:change-id="ct94691391309136"/><text:span text:style-name="T63">Durant la période 2005 – 2015, notre travail a été facilité par la définition de formats </text:span><text:change-end text:change-id="ct94691391309136"/><text:change-start text:change-id="ct94691391306928"/><text:span text:style-name="T63">standards en protéomique, l’</text:span><text:change-end text:change-id="ct94691391306928"/><text:change-start text:change-id="ct94691391403952"/><text:span text:style-name="T63">émergence de nombreux logiciels libres dans le domaine </text:span><text:span text:style-name="T64">(cf http://dx.doi.org/10.2174/1389203722666210118160946)</text:span><text:span text:style-name="T63"> et le développement en interne de nouvelles solutions </text:span><text:span text:style-name="T64">(PROTICdb, MassChroQ, X!TandemPipeline, </text:span><text:change-end text:change-id="ct94691391403952"/><text:change-start text:change-id="ct94691391399456"/>mineXpert2<text:span text:style-name="T64">)</text:span><text:change-end text:change-id="ct94691391399456"/><text:change-start text:change-id="ct94691391415008"/><text:span text:style-name="T63">.</text:span><text:change-end text:change-id="ct94691391415008"/><text:change-start text:change-id="ct94691391343008"/></text:p>
   <text:h text:style-name="P48" text:outline-level="2"><text:change-end text:change-id="ct94691391343008"/><text:change-start text:change-id="ct94691391410704"/>Système<text:change-end text:change-id="ct94691391410704"/><text:change-start text:change-id="ct94691391316128"/></text:h>
   <text:p text:style-name="P17"><text:span text:style-name="T64">Le choix de PAPPSO</text:span><text:change-end text:change-id="ct94691391316128"/><text:change-start text:change-id="ct94691391357200"/><text:span text:style-name="T64"> s’est porté d’abord sur Ubuntu puis sur Debian. Grâce au travail du groupe « Debichem » de nombreux logiciel</text:span><text:change-end text:change-id="ct94691391357200"/><text:change-start text:change-id="ct94691391356096"/><text:span text:style-name="T64">s nécessaires aux analyses de protéomique sont déjà disponibles. La distribution Debian offre un socle commun côté serveur et bureautique côté client.</text:span><text:change-end text:change-id="ct94691391356096"/><text:change-start text:change-id="ct94691391315392"/><text:span text:style-name="T64"> </text:span><text:change-end text:change-id="ct94691391315392"/><text:change-start text:change-id="ct94691391315024"/><text:span text:style-name="T65">La plateforme diffuse ses propres logiciels sous forme de paque</text:span><text:change-end text:change-id="ct94691391315024"/><text:change-start text:change-id="ct94691391412064"/><text:span text:style-name="T65">ts Debian dans un dépôt accessible publiquement. Cela permet le déploiement complet sur les serveurs et les pos</text:span><text:change-end text:change-id="ct94691391412064"/><text:change-start text:change-id="ct94691391400720"/><text:span text:style-name="T65">tes de travail de l’équipe.</text:span><text:change-end text:change-id="ct94691391400720"/><text:change-start text:change-id="ct94691391319440"/></text:p>
   <text:h text:style-name="P38" 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="ct94691391319440"/><text:change-start text:change-id="ct94691391408000"/>Les besoins en <text:change-end text:change-id="ct94691391408000"/><text:change-start text:change-id="ct94691391319072"/>stockage de la plateforme évoluent constamment en fonction des progrès techniques. <text:s/>La fréquence d<text:change-end text:change-id="ct94691391319072"/><text:change-start text:change-id="ct94691391319808"/>’acquisition et la résolution des spectromètres de masse permettent à chaque génération de grandes avancées<text:change-end text:change-id="ct94691391319808"/><text:change-start text:change-id="ct94691391403248"/> pour augmenter le nombre de protéines identifiées et quantifiées dans des échantillons de plus en plus complexes.<text:change-end text:change-id="ct94691391403248"/><text:change-start text:change-id="ct94691391394848"/></text:p>
   <text:p text:style-name="P18">Le système de stockage doit permettre <text:change-end text:change-id="ct94691391394848"/><text:change-start text:change-id="ct94691391409312"/>une adaptation en continue de la volumétrie disponible ainsi que des performances en lecture/écriture. Les solutions <text:change-end text:change-id="ct94691391409312"/><text:change-start text:change-id="ct94691391356800"/>classiques de type NAS ont été écartées pour éviter la dépendance<text:change-end text:change-id="ct94691391356800"/><text:change-start text:change-id="ct94691391401184"/> matérielle et les problèmes liés aux renouvellement des équipements.</text:p>
   <text:p text:style-name="P18">Depuis 2011, nous utilisons le stockage distri<text:change-end text:change-id="ct94691391401184"/><text:change-start text:change-id="ct94691391405520"/>bué basé sur ceph. <text:span text:style-name="T66">Il apporte une grande</text:span><text:change-end text:change-id="ct94691391405520"/><text:change-start text:change-id="ct94691391440224"/><text:span text:style-name="T66"> flexibilité et une adaptation rapide aux besoins en utilisant des serveurs standards.</text:span><text:change-end text:change-id="ct94691391440224"/><text:change-start text:change-id="ct94691391397408"/></text:p>
   <text:h text:style-name="P39" text:outline-level="2">Calcul</text:h>
   <text:p text:style-name="P19"><text:change-end text:change-id="ct94691391397408"/><text:change-start text:change-id="ct94691391320912"/>La plateforme PAPPSO est spécialisée dans les traitements en protéomique haut débit (nomb<text:change-end text:change-id="ct94691391320912"/><text:change-start text:change-id="ct94691391320544"/>reux échantillons). Pour assurer la disponibilité de nos moyens de calculs à l’ensemble des utilisateurs<text:change-end text:change-id="ct94691391320544"/><text:change-start text:change-id="ct94691391321648"/>, <text:change-end text:change-id="ct94691391321648"/><text:change-start text:change-id="ct94691391323856"/>nous utilisons le gestionnaire <text:change-end text:change-id="ct94691391323856"/><text:change-start text:change-id="ct94691391323120"/>de processus HTCondor.</text:p>
   <text:p text:style-name="P19"><text:soft-page-break/>Les besoins en calcul évoluent eux aussi en fonction <text:change-end text:change-id="ct94691391323120"/><text:change-start text:change-id="ct94691391322384"/>des instruments utilisés. Avec l’évolution des techniques, de nouvelles possibilités sont apparues dans le traitement <text:change-end text:change-id="ct94691391322384"/><text:change-start text:change-id="ct94691391443552"/>de données en protéomique exigeant elles aussi des capacités de calculs supplémentaires. Les machines dédiées au calcul doivent être ainsi renouvelées régu<text:change-end text:change-id="ct94691391443552"/><text:change-start text:change-id="ct94691391443872"/>lièrement et intégrées au fur et à mesure (comme pour le stockage).<text:change-end text:change-id="ct94691391443872"/></text:p>
   <text:h text:style-name="P44" 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="P59">L’<text:span text:style-name="T68">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 cephfs permet un accès direct aux données depuis chaque nœud de calcul, les performances ont suivies 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 pas 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="P63">Les systèmes côté serveurs et utilisateurs 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. Le stockage centralisé est disponible pour tous les postes dans une arborescence commune, 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 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="T69">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. Des postes dédiés nécessaires, ce qui limitait les capacités de traitement. Lors du passage vers les analyses shotgun, les logiciels propriétaires ont pu être avantageusement remplacés par des logiciels libres (identification des protéines avec X!Tandem). En 2008, les capacités des instruments étaient suffisantes pour pouvoir quantifier les protéines directement en spectrométrie de masse, mais les logiciels n’étaient pas adaptés. Nous avons pu développer notre propre </text:span><text:span text:style-name="T70">logiciel de quantification basé sur les idées originales des scientifiques de la plateforme. : MassChroQ. L’indépendance vis à vis des formats et des fabricants nous a permis de produire un logiciel évolutif et pérenne dès le départ, évitant l’effet « boite noire ». Ainsi, nos outils ont pu être adaptés au fur et à mesure aux nouvelles techniques et instruments, absorbant les « chocs » technologiques : doublement des fréquences d’acquisition à chaque génération (3 ans), doublement des capacités de résolution (précision de mesure des masses).</text:span></text:p>
   <text:p text:style-name="P65"><text:span text:style-name="T70">La dernière « rupture technologique » est l’apparition du timTOF pro du fabricant « Bruker ». Cet appareil dispose d’une fréquence d’acquisition 10 fois plus grande que la génération précédente, ainsi que d’une nouvelle dimension de séparation des peptides (mobilité ionique). Fait unique depuis les débuts de la protéomique, Bruker a publié les spécifications techniques de son instrument. Cela nous a permis d’adapter MassChroQ pour pouvoir utiliser directement les données </text:span><text:soft-page-break/><text:span text:style-name="T70">du constructeur, sans conversion. Nous obtenons ainsi des gains de performances remarquables par rapport aux logiciels commerciaux, ainsi que de meilleur</text:span><text:span text:style-name="T71">e</text:span><text:span text:style-name="T70">s quantifications.</text:span></text:p>
   <text:p text:style-name="P65"/>
   <text:h text:style-name="P45" text:outline-level="1"><text:span text:style-name="T25">Bilan</text:span></text:h>
   <text:p text:style-name="P66"><text:span text:style-name="T71">Le passage aux logiciels libres pour la plateforme PAPPSO a permis une maîtrise totale de ses outils, de la production des données brutes à l’interprétation biologique. Les sommes importantes économisées en licences de logiciels propriétaires (20k€ par an) ont été transférées dans la maintenance de ses 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="T72">publication d’un article de référence en métaprotéomique « nature communication » en 2021). Toutes les analyses sont complètement vérifiables et reproductibles, les logiciels étant tous disponibles librement sous licence GPLv3.</text:span></text:p>
   <text:p text:style-name="P66"/>
   <text:p text:style-name="P66"/>
   <text:h text:style-name="P33" text:outline-level="1"><text:span text:style-name="T22">P</text:span><text:span text:style-name="T55">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="T36">et utilisé dans ce </text:span><text:span text:style-name="T53">document</text:span><text:span text:style-name="T36"> </text:span>est dérivé <text:span text:style-name="T36">de celui de base</text:span> <text:span text:style-name="T36">de</text:span> LibreOffice. </text:p>
   <text:p text:style-name="P8"><text:span text:style-name="T36">Les quelques </text:span><text:span text:style-name="T37">modifica</text:span>tions <text:span text:style-name="T36">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, l’auteur 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="T36">celles </text:span><text:span text:style-name="T31">fournies </text:span><text:span text:style-name="T36">par</text:span><text:span text:style-name="T31"> LibreOffice et ainsi </text:span><text:span text:style-name="T14">disponibles </text:span><text:span text:style-name="T36">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="P36" text:outline-level="2"><text:span text:style-name="T19">Utiliser</text:span> les styles <text:span text:style-name="T38">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="T47">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="T35">l’homogénéité des</text:span> numérotation<text:span text:style-name="T38">s</text:span> de<text:span text:style-name="T35">s</text:span> titres, sous-titres, figures est respectée, <text:span text:style-name="T7">mais </text:span><text:span text:style-name="T49">cela</text:span><text:span text:style-name="T7"> garanti</text:span><text:span text:style-name="T49">t</text:span> <text:span text:style-name="T49">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="T47">Le document</text:span><text:span text:style-name="T36"> ne devrait quasiment pas </text:span><text:span text:style-name="T47">faire usage </text:span><text:span text:style-name="T36">de formatage direct. </text:span><text:span text:style-name="T47">L’option</text:span><text:span text:style-name="T40"> « </text:span><text:span text:style-name="T36">Effacer le formatage direct » </text:span><text:span text:style-name="T40">permet de </text:span><text:span text:style-name="T47">s’assurer que </text:span><text:span text:style-name="T40">les styles</text:span> <text:span text:style-name="T47">définis sont bien </text:span><text:span text:style-name="T49">appliqués sans modifications</text:span><text:span text:style-name="T40">.</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="P28">Le code source est Liberation Mono 8 points.</text:p>
   <text:p text:style-name="P28">L’utilisation du style approprié ajoute le cadre et grise le fond.</text:p>
   <text:p text:style-name="Standard"><text:soft-page-break/>Les notes de bas de page sont en 8 points<text:note text:id="ftn2" text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body>
      <text:p text:style-name="P24">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 s’attacheront, 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 l’ordre d’apparition 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="list3049355316" text:style-name="L2">
    <text:list-item>
     <text:p text:style-name="P56">Pour les articles d’une revue, on indiquera obligatoirement les auteurs, le titre de l’article, la revue, le numéro, le volume, l’année 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="P56">Pour les articles dans les actes d’un congrès, on mentionnera obligatoirement les auteurs, le titre de l’article, le titre des actes, l’année. 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="P56">Pour les livres, on citera obligatoirement le ou les auteurs, le titre, l’éditeur et l’année (il est conseillé de rajouter le lieu d’édition) <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 l’article.</text:p>
   <text:p text:style-name="Standard">Pour les références à des pages web, il conviendra d’utiliser 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="P27">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="T54">l’</text:span>article n’en sera que plus apprécié.</text:p>
   <text:h text:style-name="P37" text:outline-level="2">Marques de formatage</text:h>
   <text:p text:style-name="P5"><text:span text:style-name="T9">Pour s’assurer d’une bonne qualité de </text:span><text:span text:style-name="T31">composition</text:span><text:span text:style-name="T9"> </text:span><text:span text:style-name="T31">du document</text:span><text:span text:style-name="T9">, </text:span><text:span text:style-name="T32">il est conseillé d’</text:span><text:span text:style-name="T37">utiliser</text:span><text:span text:style-name="T32"> </text:span>l’a<text:span text:style-name="T31">ffichage des marques de formatage</text:span><text:span text:style-name="T9">. </text:span><text:span text:style-name="T37">Son activation</text:span><text:span text:style-name="T9"> </text:span>permet de <text:span text:style-name="T37">mieux </text:span>détecter quelques erreurs <text:span text:style-name="T37">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="P22"><draw:frame draw:style-name="fr1" draw:name="Image8" text:anchor-type="char" svg:width="0.847cm" svg:height="1.323cm" 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="T38">Figure </text:span><text:span text:style-name="T38"><text:sequence text:ref-name="refFigure6" text:name="Figure" text:formula="ooow:Figure+1" style:num-format="1">1</text:sequence></text:span><text:span text:style-name="T38"><text:s/>– Bouton du bandeau supérieur à activer</text:span></text:p>
   <text:h text:style-name="Heading_20_2" text:outline-level="2"><text:soft-page-break/>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 d’une légende explicite, en italique, non gras, à l’aide du style « Légende – <text:span text:style-name="T34">Figure</text:span> ». Le texte <text:span text:style-name="T54">peut alors y </text:span>fai<text:span text:style-name="T54">re</text:span> référence <text:span text:style-name="T54">ainsi</text:span> : <text:sequence-ref text:reference-format="category-and-value" text:ref-name="refFigure1">Erreur : source de la référence non trouvée</text:sequence-ref>. Il est déconseillé de créer des liens d’objets dynamiques. Il conviendra plutôt d’utiliser le menu « Insertion/Image » disponible dans le menu de LibreOffice.</text:p>
   <text:p text:style-name="P4">En cas d’insertion de figure contenant des couleurs, il est souhaitable d’en assurer la lisibilité sur une imprimante noir et blanc.</text:p>
   <text:h text:style-name="P36" 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="T54">sont utilisés</text:span>, voici quelques exemples qu’il 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 n’utiliser que deux niveaux.</text:p>
   <text:list xml:id="list2995809683" text:style-name="List_20_2">
    <text:list-item>
     <text:p text:style-name="P40">exemple de niveau 1 pour les puces (style « Liste à puces ») ;</text:p>
     <text:list>
      <text:list-item>
       <text:p text:style-name="P40"><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="P40">deuxième exemple de niveau 1 pour les puces.</text:p>
    </text:list-item>
   </text:list>
   <text:list xml:id="list2576247155" text:style-name="L3">
    <text:list-item>
     <text:p text:style-name="P57">exemple de niveau 1 pour les listes numérotées (style « Liste numérotée ») ;</text:p>
     <text:list>
      <text:list-item>
       <text:p text:style-name="P57">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="P57">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="P58">deuxième exemple de niveau 1 pour les listes numérotées.</text:p>
    </text:list-item>
   </text:list>
   <text:p text:style-name="P26">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>
   <text:list xml:id="list1816704164" text:style-name="Numbering_20_4">
    <text:list-item>
     <text:p text:style-name="P42"><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="T26">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>
    </text:list-item>
    <text:list-item>
     <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) :133–139, <text:span text:style-name="T38">j</text:span>anvier 2001.<text:bookmark-end text:name="__RefNumPara__1569_302321950"/></text:p>
    </text:list-item>
    <text:list-item>
     <text:p text:style-name="Bibliographie_20_-_20_Liste_20_de_20_références"><text:bookmark-start text:name="__RefNumPara__2647_302321950"/>Auteur3. Un exemple d’article dans les actes d’une conférence. Dans Actes de la conférence JRES2013, pages 37–49, Montpellier, décembre 2013.<text:bookmark-end text:name="__RefNumPara__2647_302321950"/></text:p>
    </text:list-item>
    <text:list-item>
     <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>
    </text:list-item>
    <text:list-item>
     <text:p text:style-name="Bibliographie_20_-_20_Liste_20_de_20_références">Auteur5. Un autre exemple d’article dans les actes en ligne d’une conférence. Dans Actes du congrès JRES20<text:span text:style-name="T35">1</text:span>7, <text:span text:style-name="T35">Nantes</text:span>, <text:span text:style-name="T38">n</text:span>ovembre 20<text:span text:style-name="T35">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="T35">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>
    </text:list-item>
   </text:list>
  </office:text>
 </office:body>
</office:document>