Conf-JRES-April-Pappso/article_jres_olivier_amoi.fodt

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<text:p text:style-name="Title"><text:span text:style-name="T31">Modèle</text:span> de larticle JRES</text:p>
<text:p text:style-name="P65">Edlira Nano</text:p>
<text:p text:style-name="P88">Associations April, </text:p>
<text:p text:style-name="P88">La Quadrature Du Net, </text:p>
<text:p text:style-name="P88">informaticienne indépendante</text:p>
<text:p text:style-name="P88"><text:a xlink:type="simple" xlink:href="mailto:eda@mutu.net" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">eda@mutu.net</text:a> / eda@laquadrature.net</text:p>
<text:p text:style-name="P70">Olivier Langella</text:p>
<text:p text:style-name="P71">Plateforme PAPPSO</text:p>
<text:p text:style-name="P71">Laboratoire GQE-Le Moulon</text:p>
<text:p text:style-name="P71">Ferme du Moulon</text:p>
<text:p text:style-name="P71">91190 Gif-sur-Yvette</text:p>
<text:p text:style-name="P71">France</text:p>
<text:p text:style-name="P71">olivier.langella@universite-paris-saclay.fr</text:p>
<text:p text:style-name="P40"/>
<text:p text:style-name="P41"><text:span text:style-name="T23">Filippo</text:span><text:span text:style-name="T83"> </text:span><text:span text:style-name="T23">Rusconi</text:span></text:p>
<text:p text:style-name="P71">Plateforme PAPPSO</text:p>
<text:p text:style-name="P71">Laboratoire GQE-Le Moulon</text:p>
<text:p text:style-name="P71">Ferme du Moulon</text:p>
<text:p text:style-name="P71">91190 Gif-sur-Yvette</text:p>
<text:p text:style-name="P71">France</text:p>
<text:p text:style-name="P71">filippo.rusconi@universite-paris-saclay.fr</text:p>
<text:p text:style-name="Titre_20_résumé">Résumé</text:p>
<text:p text:style-name="P43"><text:change-start text:change-id="ct94407799201200"/>Ce document résume les instructions aux auteurs de la conférence JRES.</text:p>
<text:p text:style-name="P43"><text:change-end text:change-id="ct94407799201200"/>Le Logiciel libre et la recherche publique partagent un objectif : le bien commun, au service de tous. Cette présentation revient sur ce que sont le bien commun et la science ouverte pour essayer de les analyser à l&apos;aide de l&apos;exemple de la plateforme scientifique Analyses protéomiques de Paris Sud-Ouest(PAPPSO).</text:p>
<text:p text:style-name="P43"><text:line-break/>PAPPSO s&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="P43"><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="P43"><text:line-break/>Comment contribuer efficacement ? Quelles sont les recommandations et obligations pour les <text:soft-page-break/>établissements publics ? Quelle licence choisir ? Comment une licence copyleft peut-elle aussi séduire les partenaires privés ? Nous apporterons des réponses et des éléments de réflexion pour corriger quelques fausses croyances et promouvoir la construction collective d&apos;une culture libre, au service du bien commun.<text:change-start text:change-id="ct94407800321840"/>Le résumé doit faire de quinze à vingt lignes. <text:span text:style-name="T40">Comme le reste du document, i</text:span><text:span text:style-name="T34">l utilise la </text:span><text:span text:style-name="T35">feuille de style Jres ; ici, </text:span><text:span text:style-name="T34">définition de</text:span><text:span text:style-name="T12"> style « </text:span><text:span text:style-name="T33">Résumé » : </text:span>écrit<text:span text:style-name="T33">ure</text:span> en italique, police avec empattement en taille 12 points. Le titre <text:span text:style-name="T33">utilisant le style </text:span>« <text:span text:style-name="T33">Titre r</text:span>ésumé » (ainsi que le titre « Mots-clefs » ci-dessous) sont en 14 points, gras, sans empattement.<text:change-end text:change-id="ct94407800321840"/></text:p>
<text:p text:style-name="Titre_20_Mots-clés">Mots-clefs</text:p>
<text:p text:style-name="Mots-clefs"><text:change-start text:change-id="ct94407800399520"/><text:span text:style-name="T66">logiciel libre, </text:span><text:change-end text:change-id="ct94407800399520"/><text:change-start text:change-id="ct94407800399760"/><text:span text:style-name="T66">IPV6, PKI, CMS, </text:span><text:span text:style-name="T61">Calmar</text:span><text:span text:style-name="T66"></text:span><text:change-end text:change-id="ct94407800399760"/><text:change-start text:change-id="ct94407800400000"/><text:span text:style-name="T66">licences</text:span><text:change-end text:change-id="ct94407800400000"/><text:change-start text:change-id="ct94407800400240"/><text:span text:style-name="T66">, </text:span><text:span text:style-name="T67">protéomique</text:span><text:change-end text:change-id="ct94407800400240"/></text:p>
<text:p text:style-name="Mots-clefs"/>
<text:p text:style-name="P89">% <text:span text:style-name="T94">Ajouter </text:span>Intro : Poser le contexte, présenter le sujet, et faire le lien entre nos parties <text:span text:style-name="T94">puis annoncer le plan.</text:span></text:p>
<text:h text:style-name="Heading_20_1" text:outline-level="1"><text:change-start text:change-id="ct94407799862176"/>Introduction<text:change-end text:change-id="ct94407799862176"/><text:change-start text:change-id="ct94407800312128"/><text:span text:style-name="T26">Plateforme danalyses protéomique</text:span><text:change-end text:change-id="ct94407800312128"/><text:change-start text:change-id="ct94407800386752"/><text:span text:style-name="T26">s</text:span></text:h>
<text:p text:style-name="P37"><text:change-end text:change-id="ct94407800386752"/><text:span text:style-name="T66">La protéomique est 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="T67">répondre à de nombreuses questions biologiques, de comprendre la physiologie ou différentes pathologie</text:span><text:span text:style-name="T83">s</text:span><text:span text:style-name="T67"> dans de</text:span><text:span text:style-name="T83">s espèces distinctes</text:span><text:span text:style-name="T67"> ou </text:span><text:span text:style-name="T83">dans des </text:span><text:span text:style-name="T67">groupes despèces (métaprotéomique). On peut connaître les protéines impliquées dans un processus biologique, ainsi que leur quantité et en déduire les caractéristiques de certains génomes ou lignées, </text:span><text:span text:style-name="T83">ou encore </text:span><text:span text:style-name="T67">comprendre la réponse physiologique liée à un stress</text:span><text:span text:style-name="T83">,</text:span><text:span text:style-name="T67"> par exemple.</text:span></text:p>
<text:p text:style-name="P19">Depuis 1997, date dapparition du terme « protéomique », les techniques utilisées nont cessé dévoluer. <text:span text:style-name="T83">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:span text:style-name="T68">Dans une expérience de protéomique, les échantillons biologiques sont préparés, les protéines extraites, séparées par chromatographie et analysées par spectrométrie de masse</text:span><text:span text:style-name="T83">.</text:span></text:p>
<text:p text:style-name="P22">Les analyses <text:span text:style-name="T83">par</text:span> spectrométrie de masse produisent de grande<text:span text:style-name="T83">s</text:span> quantité<text:span text:style-name="T83">s</text:span> de données, <text:span text:style-name="T83">directement en sortie de l&apos;instrument. Chaque fabricant a son propre format de données, qui est le plus souvent propriétaire.</text:span> <text:span text:style-name="T83">Ordinairement, les données aux formats propriétaires sont traitées par les logiciels fournis avec l&apos;instrument, eux aussi propriétaires. Comme souvent dans le domaine des formats de fichiers, c</text:span>es formats ne sont pas pérennes<text:span text:style-name="T83"> et les licences d&apos;utilisation des logiciels propriétaires sont très coûteuses</text:span>. <text:span text:style-name="T83">Il y a donc ici un problème majeur d&apos;interopérabilité.</text:span></text:p>
<text:p text:style-name="P37"><text:span text:style-name="T69">Depuis 2005, </text:span><text:span text:style-name="T83">l</text:span><text:span text:style-name="T69">a plateforme scientifique </text:span><text:span text:style-name="T83">&quot;</text:span><text:span text:style-name="T69">Analyses protéomiques de Paris Sud-Ouest</text:span><text:span text:style-name="T83">&quot;</text:span><text:span text:style-name="T69"> (PAPPSO) a fait le choix du </text:span><text:span text:style-name="T91">L</text:span><text:span text:style-name="T69">ogiciel libre pour garantir la pérennité de ses chaînes de traitement, la reproductibilité des expériences et </text:span><text:span text:style-name="T83">la </text:span><text:span text:style-name="T69">capitalisation de son savoir faire.</text:span><text:change-start text:change-id="ct94407800412240"/></text:p>
<text:p text:style-name="P23">Il est recommandé 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="T65">7</text:span></text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">.</text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T65">0</text:span></text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">.</text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link"><text:span text:style-name="T65">4</text:span></text:a><text:a xlink:type="simple" xlink:href="https://fr.libreoffice.org/download/telecharger-libreoffice/" text:style-name="Internet_20_link" text:visited-style-name="Visited_20_Internet_20_Link">)</text:a>.</text:p>
<text:p text:style-name="P37"><text:span text:style-name="T13">L</text:span>e document sera <text:span text:style-name="T13">finalement </text:span>transformé en format « Portable Document Format » (.pdf) pour la phase finale de publication.<text:change-end text:change-id="ct94407800412240"/></text:p>
<text:h text:style-name="P39" text:outline-level="2"><text:change-start text:change-id="ct94407800429200"/>Taille des articles<text:change-end text:change-id="ct94407800429200"/><text:span text:style-name="T21">Transition d</text:span><text:span text:style-name="T22">es</text:span><text:span text:style-name="T21"> logiciel</text:span><text:span text:style-name="T22">s</text:span><text:span text:style-name="T21"> propriétaire</text:span><text:span text:style-name="T22">s</text:span><text:span text:style-name="T21"> au </text:span><text:span text:style-name="T22">L</text:span><text:span text:style-name="T21">ogiciel libre</text:span></text:h>
<text:p text:style-name="P37"><text:change-start text:change-id="ct94407800430096"/>Larticle doit faire entre 5 et 10 pages.<text:change-end text:change-id="ct94407800430096"/><text:span text:style-name="T70">Le passage progressif au </text:span><text:span text:style-name="T83">L</text:span><text:span text:style-name="T70">ogiciel libre a permis une rationalisation de lutilisation des ressources informatiques. Nous sommes passés de postes dédiés à licence unique</text:span><text:span text:style-name="T83"> pour usage</text:span><text:span text:style-name="T70"> unique </text:span><text:span text:style-name="T71">à une infrastructure collective combinant stockage, calcul et enchaînement des traitements depuis nimporte quel poste de travail.</text:span></text:p>
<text:p text:style-name="P37"><text:span text:style-name="T72">Durant la période 2005