Conf-JRES-April-Pappso/amue/article_amue.fodt

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<office:meta><meta:initial-creator>Olivier Langella</meta:initial-creator><meta:creation-date>2022-07-04T09:54:55.776571844</meta:creation-date><dc:date>2022-07-06T12:37:58.044156812</dc:date><dc:creator>Filippo Matteo Rusconi</dc:creator><meta:editing-duration>PT3H43M12S</meta:editing-duration><meta:editing-cycles>12</meta:editing-cycles><meta:generator>LibreOffice/7.0.4.2$Linux_X86_64 LibreOffice_project/00$Build-2</meta:generator><meta:document-statistic meta:table-count="0" meta:image-count="0" meta:object-count="0" meta:page-count="1" meta:paragraph-count="8" meta:word-count="435" meta:character-count="2999" meta:non-whitespace-character-count="2572"/></office:meta>
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<text:p text:style-name="Standard">Logiciels libres <text:span text:style-name="T5">et recherche scientifique</text:span> : à la recherche du bien commun</text:p>
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<text:p text:style-name="Standard">Le logiciel libre et la recherche publique partagent un <text:span text:style-name="T5">même </text:span>objectif : le bien commun, au service de tous. Les deux semblent faits l&apos;un pour l&apos;autre. Mais qu&apos;en est-il en réalité?</text:p>
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<text:p text:style-name="P2">Dans les laboratoires, <text:span text:style-name="T5">par exemple</text:span>, loutil informatique est souvent basé sur des logiciels propriétaires, <text:span text:style-name="T5">à cause de linertie</text:span> et <text:span text:style-name="T5">d</text:span>es <text:span text:style-name="T5">fabricants</text:span> de matériel scientifique qui ne fournissent les logiciels et le support que pour <text:span text:style-name="T5">la</text:span> plateforme <text:span text:style-name="T5">de bureautique dominante</text:span>.</text:p>
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<text:p text:style-name="P1"><text:span text:style-name="T1">Au travers de l</text:span>exemple de la plateforme de protéomique PAPPSO (Plateforme d&apos;Analyses Protéomique de Paris Sud-Ouest http://pappso.inra.fr/), <text:span text:style-name="T2">nous avons démontré quune transition vers le logiciel libre était possible </text:span><text:span text:style-name="T5">tout au</text:span><text:span text:style-name="T2"> bénéfice </text:span><text:span text:style-name="T5">de </text:span><text:span text:style-name="T2">la « </text:span><text:span text:style-name="T5">S</text:span><text:span text:style-name="T2">cience ouverte »</text:span>.</text:p>
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<text:p text:style-name="Standard">PAPPSO s&apos;est dotée au fil des années et des besoins, d&apos;une infrastructure informatique complète : réseau, serveurs, stockage, calcul et postes personnels, basée en totalité sur des systèmes <text:span text:style-name="T5">dexploitation </text:span>et <text:span text:style-name="T5">des </text:span>logiciels libres. <text:span text:style-name="T5">L</text:span>a plateforme développe elle-même plusieurs logiciels sous licence libre et en particulier toute la chaîne de traitement<text:span text:style-name="T5"> </text:span>des données <text:span text:style-name="T5">de </text:span>protéomique,<text:span text:style-name="T5"> </text:span>depuis leur <text:span text:style-name="T5">production par</text:span> <text:span text:style-name="T5">le</text:span>s instruments jusqu&apos;à leur analyse statistique finale : <text:span text:style-name="T6">mineXpert2</text:span>, <text:span text:style-name="T6">X!</text:span><text:span text:style-name="T7">T</text:span><text:span text:style-name="T6">andemPipeline</text:span>, <text:span text:style-name="T6">MassChroQ</text:span>, <text:span text:style-name="T6">PROTICdb</text:span> (liste complète des logiciels <text:span text:style-name="T5">à</text:span> http://pappso.inra.fr/bioinfo/).</text:p>
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<text:p text:style-name="P4"><text:span text:style-name="T2">C</text:span>e choix s&apos;est opéré <text:span text:style-name="T8">inéluctablement</text:span>, dans un environnement scientifique où la maîtrise fine des logiciels est <text:span text:style-name="T8">consubstantielle à</text:span> <text:span text:style-name="T5">la</text:span> reproductibilité des traitements, <text:span text:style-name="T8">où leur </text:span>optimis<text:span text:style-name="T8">ation</text:span> <text:span text:style-name="T5">en </text:span>améliore le fonctionnement<text:span text:style-name="T5">, </text:span><text:span text:style-name="T8">pour, </text:span><text:span text:style-name="T7">in fine</text:span><text:span text:style-name="T5">, </text:span>faire avancer l<text:span text:style-name="T5">es</text:span> technique<text:span text:style-name="T5">s </text:span><text:span text:style-name="T8">et </text:span><text:span text:style-name="T5">la recherche</text:span>. <text:span text:style-name="T5">Cette</text:span><text:span text:style-name="T2"> maîtrise apporte à PAPPSO une agilité extrême, </text:span><text:span text:style-name="T8">lui </text:span><text:span text:style-name="T2">permet</text:span><text:span text:style-name="T5">t</text:span><text:span text:style-name="T8">ant</text:span><text:span text:style-name="T2"> </text:span><text:span text:style-name="T8">d</text:span><text:span text:style-name="T2">e développe</text:span><text:span text:style-name="T8">r</text:span><text:span text:style-name="T5"> </text:span><text:span text:style-name="T2">ses propres idées, </text:span><text:span text:style-name="T8">de s</text:span><text:span text:style-name="T2">adapt</text:span><text:span text:style-name="T8">er</text:span><text:span text:style-name="T2"> </text:span><text:span text:style-name="T5">rapide</text:span><text:span text:style-name="T8">ment</text:span><text:span text:style-name="T5"> </text:span><text:span text:style-name="T2">aux nouvelles techniques </text:span><text:span text:style-name="T8">et aux nouveaux instruments</text:span><text:span text:style-name="T2"> sans </text:span><text:span text:style-name="T8">fragilisation</text:span><text:span text:style-name="T5"> de</text:span><text:span text:style-name="T2"> son organisation. </text:span><text:span text:style-name="T3">Depuis </text:span><text:span text:style-name="T5">dix</text:span><text:span text:style-name="T3"> ans, le logiciel libre et lutilisation des formats </text:span><text:span text:style-name="T5">de données </text:span><text:span text:style-name="T3">standard nous a </text:span><text:span text:style-name="T8">ainsi</text:span><text:span text:style-name="T3"> permis dassurer la continuité des projets, </text:span><text:span text:style-name="T8">avec à la clef dimportantes </text:span><text:span text:style-name="T5">contributions</text:span><text:span text:style-name="T4"> à lécosystème du logiciel libre en protéomique </text:span><text:span text:style-name="T5">(a</text:span><text:span text:style-name="T4">lgorithmes </text:span><text:span text:style-name="T5">novateurs), </text:span><text:span text:style-name="T8">en partie grâce à la réutilisation </text:span><text:span text:style-name="T5">de</text:span><text:span text:style-name="T4"> fonctionnalités </text:span><text:span text:style-name="T8">libres </text:span><text:span text:style-name="T4">développées par dautres équipes.</text:span></text:p>
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<text:p text:style-name="Standard">De nombreux logiciels libres de pointe sont issus du monde de la recherche publique, comme en témoigne en partie la forge du code source du secteur public. De nombreux logiciels connus et utilisés largement en sont issus : la distribution Debian GNU/Linux, le langage OC<text:span text:style-name="T5">a</text:span>ml, Scilab, Sympa, Lodel <text:span text:style-name="T5">et</text:span> VLC, <text:span text:style-name="T8">ce dernier</text:span> né d&apos;un projet d&apos;étudiants de <text:span text:style-name="T5">lEcole c</text:span>entrale Paris.</text:p>
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<text:p text:style-name="Standard">L&apos;environnement de la recherche publique, éloigné d&apos;impératifs économiques immédiats, en contact direct avec un milieu hautement qualifié, riche de par la diversité des savoirs et la qualité des échanges, constitue un atout pour le développement efficace de<text:span text:style-name="T8">s</text:span> logiciels libres. C&apos;est d&apos;ailleurs cet environnement <text:span text:style-name="T8">et</text:span> ce savoir faire que les entreprises privées apprécient et recherchent <text:span text:style-name="T5">dans le secteur public de la recherche</text:span>.</text:p>
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