User:Timothee Flutre/Notebook/CR AGAP/2014/01/10: Difference between revisions

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==Bookmarks for INRA, CIRAD and SupAgro==
==Bookmarks for INRA, CIRAD, SupAgro, and more==
* I have been hired by the INRA, in the department "Plant biology and breeding" (BAP in French), but the laboratory in which I am working, AGAP, depends on several research institutes: INRA, CIRAD and Montpellier SupAgro. The primary goal of such an institutional organization is to build a lab to "encompass a wide range of skills and be a leading platform for applied plant biology and genetics", which is a good endevaour. However, on a daily basis, this is particularly challenging as information is scattered around, and each person needs its own access rights to the tools used by each institute. This web page hence aims at providing a list of links to navigate easily among all sources of information.
* I have been hired by the INRA, in the department "Plant biology and breeding" (BAP in French), but the laboratory in which I am working, AGAP, depends on several research institutes: INRA, CIRAD and SupAgro. The primary goal of such an institutional organization is to build a lab to "encompass a wide range of skills and be a leading platform for applied plant biology and genetics", which is a good endevaour. However, on a daily basis, this is particularly challenging as information is scattered around, and each person needs its own access rights to the tools used by each institute. This web page hence aims at providing a list of links to navigate easily among all sources of information.


* '''Institutions:'''
* '''Institutions:'''
** [https://en.wikipedia.org/wiki/Institut_national_de_la_recherche_agronomique INRA]: [http://www.inra.fr/en web site], [https://intranet.inra.fr/ intranet], [https://intranet.annuaire.inra.fr/accueil.action directory] (annuaire)
** [https://en.wikipedia.org/wiki/Institut_national_de_la_recherche_agronomique INRA]: [http://www.inra.fr/en web site], [https://intranet.inra.fr/ intranet], [https://intranet.annuaire.inra.fr/accueil.action directory]
*** BAP: [http://www.bap.inra.fr/en web site] and [https://intranet6.inra.fr/bap intranet]
*** BAP: [http://www.bap.inra.fr/en web site], [https://intranet6.inra.fr/bap intranet]
*** centre of Montpellier: [http://www.montpellier.inra.fr/ web site] and [https://intranet.montpellier.inra.fr/ intranet]
*** centre of Montpellier: [http://www.montpellier.inra.fr/ web site], [https://intranet.montpellier.inra.fr/ intranet], [http://www.supagro.fr/web/UserFiles/Flash/plan-campus.html map], [https://web.supagro.inra.fr/intranet/trombino/ directory]
** [https://en.wikipedia.org/wiki/Centre_de_coop%C3%A9ration_internationale_en_recherche_agronomique_pour_le_d%C3%A9veloppement CIRAD]: [http://www.cirad.fr/en/home-page web site] and [https://intranet.cirad.fr/ intranet]
** [https://en.wikipedia.org/wiki/Centre_de_coop%C3%A9ration_internationale_en_recherche_agronomique_pour_le_d%C3%A9veloppement CIRAD]: [http://www.cirad.fr/en/home-page web site], [https://intranet.cirad.fr/ intranet] ([https://sso.cirad.fr/login authentification] if outside CIRAD), [http://intranet-search.cirad.fr/agents directory], [http://www.cirad.fr/var/cirad/storage/original/application/05038b0c55a79c3d0f2f420aa7025e4d.swf map]
** [https://fr.wikipedia.org/wiki/Centre_international_d%27%C3%A9tudes_sup%C3%A9rieures_en_sciences_agronomiques SupAgro]: [http://www.supagro.fr/web/en/ web site] and [https://www.supagro.fr/web/intranet/ intranet]
** [https://fr.wikipedia.org/wiki/Centre_international_d%27%C3%A9tudes_sup%C3%A9rieures_en_sciences_agronomiques SupAgro]: [http://www.supagro.fr/web/en/ web site], [https://www.supagro.fr/web/intranet/ intranet], [http://www.supagro.fr/web/UserFiles/Flash/plan-campus.html map], [https://web.supagro.inra.fr/intranet/trombino/ directory]
** AGAP: [http://umr-agap.cirad.fr/en web site] and [https://intranet-umr-agap.cirad.fr/ intranet]
** AGAP: [http://umr-agap.cirad.fr/en web site], [https://intranet-umr-agap.cirad.fr/ intranet]
** [http://en.wikipedia.org/wiki/Agropolis_Fondation Agropolis Fondation]: [http://www.agropolis-fondation.fr/ web site]


* '''Tools:'''
* '''Tools:'''
** visioconference for academics: [http://evo.renater.fr/ SeeVogh]
** SupAgro:
** SupAgro provides my most basic tools:
*** webmail: [https://webmail.supagro.inra.fr/services/portal/ Horde]
*** email: [https://web.supagro.inra.fr/horde3/imp/login.php Horde]
*** [http://www.montpellier.inra.fr/intranet/intracampus/reservations/viti/ bookings] for team "vigne" (rooms, videoproj, etc; Aurelie Pedrola for Ferguson's room), [https://www1.montpellier.inra.fr/intranet/intracampus/reservations/R_Tableau_reservation.php?type=salle_arbo room MISTEA/AGAP], [https://reservations-vehicules.inra.fr/ cars]
*** mailing lists: [https://listes.supagro.inra.fr/sympa/ Sympa]
*** mailing lists: [https://listes.supagro.inra.fr/sympa/ Sympa] (umr-agap-daav, umr-agap-ge2pop, umr-davem-bioinfo)
** at INRA's national level, the DSI (direction des systèmes informatiques) also provides a bunch of [https://intranet6.inra.fr/systemes-information/Offre-de-service useful tools], among which
*** [http://web.supagro.inra.fr/pmb/opac_css/index.php library]
*** mailing lists: [https://listes.inra.fr/sympa Sympa]
*** VPN client: [https://web.supagro.inra.fr/intranet/uic/index.php?post/2014/09/11/Installation-OpenVPN OpenVPN], [https://web.supagro.inra.fr/intranet/BAO/Forti/ Fortinet]
*** IT help: [https://web.supagro.inra.fr/intranet/uic/index.php EIC]
** INRA (notably via the [https://intranet6.inra.fr/systemes-information/Offre-de-service DSI])
*** mailing lists: [https://listes.inra.fr/sympa Sympa] (such as the one on [https://listes.inra.fr/sympa/info/selection-genomique-inra genomic selection], [https://listes.inra.fr/sympa/info/nirs NIRS])
*** spaces for collaborative projects: [https://collaboratif.inra.fr/silverpeas Silverpeas]
*** shared online calendars: [https://agenda.inra.fr/ YaZiba]
*** shared online calendars: [https://agenda.inra.fr/ YaZiba]
*** shared large files: [https://echange-fichiers.inra.fr/ FileX]
*** shared large files: [https://echange-fichiers.inra.fr/ FileX]
*** spaces for collaborative projects: [https://collaboratif.inra.fr/silverpeas Silverpeas]
*** visioconference: [https://wiki.inra.fr/wiki/visio/ visio]
*** files in cloud: [https://intranet6.inra.fr/systemes-information/Offre-de-service/Communication-et-echanges/Partage-securise-de-fichiers-cloud?ticket=ST-387973-tfJxa2hv5PQYceEgObWr-cas YazibaDrive]
*** management of external agents: [https://www7.inra.fr/admin_appli/ldap/main LDAP Externes] ([http://doctech.jouy.inra.fr/inra/informatique/projets/Ldap/Utilisation_Application_gestion_LDAP_externe.pdf doc])
*** spaces for collaborative editing: [https://wiki.inra.fr/ Xwiki]
*** spaces for collaborative editing: [https://wiki.inra.fr/ Xwiki]
*** [https://belinra.inra.fr/ libraries]
*** [http://www.mathinfo.inra.fr/en maths-info]
*** [https://elearning.formation-permanente.inra.fr/ ''e''learning] of the Formation Permanente
*** PEPI [http://www6.inra.fr/pepi/Ingenierie-Bio-Informatique-et-Statistique-pour-les-donnees-haut-debit-IBIS IBIS] (bioinfo and biostat)
*** missions: [https://intranet.inra.fr/Produits/ulysse/Ulysse/ Ulysse]
*** leave days: [https://rh-production.s2i.inra.fr/hra-space/saml HR Access]
*** bug tracker: [https://intranet.inra.fr/mantis-INRA/login_page.php Mantis]
** CIRAD:
*** mailing lists: [http://sympa.cirad.fr/sympa/ Sympa] (biostatsagap: first log in to CIRAD intranet, then log in to Sympa)
*** personal online space: [https://espace-perso.cirad.fr/c/portal/login Espace perso]
*** spaces for collaborative projects: [https://collaboratif.cirad.fr/share/page/repository Alfresco]
*** shared large files: [http://filex.cirad.fr/ FileX]
*** online talks: [http://amphi-tv.cirad.fr/ AmphiTV] (possibly live)
*** VPN client: [ftp://ftp.cirad.fr/cirad/fortinet/ Fortinet]
** visioconference for academics: [http://evo.renater.fr/ SeeVogh], [https://jitsi.visio.renater.fr/ Jitsi]


* '''Computing platforms:''' especially high performance computing resources (HPC, that is computer clusters)
* '''Computing platforms:''' especially high performance computing resources (HPC, that is computer clusters)
** URGI: [https://urgi.versailles.inra.fr/ web site], [https://urgi.versailles.inra.fr/Platform/User-support get account] (need fixed IP, then ssh -Y tflutre@gpi.versailles.inra.fr), support (urgi-support@versailles.inra.fr)
** URGI: [https://urgi.versailles.inra.fr/ web site], [https://urgi.versailles.inra.fr/Platform/User-support get account] (need fixed IP or [https://acces-versailles.versailles.inra.fr/ not], then ssh -Y tflutre@saruman.versailles.inra.fr), support (urgi-support@versailles.inra.fr)
** SouthGreen: [http://www.southgreen.fr/ web site], [http://www.southgreen.fr/content/computer-facilities get account] (need [https://vpn-montpellier.cirad.fr/ VPN], then ssh -Y flutre@marmadais.cirad.fr), [http://www.southgreen.fr/content/report-problem support]
** SouthGreen: [http://www.southgreen.fr/ web site], [http://www.southgreen.fr/content/computer-facilities get account] (need [https://vpn-montpellier.cirad.fr/ VPN], can also be open via the Fortinet client from SupAgro via ./forticlientsslvpn_cli --server vpn-montpellier.cirad.fr:443 --vpnuser timothee.flutre, and then ssh -Y flutre@marmadais.cirad.fr), [http://www.southgreen.fr/content/report-problem support], use qlogin -q bigmem.q to get X11 forwarding from compute nodes
** Migale: [http://migale.jouy.inra.fr/ web site], [http://migale.jouy.inra.fr/?q=ressources get account] (then ssh -Y tflutre@migale.jouy.inra.fr), support (help.migale@jouy.inra.fr)
** Migale: [http://migale.jouy.inra.fr/ web site], [http://migale.jouy.inra.fr/?q=ressources get account] (then ssh -Y tflutre@migale.jouy.inra.fr), support (help.migale@jouy.inra.fr)
** GenOuest: [http://www.genouest.org/ web site], [http://genoweb1.irisa.fr/AppliESIB/access/access-en.php get account] (need fixed IP, then ssh -Y tflutre@genocluster2.irisa.fr), support (support@genouest.org)
** GenOuest: [http://www.genouest.org/ web site], [http://genoweb1.irisa.fr/AppliESIB/access/access-en.php get account] (ssh -Y tflutre@genossh.genouest.org), support (support@genouest.org)


* '''Resources:'''
* '''Miscellaneous:'''
** [http://www.mathinfo.inra.fr/en maths-info]
** [https://www.abcontrats.inra.fr/ portail juridique] de l'INRA, [http://www.supagro.fr/web/pages/?idl=19&page=536 Agro Valo Méditerranée]
** [https://elearning.formation-permanente.inra.fr/ online learning]
** GNU/Linux distribution by an INRA lab: [https://2ic.pepi.inra.fr/index.php/poste-de-travail/systeme-dexploitation/520-distribution-debian-customisee-pour-une-utilisation-bureautique Debian PAPPSO]
** [https://belinra.inra.fr/ online libraries]
** [http://www.math.univ-montp2.fr/SPIP/sem.php3?a=programme&sem=13 Séminaire de Probabilités et Statistique] de Montpellier (mailing list [http://www.math.univ-montp2.fr/~pudlo/Semstat/_.html semstat])
** Computational Biology Institute of Montpellier ([http://www.ibc-montpellier.fr/ IBC]): mailing list [https://listes.lirmm.fr/sympa/info/ibc-all ibc-all]
** Labo d’Informatique, de Robotique et de Microélectronique de Montpellier ([http://www.lirmm.fr/ LIRMM]): [https://listes.lirmm.fr/sympa/ mailing lists]
** Société Française de Bio-Informatique ([http://www.sfbi.fr/ SFBI]): [http://listes.sfbi.fr/wws/info/bioinfo mailing list] ("liste bioinfo")
** mailing lists on "evolution": [https://listes.univ-montp2.fr/sympa/d_read/evolmontp/divers/evolmontp_mode_demploi.txt evolmontp], [https://listes.univ-montp2.fr/sympa/d_read/evolfrance/divers/evolfrance_mode_demploi.txt evolfrance], [http://evol.mcmaster.ca/evoldir.html evoldir]
** mailing list of the International Grape Genome Program ([http://www.vitaceae.org/index.php/Communication_Resources_for_Grape_Researchers IGGP])


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Revision as of 08:24, 16 December 2014

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Bookmarks for INRA, CIRAD, SupAgro, and more

  • I have been hired by the INRA, in the department "Plant biology and breeding" (BAP in French), but the laboratory in which I am working, AGAP, depends on several research institutes: INRA, CIRAD and SupAgro. The primary goal of such an institutional organization is to build a lab to "encompass a wide range of skills and be a leading platform for applied plant biology and genetics", which is a good endevaour. However, on a daily basis, this is particularly challenging as information is scattered around, and each person needs its own access rights to the tools used by each institute. This web page hence aims at providing a list of links to navigate easily among all sources of information.
  • Computing platforms: especially high performance computing resources (HPC, that is computer clusters)
    • URGI: web site, get account (need fixed IP or not, then ssh -Y tflutre@saruman.versailles.inra.fr), support (urgi-support@versailles.inra.fr)
    • SouthGreen: web site, get account (need VPN, can also be open via the Fortinet client from SupAgro via ./forticlientsslvpn_cli --server vpn-montpellier.cirad.fr:443 --vpnuser timothee.flutre, and then ssh -Y flutre@marmadais.cirad.fr), support, use qlogin -q bigmem.q to get X11 forwarding from compute nodes
    • Migale: web site, get account (then ssh -Y tflutre@migale.jouy.inra.fr), support (help.migale@jouy.inra.fr)
    • GenOuest: web site, get account (ssh -Y tflutre@genossh.genouest.org), support (support@genouest.org)


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