| 1 | | [[PageOutline]] |
| 2 | | |
| 3 | | = List of Proteios Wiki Pages = |
| 4 | | |
| 5 | | == Introduction == |
| 6 | | |
| 7 | | This page contains a list of Proteios wiki pages. |
| 8 | | |
| 9 | | * A wiki page is normally listed under the first wiki page linking to it, but exceptions may occur, in order to keep wiki pages with related contents listed together. |
| 10 | | * Not all wiki pages are guaranteed to be included in the list. |
| 11 | | * Some wiki pages may occur more than once in the list. |
| 12 | | * Some links to non-wiki pages are included, if the links were included on a wiki page in a list with wiki links. |
| 13 | | |
| 14 | | == Links to Proteios Wiki Pages == |
| 15 | | |
| 16 | | 1. [wiki:WikiStart Proteios Wiki Start Page] |
| 17 | | 1. [wiki:MoreAboutProteios About Proteios Software Environment] |
| 18 | | 1. [wiki:ProteiosListOfWikiPages List of Proteios Wiki Pages] |
| 19 | | 1. [wiki:Releases Proteios Software Environment releases] |
| 20 | | 1. [wiki:Download Download] |
| 21 | | 1. [wiki:KnownIssuesProteios Known Issues] |
| 22 | | 1. [wiki:Problems Known problems] |
| 23 | | 1. [wiki:Manual Proteios SE Manual] |
| 24 | | 1. [wiki:SomeConceptsInProteios Some Concepts in Proteios SE] |
| 25 | | 1. [wiki:UserGuide User Guide] |
| 26 | | 1. [wiki:WorkingWithAccounts Working With Accounts] |
| 27 | | 1. [wiki:WorkingWithExtensions Working With Extensions] |
| 28 | | 1. [wiki:ExtensionManual Extension Manual] |
| 29 | | 1. [wiki:ImplementAction Implement Action] |
| 30 | | 1. [wiki:ImplementPlugin Implement Plugin] |
| 31 | | 1. [wiki:PluginConfiguration Plugin handling] |
| 32 | | 1. [wiki:WorkingWithProjects Working With Projects] |
| 33 | | 1. [wiki:WorkingWithFiles Working With Files] |
| 34 | | 1. [wiki:SharingData Sharing information] |
| 35 | | 1. [wiki:FTPServerUsage Proteios FTP Server Usage] |
| 36 | | 1. [wiki:WorkingWithSamples Samples and sample tracking] |
| 37 | | 1. [wiki:WorkingWithHitReports Working With Hits Reports] |
| 38 | | 1. [wiki:GelBasedReport Generating a report for a gel-based project] |
| 39 | | 1. [wiki:ExQuest ExQuest import] |
| 40 | | 1. [wiki:HitsReportTableFeatures Hits Report Table Features] |
| 41 | | 1. [wiki:Filters Filters] |
| 42 | | 1. [wiki:HitsReportTablePrideXmlExport PRIDE 2.1 XML Export] |
| 43 | | 1. [wiki:OverviewOfGeneratedPrideXmlFile Overview of the Generated PRIDE XML Export File ] |
| 44 | | 1. [wiki:WorkingWithSpectrumSearches Search results] |
| 45 | | 1. [wiki:SharingData Sharing information] |
| 46 | | 1. [wiki:DIGEAnalyzer DIGE Analyzer] |
| 47 | | 1. [wiki:ExQuest ExQuest import] |
| 48 | | 1. [wiki:Webservice Webservice] |
| 49 | | 1. [wiki:XTandemSearchEngineInterface X!Tandem Search Engine Interface] |
| 50 | | 1. [wiki:Installation Proteios 2 Installation] |
| 51 | | 1. [wiki:BuildProteios Build Proteios from Source Code] |
| 52 | | 1. [wiki:DetaildBuildInstructions Detailed Build Instructions] |
| 53 | | 1. [wiki:SettingUpEclipse Setting up Eclipse] |
| 54 | | 1. [wiki:MySQLremote How to grant rights for remote access to a MySQL server] |
| 55 | | 1. [wiki:Update Update] |
| 56 | | 1. [wiki:ServerAdministration Proteios SE server administration] |
| 57 | | 1. [wiki:TomcatApacheSSLConfigurationHints Tomcat/Apache Web Server/SSL Configuration Hints] |
| 58 | | 1. [wiki:FTPServer Proteios FTP Server] |
| 59 | | 1. [wiki:FTPServerUsage Proteios FTP Server Usage] |
| 60 | | 1. [wiki:ThirdPartyLicenses Third Party Licenses] |
| 61 | | 1. [wiki:Developers Information for Developers] |
| 62 | | 1. [wiki:SomeConceptsInProteios Some Concepts in Proteios SE] |
| 63 | | 1. [http://www.proteios.org/htdocs/generated_schema.html Database Schema] ''(Non-wiki page)'' |
| 64 | | 1. [wiki:ExtensionManual Extension Manual] |
| 65 | | 1. [wiki:ImplementAction Implement Action] |
| 66 | | 1. [wiki:ImplementPlugin Implement Plugin] |
| 67 | | 1. [wiki:SettingUpEclipse Setting up Eclipse] |
| 68 | | 1. [wiki:BuildProteios Build Proteios from Source Code] |
| 69 | | 1. [wiki:DetaildBuildInstructions Detailed Build Instructions] |
| 70 | | 1. [wiki:SettingUpEclipse Setting up Eclipse] |
| 71 | | 1. [wiki:JavaDoc JavaDoc] |
| 72 | | 1. [wiki:TicketManual Ticket Manual ] |
| 73 | | 1. [wiki:SubversionSpecificLogCommands Subversion usage] |
| 74 | | 1. [wiki:Testing Testing] |
| 75 | | 1. [wiki:UnitTestsJunitBackground Unit Tests and JUnit - Background] |
| 76 | | 1. [wiki:JunitFourAndAlternatives JUnit 4 Issues and Alternatives] |
| 77 | | 1. [wiki:JwebUnitPackageDependenciesLatestReleases jWebUnit Package Dependencies for Latest Releases] |
| 78 | | 1. [wiki:jWebUnitCompilePackageTest jWebUnit Compile Test for Used Packages] |
| 79 | | 1. [wiki:TestPackageAlternatives Test Package Alternatives] |
| 80 | | 1. [wiki:TableFactoryUse TableFactory Use] |
| 81 | | 1. [wiki:NamingConventions Naming Conventions] |
| 82 | | 1. [wiki:LoggingGuidelines Logging Guidelines] |
| 83 | | 1. [wiki:UsefulLinks Useful Links] |
| 84 | | 1. [wiki:ThirdPartyLicenses Third Party Licenses] |
| 85 | | 1. [wiki:TomcatApacheSSLConfigurationHints Tomcat/Apache Web Server/SSL Configuration Hints] |
| 86 | | 1. [wiki:ReleaseProcedure Release Procedure] |
| 87 | | 1. [wiki:Specification Specification] |
| 88 | | 1. [wiki:ServiceUserAdministration User management] |
| 89 | | 1. [wiki:UseCaseCreateNewAccount UseCase Create New Account] |
| 90 | | 1. [wiki:UseCaseRemoveAccount Use Case Remove Account] |
| 91 | | 1. [wiki:ServiceRolePermissions Role based permissions] |
| 92 | | 1. [wiki:ServiceDataSharing Data sharing] |
| 93 | | 1. [wiki:UseCaseSharingDirectory Use Case Sharing Directory] |
| 94 | | 1. [wiki:ServiceFileUpload Uploading a set of files] |
| 95 | | 1. [wiki:ServiceDataImport Data import of different formats, e.g. mzData, PKL] |
| 96 | | 1. [wiki:ServiceSearchAndFilter Data searching/filtering] |
| 97 | | 1. [wiki:ServiceSampleManagement Sample Management] |
| 98 | | 1. [wiki:UseCaseCreateNewSample Use Case Create New Sample] |
| 99 | | 1. [wiki:ServiceProjectManagement Project management] |
| 100 | | 1. [wiki:UseCaseCreateNewProject Use Case Create New Project] |
| 101 | | 1. [wiki:ServiceReportGeneration Report generation] |
| 102 | | 1. [wiki:ServiceDataAnnotation Data annotation] |
| 103 | | 1. [wiki:ServiceNotificationManagement Notification management ] |
| 104 | | 1. [wiki:UseCaseCreateNewAccount Use Case Create New Account] |
| 105 | | 1. [wiki:UseCase2DGelBased 2D Gel-based proteomics workflow] |
| 106 | | 1. [wiki:UseCaseMSTypes Different mass spectrometry modes to handle] |
| 107 | | 1. [wiki:MSFileNames File Naming] |
| 108 | | 1. [wiki:GelReport Gel Report] |
| 109 | | 1. [wiki:UseCaseQuantitativeLCMS Quantitative LC-MS use case] |
| 110 | | 1. [wiki:UseCaseMSTypes Different mass spectrometry modes to handle] |
| 111 | | 1. [wiki:UseCaseBiochemistryBroad Dep of Biochemistrys broad view of aim with Proteios ] |
| 112 | | 1. [wiki:UseCaseBiochemistry2DgelBased Biochemistry 2DGel-based workflow] |
| 113 | | 1. [wiki:UseCaseExample How to write a Use Case] |
| 114 | | 1. [wiki:LoginToWikiUseCase Login to Proteios wiki] |
| 115 | | 1. [wiki:DatabaseModelMS Mass Spectrometry part of the Proteios database] |
| 116 | | 1. [wiki:GeneralActivity General Activity Diagrams] |
| 117 | | |
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