userguide:ihm
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userguide:ihm [2008/10/09 10:13] 132.168.73.247 créée |
userguide:ihm [2009/12/01 15:17] (current) 132.168.73.124 |
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| - | ===== L'interface graphique ===== | + | ===== Graphical User Interface ===== |
| {{ :userguide:ihm_irma.png |}} | {{ :userguide:ihm_irma.png |}} | ||
| - | L'interface graphique d'IRMa est composé de deux panels de navigation à gauche et à droite de la fenêtre et d'un ensemble de vues détaillées au centre. | + | IRMa main window is splitted in three panels : the left one allow users to browse protein hits, the rigth one shows submitted queries and peptide sequences matching this queries. The center panel contains tabs representing Protein hit details, Search parameters, Query details and the list of identified proteins. |
| - | **__La partie gauche__** (navigation par protéines) représente sous la forme d'une hiérarchie de hits les différents élements de l'identification : | + | ==== Browse protein hits ==== |
| - | * les hits {{:userguide:protein.png|}} | + | |
| - | * les peptides {{:userguide:peptide.png|}} | + | |
| - | **__La fenêtre centrale__** est dédié aux vues détaillées des éléments de l'identification. La vue la plus utilisée est celle qui détaille le contenu d'un hit. Les informations suivantes sont visibles dans cette vue : | + | Hierarchical representation of protein hits : |
| + | * protein hits {{:userguide:protein.png|}} | ||
| + | * peptides {{:userguide:peptide.png|}} | ||
| - | * La description de la proteine principale, son score, masse, pI, couverture, etc. | + | ==== Center panel ==== |
| - | * La liste des protéines qui matchent pour un même ensemble ou pour un sous ensemble des peptides. | + | |
| - | * Les peptides qui matchent pour ce hit. | + | === Protein Hit details === |
| + | |||
| + | This pane displays the proteins and the set of peptides collapsed into the selected hit : | ||
| + | |||
| + | * The "main" protein details : description, score, mass, pi, coverage, etc. | ||
| + | * The collection of proteins matching the same set of peptides or a sub-set of this peptides. | ||
| + | * The set of peptides collapsed into this hit according to their category : significant, ambiguous or duplicated. | ||
| + | * Some additional informations associated to the "main" protein (emPAI, ...) | ||
| {{ :userguide:irma_prot.png |}} | {{ :userguide:irma_prot.png |}} | ||
| - | Il est possible d'effectuer les opérations suivantes sur cette vue : | + | At the top of this pane, a toolbar allow users to : |
| - | * Obtenir la vue Mascot d'un peptide (peptide view) via une connexion au serveur Mascot. Pour ce faire, il faut sélectionner un peptide dans l'un des tableaux et presser la barre d'espace. | + | * access Mascot Protein View page{{:userguide:viewpg.png|}} |
| - | * Invalider un peptide en sélectionnant un ou plusieurs peptides dans le tableau des peptides significatifs et en pressant la touche A (pour Ambigu). | + | * access protein description provided by public datasource {{:userguide:webprotein.png|}} |
| + | * delete the selected hit from the result if it does not contains any more significant PSM | ||
| + | * group the selected hit with another one if IRMa detect that the set of PSM classified as significants is a subset of PSM belonging to another hit. | ||
| + | |||
| + | The user can replace the main protein by choosing another protein among the list of proteins identified by the same set of PSM (right-clic on the protein you want to set as the new "main" protein). | ||
| + | |||
| + | |||
| + | By selecting a PSM, users can : | ||
| + | * Acces Mascot peptide view (select PSM and press space bar or rigth-clic for contextual menu). | ||
| + | * Classify a ambiguous a selected PSM (select PSM and press A for Ambiguous). | ||
| + | |||
| + | === Query details === | ||
| + | |||
| + | Displays potential peptide sequence matches of the selected query. Right-clic on a PSM to display the annotated spectra of the selected peptide and the ion fragment matches. | ||
| + | |||
| + | === Search Parameters === | ||
| + | |||
| + | Informations about the search : taxonomy, parameters, source file, etc. | ||
| + | |||
| + | === Proteins List === | ||
| - | **__La partie droite__** (navigation par query) représente sous la forme d'une hiérarchie de query de l'identification : | + | For each hit in the identification result, display accession, description, score, matches count, etc of the main protein |
| - | * les query {{:userguide:query.png|}} | + | |
| - | * les peptides {{:userguide:peptide.png|}} | + | |
| - | * les hits {{:userguide:protein.png|}} | + | |
| - | La barre d'outils placée en haut de la fenêtre permet de réaliser les opérations suivantes : | + | **__right pane__** (query-centric browser) hierarchical representation of the queries : |
| + | * queries {{:userguide:query.png|}} | ||
| + | * peptides {{:userguide:peptide.png|}} | ||
| + | * hits {{:userguide:protein.png|}} | ||
userguide/ihm.1223539992.txt.gz · Last modified: 2008/10/09 10:13 by 132.168.73.247
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