User interface

NBX

The NBX for NuGO members
Goal of the project
Setup of the NBXs
Getting access
Authentication procedure
User interface
Help infrastructure

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Homepage | User interface

The user interface of the NBX

Upon opening an NBX's URL the user is presented with the screen as shown in the screenshot below:

The opening page shows which NBX the user is connected to and contains a short text, giving some basic information and links to some tools that can be used to connect to the NBX, other than via the web-interface. On top of the page, several tabs are presented that offer possibilites to directly use facilities installed on the NBX. The Bio-Linux4 and CMS links are for administrators.

The Desktop tab opens a java applet or an NX client window that - after prompting for the username and password - grants access to the Desktop of the NBX from any other computer using default settings. For better performance one can use SSH or VNC. After logging on, the desktop is shown, containing icons to several progams and locations containing data available for the user:

Some of the tools available are developed by NuGO members (Eu.Gene, Pathvisio, Wikipathways) or licenced by NuGO (GeneGo, two Genomatix tools).

The EMBOSS tab gives access to the EMBOSS suite of bioinformatics applications. The GenePattern tab gives access to another set of tools available. Tools written in a set of scripting/programming languages (Java, R, Matlab) can be added to the system, in fact several of those have been specifically developed in-house for NuGO use such as toosl for microarray quality control, preprocessing and analysis, and Gene Ontology analysis. The quality control module automatically links to a central dedicated R server that allows analysis of large data sets, without posing any extra complexity to the user. GenePattern also enables building 'pipelines' by linking up several tasks. Finally, the nutriBASE tab gives access to one of NuGO's data storage and sharing system mainly for Affymetrix microarray data. This system has been partly developed within NuGO, based on BASE2. It allows direct export of experiments in a format suitable for upload into EBI's ArrayExpress.