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We used the integrated tools of the HIS (ORBIS® from Agfa Healthcare) [ 18] to create a form which contains all relevant survival data for KM-plots and integrated it into the clinical workflow.
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A cluster analysis with the 12 type strains was performed, using the integrated tools of the MALDI Biotyper 2.0 software package.
The forms and pertinent data reports were implemented using the integrated tools of the local CIS.
False discovery rate (FDR) analysis was also performed using the integrated tools in ProteinPilot.
The false discovery rate (FDR) analysis was performed using the integrated tools in ProteinPilot software and a confidence level of 95% was set to exclude false positive sequence identifications by analyzing the specificity and the quality of results with decoy database searching.
Structural searches were performed using the integrated tool InterProScan [43].
I have explored the structures of all these proteins using the integrated tool InterProScan (see Methods).
First, the cantilevers spring constant was determined using the integrated tool of a JPK BioAFM (atomic force microscope, JPK Instruments AG).
According to the official guidelines from the DLQI questionnaire, the BDI, the HAMD, the YMRS and the HADS all forms were parameterised using the integrated tool (ORBIS® Composer) of the local clinical information system ORBIS® by Agfa Healthcare [ 31].
Structural analyses of the ubiquilin proteins were performed using the integrated tool InterProScan [ 92] (available online at http://www.ebi.ac.uk/Tools/pfa/iprscan/). Microarray data were obtained from the public repositories in which the datasets from the studies cited along the text were deposited.
All sequences were aligned using the integrated aligner tool and the fast aligner option, followed by manual alignment of the sequences to closely related sequences in the ARB database.
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