Demo walk through

This is a step-by-step description of creating a data analysis with the Bioinformatik Studio. Before you start, make sure that you have two files in FASTA format for analysis (in the folder example_data/flatfile you should find the two files positive.fasta and negative1.fasta) and a local R software installation with the right path set in Configuration. It is also important, that you have menus with proper engines to work with the raw data (you can create them with the Menu Customizer, for this example we will need AaDistribution for an analysis of the amino acid distribution) and the right connections (to AaDistributionBoxPlot and AaDistributionHistogram) in the Engine Manager .
First, you have to select the raw data to analyse. This data can be obtained by a flat file (like FASTA) or a database. In this example, we first work with the flat files.

  1. Click on Input and select Flat File.
A dialog will appear where the format of the file has to be choosen
  1. Choose FASTA, click OK
The next dialog will ask for the type of data in the file
  1. Choose Protein, click OK
  2. Choose file positive.seq
Another dialog will ask for a desciption of the file. The description will show in the input table.
  1. Enter a description or leave the default (filename)
In the input table, the new entry will show up with the description provided above. A right-click on the entry will open a popup menu. There is it possible to change the description or remove the entry from the table.
Now we need an engine to create an result. (If there is no menu, create it first in the Menu Customizer). We want to compare the distibution of the two input sets (FASTA files).
  1. Select the two input sets in the input table (positive.seq and negative1.seq)
  2. Choose AaDistribution from the menu.
As you click on the menu entry, the Bioinformatic Studio will run that engine (as you can see in the statusbar, a progressbar will appear).
As soon as the engine result is created, it will be shown in the result table Now the data is ready for a statistical test or a visualisation.