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Gene Function Inference in Deletion Mutants 7Fig. 2. The main BDrun window, with the parameters to be set on the left and themessage window on the right. The sets of parameters on the bottom left allows to runBD on a remote machine, and to select a variant of the algorithm. BD is controlled bythe set of buttons at the bottom (operations).1. The data must be loaded by using the [Load] button. The file Fr764_228_ratio.txtmust be chosen and the uncertainty file Fr764_228_ratio.unc must be present inthe same directory. If successful, the left textual display gives the message:read:/home/ghbidaut/data/Rosetta_Compendium/Fr764_228_ratio.uncread:/home/ghbidaut/data/Rosetta_Compendium/Fr764_228_ratio.txt.Next, the following parameters need to be reviewed and fixed:• tag: this is the current experiment tag, used to identify the output.• dir: this is the current working directory.• Ensemble: this is the number of Markov chains used simultaneously forsearching a solution. For now, the current implementation of BD is limitingthis value to one so this cannot be changed by the user.• Niter: the number of Markov chain iterations. 3000 is a reasonable value in thisanalysis.• Nshow: this provides the number of steps of the Markov chain between snapshotsduring sampling. The default value (500) is left as is.• Iseed: this is the random seed that will determine the position of the MarkovChain in the solution space. Saving this seed value allows the exact reproducibilityof the decomposition.