The line:

use Bio::Tools::pICalculator;
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asks perl to load Bio/Tools/pICalculator.pm, which is "missing" in your setup. You should probably correct the previous line:

use lib "System/common"; # wiped "/Bio/Tools" away
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to show perl where the library is (note that the "Bio/Tools" part is handled directly by perl).

Update: definitively ++Tanktalus for the note about relative paths in use lib.