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This overview compares tools like Bioclipse and Pipeline Pilot, highlighting their impact on userscripts.
Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, discussing and comparing different offerings like Pipeline Pilot, Taverna, and KNIME.
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Egon Willighagen (2007) studied this question.
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