Knime uses a visual programming language to connect data flows through function blocks, which makes it a natural and self-explanatory GUI for data pipelines
It has broad application, including scientific data preparation.
Knime integrations
e.g. Knime : Community Extensions : Bioinformatics and Next Generation Sequencing Extensions
which includes : knime4bio :
"Knime4Bio is a set of nodes for KNIME used to analyse data produced by the next-generation-sequencing (NGS) technologies. Most of the nodes are used to filter and annotate VCF (Variant Call Format) files, some nodes can be used to query the NCBI databases, the mysql ucsc server, etc..."
That could be useful for Pretzel users preparing data for input to Pretzel, and Pretzel could be integrated as an output functional block - that seems like a good student project because it is interesting, flexible (can be split into stages), and probably a reasonable size - for a simple initial integration.
About Knime
Knime uses a visual programming language to connect data flows through function blocks, which makes it a natural and self-explanatory GUI for data pipelines It has broad application, including scientific data preparation.
Knime integrations
e.g. Knime : Community Extensions : Bioinformatics and Next Generation Sequencing Extensions which includes : knime4bio : "Knime4Bio is a set of nodes for KNIME used to analyse data produced by the next-generation-sequencing (NGS) technologies. Most of the nodes are used to filter and annotate VCF (Variant Call Format) files, some nodes can be used to query the NCBI databases, the mysql ucsc server, etc..."
That could be useful for Pretzel users preparing data for input to Pretzel, and Pretzel could be integrated as an output functional block - that seems like a good student project because it is interesting, flexible (can be split into stages), and probably a reasonable size - for a simple initial integration.