3.4 Implementation and web interface
We implemented the layout algorithm in C++ and tested it on a 2.8 GHz Pentium computer running the Fedora Core 3 operating system. Our software contains two executable programs. The first executable, layout, implements the layout algorithm. It takes a text file describing the biclusters as input and outputs the layout in a simple textual format that specifies the order of the rows and columns in the layout and the corners of each bicluster in the layout. The second executable, drawlayout, uses the computed layout and the original data set as input and produces an image corresponding to the layout.
If the input data contains a large number of biclusters, the layout may contain too many rows and/or columns for the user to navigate with ease. To alleviate this problem, we have also developed a simple web-based interface that allows the user to upload a file containing computed biclusters and a file containing the original data, and query the layout with the names of rows and columns. The interface invokes layout and drawlayout on the biclusters that contain the query rows/columns and highlights the matching biclusters, rows, and columns in the resulting layout. The interface allows the user to specify whether the data is real-valued or binary, whether the layout should contain only the matching biclusters, and whether the query should be a conjunction or disjunction of the search terms.