Justin, Here is a copy of the to do list I recently sent to the others: The next step is to build a list, not of analysis tools, but of dynamic client-side interfaces. EMBOSS will take care of the big analysis tools for us. For now, here is a brief list of some dynamic "loci" I've been thinking of. Please feel free to add to this: (1) Benchtop/workspace. GUI representation of all data objects (files, documents, graphs) and possibly various loci. Also may be used for automation of analyses (recall GCL?). (2) File translation interface: to read in various DNA/protein document formats and convert them to XML. Also may be used to query databases and sort/compile documents. (3) Sequence visualization/editing tool: to manipulate DNA/protein sequences (4) Sequence comparison tool: to show multiple sequences aligned or translated. May also perform some functions of (6) (5) 3D visualization tool: to display molecules as 3D structures, with emphasis on a schematic/cartoon representation. (6) Graphing tool: to display plots against sequences and to make simple graphs. Some may argue this isn't needed, but I need it for my programs, so others may too ;-) (7) HTML browser implementation: separate from the other tools, this would be a way for anyone with a browser to access analysis loci. The best approach may be for each of us to pick a single tool to concentrate on. And remember, most of these tools will be XML browsers of a sort. We should also make a list of "trivial" analysis/conversion tools for the client-side. Jeff -- J.W. Bizzaro Phone: 617-552-3905 Boston College mailto:bizzaro at bc.edu Department of Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ --