We describe a set of problems and a proposed solution using a collaborative computing platform developed at UVM, the UVM BioDesktop, http://biodesktop.uvm.edu.  We support both serving public sequence data and managing this data privately in a hierarchical folder system using a familiar graphical interface.  The UVM BioDesktop supports creating, modifying, querying, annotating, and exporting sets of Genbank Entries, alignments, structures and other biological objects.  In the UVM BioDesktop a suite of perl programs manages an HTML interface, manages a file/folder system using a MySQL relational database, and queries GenBank using programs based on the NCBI C++ toolkit.  We describe use of the UVM BioDesktop for creation of mutation databases; a LIMS for a group that handles data related to combinatorial peptide library screens; and a protein sequence pipeline that identifies and classifies protein sequences containing a specified domain.