The US LIMS provides a user-friendly web portal to the data storage and supercomputer analysis methods. All routines are programmed in XHTML, PHP and Perl, and adhere to the W3C strict coding standard (http://www.w3.org/TR/xhtml1) to assure platform and browser independence. Each user is authenticated to a MySQL database, a separate instance belonging to each participating institution. Users are given a permission level which determines their role in the system (i.e. administrator, user, collaborator, analyst), and determines which data in the database can be accessed by the user. Any user can choose to share selected datasets from their own data with any other users to facilitate collaborations. The LIMS further offers web forms for the entry of peptide and nucleic acid sequences, buffer composition, upload of ancillary image data, as well as a virtual laboratory notebook for the annotation of projects and a place to provide experimental details. An interface for the retrieval of experimental and ancillary data as well as data analysis results is available as well. The supercomputer interface is used to enter analysis parameters and submit experimental analysis projects to the supercomputer clusters. Database tables in the US LIMS collect analysis results from the supercomputer, including submission parameters so analyses can be repeated in case of a malfunction. One of several clusters can be chosen for submission of compute-intensive jobs, and a detailed job queue informs the users about the status of their jobs, and permits job resubmission or job canceling. Supercomputer statistics such as used CPU time and performance are stored in database tables to permit accounting of computing allocations. Data analysis results are stored as compressed archives, whose contents are parsed by a web application that automatically generates a dynamically coded HTML file which presents the results through a browser as a well organized web page containing links to visualization images, ASCII formatted spreadsheets, and data analysis result reports generated by UltraScan.