Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological macromolecules. MMQL portends to be intuitive with a simple syntax, so that from a user's perspective complex queries are easily written. A number of basic queries and a more complex query--determination of structures containing a five-strand Greek key motif--are presented to illustrate the strengths and weaknesses of the language. The predominant features of MMQL are a filter and pattern grammar which are combined to express a wide range of interesting biological queries. Filters permit the selection of object attributes, for example, compound name and resolution, whereas the patterns currently implemented query primary sequence, close contacts, hydrogen bonding, secondary structure, conformation and amino acid properties (volume, polarity, isoelectric point, hydrophobicity and different forms of exposure). MMQL queries are processed by MMQLlib; a C++ class library, to which new query methods and pattern types are easily added. The prototype implementation described uses PDBlib, another C(++)-based class library from representing the features of biological macromolecules at the level of detail parsable from a PDB file. Since PDBlib can represent data stored in relational and object-oriented databases, as well as PDB files, once these data are loaded they too can be queried by MMQL. Performance metrics are given for queries of PDB files for which all derived data are calculated at run time and compared to a preliminary version of OOPDB, a prototype object-oriented database with a schema based on a persistent version of PDBlib which offers more efficient data access and the potential to maintain derived information. MMQLlib, PDBlib and associated software are available via anonymous ftp from cuhhca.hhmi.columbia.edu.

The variation among mobile devices has led to various approaches for the presentation of data. In general, these approaches work well when a specialized application is developed for a given device, but do not work as well when generally available web pages are used as the source. Various approaches have been proposed and used for the display of web pages, most recently the proposal for HTML Mobile Profile. The evolution and implementation of this standard have opened the possibility of near-universal support for mobile device web display through conversion of web pages into a form consistent with HTML Mobile Profile. RIML, a markup language developed by the Consensus project took a major step in this direction with a system that includes an enhanced markup language, a database of device characteristics, and a translation engine. It introduced a rich set of mapping concepts, but the extensions to HTML make it unrealistic to reach widespread implementation. Our approach is similar to the approach of Consensus, but instead uses existing HTML syntax to provide translation pragma. The pragma defined in the HTML guides translation engine that breaks the page into a deck-of-cards, with the appropriate links between cards. We approach the problem of transforming existing web pages into wireless content by dividing it into three separate problems: the conversion of unstructured or invalid web pages into valid pages (XHTML), the transformation of valid pages into a markup suitable for mobile devices (XHTML-MP), and finally, the formatting of the resulting documents such that they are suitable for display on wireless devices. The pragma specified in the HTML guides these steps, particularly the formatting of the document wireless display.