A Tcl-based SRS v. 4 interface

Abstract

A new SRS (Sequence Retrieval System) user interface has been developed for SRS v.4. Key features are the support of simple character-oriented (ASCII, VT100) terminals by coding in Tcl augmented by some dedicated Curses calls, support of graphics terminals in an X-Windows version by using the Tk extension to Tcl, and support of a client/server environment by using the TDP extension to Tcl. The Sequence Retrieval System (SRS) is a powerful tool for the fast extraction of information from flat file libraries (Etzold and Argos, 1993) and has rapidly established itself as a major research instrument for the bio-informatics community. Internally the system employs a query language, which is user accessible through either a command-line user interface, 'getz', or a more user friendly, character-oriented window interface. For SRS versions up to release v. 3, this window interface supported VT100-compatible terminals. Because of major changes in the underlying SRS libraries, the v. 3 interface became fully incompatible with the most recent version of SRS (v. 4.x). Thus the many users with only a simple terminal/terminal emulator connection were either deprived of access to SRS, or were forced to use the ASCII WWW client LYNX. This prompted us to develop a character-oriented SRS v. 4 window interface with the look and feel of its SRS v. 3.1 predecessor and coded to be as library independent as possible to maintain compatibility with future SRS releases. In addition, some 'extensions' were coded to widen the applicability to graphics terminals and to a client/server environment. At the time of preparation of this paper, the SRS interface described had been implemented in one form or another on most EM Bnet nodes and on all the platforms given in Table II. The code has been stored at the EMBL in Heidelberg, where it will be available, with installation instructions and scripts, as part of the SRS distribution.