Premium
A flexible and easy to use molecular biology workbench efficiently developed in Tcl/Tk
Author(s) -
Pohle HansPeter,
Drescher Bernd
Publication year - 2000
Publication title -
software: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.437
H-Index - 70
eISSN - 1097-024X
pISSN - 0038-0644
DOI - 10.1002/1097-024x(200010)30:12<1433::aid-spe348>3.0.co;2-i
Subject(s) - workbench , computer science , programming language , software , process (computing) , sequence (biology) , software engineering , operating system , visualization , data mining , biology , genetics
We describe the design and implementation of a workbench for molecular biology that allows the easy integration of analysis tools. The software is implemented in Tcl/Tk using the [incr Tcl] extension that provides object‐oriented programming. The program is called tkGDE and consists of four main parts. The sequence editor allows the user to perform basic editing operations on biomolecule sequences. The graphical annotation editor gives the user a graphical overview of all annotated features of a sequence. The output manager retains information on the results produced by the analysis tools. The bundle control allows several tools to run automatically, passing data from one tool to the next. Tools are integrated into the system by describing their properties in a configuration file, which drastically reduces the time needed for integration. We present results proving that Tcl/Tk has been misjudged to be slow and unsuited for large projects. To achieve sufficient performance we exploited special features of Tcl/Tk, namely idle tasks and the capabilities built into the Tk canvas widget. The system consists of more than 34000 lines of [incr Tcl] code in 182 classes. The whole development process took about one person‐year. Copyright © 2000 John Wiley & Sons, Ltd.