Vect: An Automatic Visual Perl Programming Tool for Nonprogrammers
Hui-Hsien Chou. Vect: An Automatic Visual Perl Programming Tool for Nonprogrammers. BioTechniques, Vol. 38, No. 4: pp 615-621, Apr 2005.
Modern high-throughput biological research produces enormous amount of data that must be processed by computers, but many biologists dealing with these data are not professional programmers. Despite increased awareness of interdisciplinary training in bioinformatics, many biologists still find it difficult to create their own computational solutions. VECT, the Visual Extraction and Conversion Tool, has been developed to assist nonprogrammers to create simple bioinformatics without having to master a programming language. VECT provides a unified graphical user interface for data extraction, data conversion, output composition, and Perl code generation. Programming using VECT is achieved by visually performing the desired data extraction, conversion, and output composition tasks using some sample user data. These tasks are then compiled by VECT into an executable Perl program, which can be saved for later use and can carry out the same computation independently of VECT. VECT is released under the GNU General Public License and is freely available for all major computing platforms including Macintosh® OS X, Linux, and Microsoft® Windows® at www.complexcomputation.org
UBViz: a software tool for exploring metabolic pathways in 3-D space
Song Li and Hui-Hsien Chou. UBViz: a software tool for exploring metabolic pathways in 3-D space. BioTechniques, Vol. 38, No. 4: pp 540-542, Apr 2005.
In this paper, we introduce a novel approach to bringing metabolic pathways into 3-D space. Compared with the aforementioned system, this approach has several advantages. First, our system, UBViz, only needs logical descriptions of the pathways from the data providers and performs the 3-D layout algorithm locally. As a result, less data is needed to be transferred through the network, since the coordinate information is not needed by UBViz. Second, the UBViz's XML interface enables existing XML format pathway files from KEGG to be immediately usable; no change on the KEGG side is needed. Therefore, UBViz's users can make use of all existing database resources, such as the pathway data KEGG provides, and benefit from modern computer 3-D technology immediately without requiring the data providers to expend any effort. Finally, UBViz is a standalone highly efficient C++ program that does not depend on any other software to execute and is easily installable by end-users.
Availability: UBViz is distributed under the Gnu General Public License and can be downloaded from www.complexcomputation.org/download/UBViz/index.html. UBViz is available on all major computing platforms including Windows, Linux, and Mac® OS X.