Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software e...

Pise: Software for Building Bioinformatics Webs

Pise is interface construction software for bioinformatics applications that run by command-line operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses. It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web se...

Bioinformatics & Knowledge Engineering

Two softwares used for sequence alignment and searches are BioJava and BioPerl Comparison between these two tolls is shown. There are several software engineering issues such as software reuse, component-based software engineering, cleanroom engineering. We are discussing here software reuse (reusable objects). What kind and amount of bimolecular data is available and how to encode that data an...

Software patents in Bioinformatics

Bioinformatics has published papers describing new software for over 20 years (Nilsson and Klein 1985). During this time the world of software has changed considerably particularly with the irresistible rise of initiatives to build freely accessible software as has opening access to data resources. The Internet and the Web have also changed the way we use and distribute software. This social an...

Structural Bioinformatics for Protein Engineering