The Java Environment for Nature-Inspired Approaches (JENA): A Workbench for BioComputing and BioModelling Enthusiasts

The term biocomputing subsumes a growing variety of effective concepts, strategies, and algorithmic techniques adopted from facets of biological information processing. In an highly interdisciplinary manner, underlying principles succeed in getting identified, understood, and transferred into the practice of computer science. Resulting models and simulation systems widely differ in their level of abstraction from almost realistic up to strongly idealised. Corresponding implementations have been categorised into microscale, mesoscale, and macroscale, but an interscale approach able to bridge existing gaps in between is still missing. Within an ongoing long-term project we are going to incorporate modelling components and descriptive instruments from different scales into a common programming workbench making the process of abstraction and concretion visible when elucidating a problem solution strategy throughout the scales. For instance, a DNA strand might be simply captured by a name, more detailed by a sequence of bits, eventually by its primary and secondary structure mentioning all involved nucleotides and nucleotide pairs, and finally by its tertiary structure expressing the spatial positions of all atoms bonded to each other. Analogously, chemical reactions and physical processes can be specified at various levels of abstraction. Our workbench has been designed as an experimental system open for successive extension along with student’s contributions by integration of more and more issues from biocomputing. We present the current status of the project together with its underlying software design concept implemented in Java. A case scenario addressing double-stranded DNA and separation of DNA pools by length using gel electrophoresis demonstrates the practicability of the workbench.