Find the paper in PDF and more information about the conference here

Free Software In Biology Using Debian-Med: A Resource For Information Agents and Computational Grids

28 April 2005


The development of Free Software has much in common with scientific research: the sharing of knowledge and to make progress.

Software in science co-evolves with data that is available to feed it. In the data driven molecular sciences, the information technology is particularly concerned to ease the data flow between applications. This is of particular importance because of the biological data's heterogeneity while individual entries are strongly semantically interdependent. Bioinformatics has developed technologies to communicate between data and tools.

With agent and grid technologies, Computer Science has developed means to operate across multiple databases, hereto also connecting otherwise independent institutes across the world. For the agent community for the access of standard technologies and databases, and for the grid technologies in particular, a common problem is the accessibility of information sources in respective local installations. These may differ in version, location or access permissions. Because of these differences, a common infrastructure still requires considerable local maintenance, particularly for the incorporation of novel data sources.

For computational grids, VOs determine installation paths and inter-institutional access permissions. The actual work for implementing such a agreements is imposed on the respective site's maintainer. A further unresolved issue is the heterogeneity of underlying hardware. This paper describes Debian-Med, a special interest group within the Debian Linux organisation, aiming to provide a hardware-independent common view on Free software and databases for medical and biological research, and stresses its possible impact on the community as a backbone of grids and information agents in computational biology.

CDD Custom Debian Distribution
BOINC Berkeley Open Infrastructure for Network Computing
BTS Bug Tracking System
DFSG Debian Free Software Guidelines
EBI European Bioinformatics Institute
LSB Linux Standard Base
RE Runtime Environment
SETI Search for Extraterrestrial Intelligence
SRS Sequence Retrieval System
VO Virtual Organisation

Andreas Tille 2005-05-13