Next: Introduction
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 |