Community-driven computational biology with Debian Linux

Abstract

BackgroundThe Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments.ResultsThe Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software.ConclusionsDebian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

Beyond epitopes: Future and application of computational vaccinology

“…[3][4][5][6][7] Aside of those pre-boxed methods computational workflows binding heterogeneous (island) methods together into combined processes, often involving linking of annotation sources for decision making, have become popular. 8,9 Many existing methods are certainly of high technological quality, but need more intensive testing and feedback by the vaccine community for full evaluation of relevance and tuning for applied vaccinology. In this context, computational vaccinologists should be understood as partners, and certainly not rivals.…”

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

“…The Debian GNU/Linux distribution provides base systems for the Docker images and has a rich repository of scientific software with special interest groups for science in general, and additional efforts, for example Astronomy, Bioinformatics and Chemistry (https://blends.debian.org/ med/tasks/) [27]. The Bioconda community provides additional packages homogeneously for all Linux distributions and macOS.…”

“…Debian and its derivatives share the deb package format with a long history of community support for bioinformatics packages [26,27].…”

EMBnet.journal 19 Suppl. B

“…The binaries can already be integrated (Krabbenhöft et al, 2008) with Taverna and remote resources be added (Möller et al, 2010). Bio-Linux ships with Taverna as it comes from the developers' website.…”

“…Debian Med (Möller et al, 2010) and Bio-Linux (Field et al, 2006) provide the necessary glue for distribution of individual tool updates back to the wider community. This is achieved by packaging and distributing the tools in the context of these larger tool repositories.…”