Projects in Computational Biology
Genome annotation projects
With the help of the MIGenAS infrastructure, a number of microbial genomes, among them some highly relevant model organisms, were “finished” and published (see below for references), several other projects are currently in progress. Key components which are employed here comprise the Phred/Phrap assembler package (ported by MPCDF to 64-bit Linux and parallelized for running on large shared-memory systems), GenDB (MPCDF installation of GenDB 2.0, 2.2), the MIGenAS web toolkit, HaloLex, and relevant sequence and annotation databases.
One of the highlights in this area was the analysis of ancient DNA from a Siberian Mammoth fossil, for which considerable parts of the computational analysis were conducted with the MIGenAS infrastructure.
Many projects and working groups are taking advantage of dedicated support in the form of general and bioinformatics-specific user support and application consulting, hardware resources, etc.
Hosting, housing and consulting
MPCDF provides consulting to several bioinformatics-related projects and houses and hosts hardware and various web applications, e.g.
Galaxy (https://www.bioinfo.mpg.de/galaxy): Galaxy is an open source, web-based platform for data intensive biomedical research. The MPCDF is operating a Galaxy instance for the MPG, in collaboration with several Max Planck Institutes.
Movebank (http://www.movebank.org): a free, online database of animal tracking data (developed at MPI for Ornithology and collaborators)
MIGenAS toolkit (2005-2017) web-based toolkit and workflow engine for integrated sequence analysis (developed at MPCDF):
HaloLex (https://www.halolex.mpg.de): comprehensive annotation and information system for prokaryotic genome and proteome data (developed at MPI of Biochemistry and MPCDF) access restricted/on request
EUCLIS (2006-2019) a comprehensive information system for the EU Chronobiologists (developed at LMU Munich and MPI of Biochemistry)