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Parallel DNA sequence assembly

In the BmBF-funded research project NGSgoesHPC to improve HPC approaches to DNA assembly, we were involved with developing non-blocking code versions based on the parallel de novo sequence assembler PASHA.The project was coordinated by Cologne University and involved Bull, Intel, and several research partners.

Funding: BMBF #01IH11003A (2011 - 2014)

Analysis methods for protein folding and aggregation simulations using MCMC

Development of a software library MCMine to analyze large scale simulations of peptide aggregation and protein folding.

Statistical analysis is key for understanding the conformational ensembles generated in MCMC simulation. Extracting meaningful results from millions of conformations generated in a simulation run requires novel parallel analysis methods for fast cluster detection, structural analysis, and energetic evaluation of conformations.

Partners: Prof. Yanjie Wei, Shenzhen Institutes of Advanced Technology.

Funding: Joint OCPC & JSC funding