ELaSTIC similarity graphs construction from massive biological sequence collections. The method is designed to detect pairwise similarities in data sets with millions of DNA/RNA or protein sequences without aligning all sequences against each other. Currently, we are extending the method into a long reads DNA assembler.
Understanding Fluid Flow large-scale study involving a cloud-like computational federation to investigate a flow behavior in micro-channels. The experiment harvested 2,897,390 core-hours from 10 HPC centers around the world. Currently, we are using results of the experiment to solve the inverse problem of flow design.
Faster2 is a simple yet powerful and extensible C++11 framework for working with FASTA and FASTQ files. Developed mostly to facilitate our testing workflows.
TINGe & GeNA systems biology parallel framework for gene networks inference. The software can handle whole genome expression data, and it has been successfully used to reconstruct the largest to date gene network of Arabidopsis thaliana. It also provides Cytoscape plugin and standalone application for analysis of gene regulatory networks using approach akin to the PageRank algorithm.
Parallel-TCoffee parallel multiple sequence aligner able to align thousands of sequences using the T-Coffee scoring method.
Libpnorm a C/C++ high performance library for scheduling pairwise computations on Cell processors taking into account local memory limitations.