High throughput data at different biological levels (e.g DNA, RNA, protein, or species population level) have currently become a routine for a great number of research fields in biology.
When it comes to ecology, biodiversity and evolution, the more such data become available, the more the requirements in processing and analysis rise. These requirements include not only improved algorithms, but also high computational power; power exceeding by far and large the desktop computer capacity.
To this end, the Institute of Marine Biology Biotechnology and Aquaculture (IMBBC) of the Hellenic Centre for Marine Research (HCMR), has built a High Performance Computing (HPC) system named “zorbas”.
Up today, IMBBC and “zorbas” mostly focus on:
- non-model organism next-generation sequencing data analysis,
- environmental -omics
- large-scale ecology & biodiversity data analysis.
Available softwares, maintained by dedicated personnel, allow raw read pre-preprocessing, whole genome de novo assembly, genome annotation, variant discovery, population genomic analyses, RNA-Seq, phylogenomics, metabarcoding analyses, biodiversity index calculation, and ecological data analysis (available also through the web interface of RvLab).
As bioinformatic analyses is common to imply considerable memory requirements, “zorbas” current capacity comprises 5TB total RAM (up to 1.5TB available on a single node) Launched in 2010, zorbas accommodates more than 200 state-of-the-art software suites.
Since pipelines and workflows are quite common in bioinformatics, systematic efforts have focused on pipeline parallelization and containerization (mainly Singularity-based). This way, both the decrease of the computational time needed, the sharing of code and reproducibility are encouraged the most.
Ongoing collaborations with the LifeWatch ERIC, EMBRC ERIC, and the ELIXIR Research Infrastructures aim at sharing resources and accumulated expertise to the broader pertinent Hellenic and European bioinformatics and biology communities.
Funding for establishing the IMBBC HPC has been received by the MARBIGEN (EU REGPOT) project, LifeWatchGreece and CMBR (Centre for the study and sustainable exploitation of Marine Biological Resources) Research Infrastructures (ESFRIs).