Imbbc Hpc Publication
Our manuscript on the history, the usage and the scnientific impact of the IMBBC HPC facility over the last 10 years was just published on the GigaScienece journal.
Have a look overe here.
Our manuscript on the history, the usage and the scnientific impact of the IMBBC HPC facility over the last 10 years was just published on the GigaScienece journal.
Have a look overe here.
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
The Dark mAtteR iNvestigator darn
software tool for the identification of the unassigned sequences of COI data is on the road!
Here you may find the corresponding pre-print!
darn
is available as a Docker image.
You may find more about how to install and how to use darn
through its GitHub repository.
Text-mining and data integration.
Really glad about dingo being accepted at BOSC2021.
We will be there with our e-poster!
Thanks for the event @OBF_BOSC!
e-See you all there!
Really glad about dingo being accepted at the annual Bioinformatics Open Source Conference 2021 BOSC2021.
We will be there with our e-poster!
Thanks for the event @OBF_BOSC!
e-See you all there!
Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The conditions in these environments, i.e., high temperatures, low pH values and high concentration of heavy metals, often resemble harsh industrial settings. Thus, these environments may serve as pools of enzymes of enhanced catalytic properties that may provide benefits to biotechnology. Here, we screened 11 metagenomic libraries previously constructed from microbial mat samples covering the seafloor and the polymetallic chimneys of Kolumbo volcano as well as mat samples from Santorini caldera, to mine, in silico, genes associated with bioenergy applications.
The First international conference on the use of DNA for water biomonitoring is here!
Both PEMA and DARN have earned a spot there and will be presented as oral talks!
You may see the complete program here.
Thanks @DNAquaNet!
See you all there!
The Microbiome Data Analyses Workshop has opened its registration!
A series of great topics and software will be covered!
PEMA will be there for a full hands-on tutorial!
Even online, hope to e-meet you all there!
In the framework of Google Summer of Code 2021 the GeomScale group has proposed, among others, a bio project!
We will use volesti
to sample on the flux space of metabolic networks and investigate potential microbial interactions.
For more inforamtion, you may check the project here.