BAC supports Bioinformatics, Analytics, scientific Computing and data management in the Stazione Zoologica Anton Dorhn. BAC is today specialized in offering support in the following areas:
- Computing Facilities
- Web-based platforms
- GIS and Ecological modelling
- Data management
- Education and Training
- High performance Computing.
BAC offers access (via ssh) to a High Performace Computing (HPC) cluster.
Linux operating system knowledge is a prerequisite to access and use the HPC facilities.
The cluster is running under Debian GNU/Linux and is composed of nine nodes. Each node offers 32 physical cores and 1TB RAM each. The setup includes a high-performance parallel storage where users can store their data while analysis are ongoing. We do not consider this enough for SZN scientists demand but we are expanding thanks to istitutional plannings.
The HPC cluster offers plenty of ready to use software tools (https://bioinfo.szn.it/tools/). In addition, BAC can install tools (or upgrade tools already available) on demand.
User jobs can be submitted via a well-documented and popular workload manager (SLURM), but in case you are not familiar with the above technology, BAC can provide ad-hoc planned training on this specific subject (see details at the end of this document on how to). Periodic Unix courses could be planned for non-expert users upon request.
MPI tasks are generally supported via OpenMPI-SLURM integration. Support for particular setups is offered and is intended as a collaboration that needs to be planned by a specific partnership agreement with BAC that will be approved in RIMAR.
- Storage facilities.
BAC aims to offer storage service by different strategies, tailored to your needs. Short and long term storage of your data or backup copies will be agreed on a case-to-case basis due to availability of resources. Please notice that no institutional resources are available at the moment.
You can offer a budget to contribute to a storage resource expansion plan in charge of BAC consulting and support for maintenance. This means that X% of this resource will be dedicated to your effort and (100-X)% will be reserved to the service, to support all SZN BAC users. Agreements on the X can be fixed upon specific requirements.
- Support for Unix based systems
BAC offers expertise for planning, deploying, tuning and maintaining HPC facilities and servers. BAC users are encouraged to use BAC computing facilities. Contributions to update/expand the SZN computing facilities are more than welcome. Personal clusters or servers are deeply discouraged. Configuring these efforts is upon official agreements with you, BAC and RIMAR.
If our systems do not suit your needs, we will be glad to support your “computing demanding” projects or tasks. This is considered support in our ticketing service. Agreements will be reached with you, BAC and RIMAR.
If you want to setup your own system for specific, reasonable reasons, we can offer HPC systems and network engineering consulting services, upon official agreements approved by you, BAC and RIMAR.
BAC offers support in the field of bioinformatics and omics sciences, providing strategies and tools for several types of data analysis:
- Related omics
Example of services offered:
- Comparative analysis (orthology/paralogy prediction)
- RNA-seq and related (from cleaning to DEGs calling)
- Functional annotation and domain identification
- Metagenomics and metabarcoding
- OTU/ASVs/sOTUs table analysis
- Three-dimensional protein structure prediction by homology modelling
BAC has the capabilities to support your relevant projects setting up web-based platforms and databases. Example of services offered:
- Database and platform design
- Genoma: a platform for exploring genomic information of species of interest for Marine Biology (under development,currently 14 species are included)
- Pseudo-nitzschia multistriata genome portal: a dedicated platform for the exploitation of the genomic content of this diatom, including a genome browser and a BLAST SERVER
- Geographical Information Systems:
- BLAST services
- TARA BLAST server
GIS AND ECOLOGICAL MODELLING
The BAC unit supports data management and analysis for georeferenced collections based on Geographic Information System (GIS) supporting spatial analysis, niche models and remote sensing applications.
- Data mapping through GIS software/tools
- Support in data organization
- Data integration using public collections
- Spatial analysis of environmental/biological data
- Ecological modelling (e.g., species distribution models and ecological niche models)
Example of services offered:
BAC provides guidelines, formats and standards to organize data and metadata collections produced by SZN researchers according to the European directives for OPEN DATA management, in respect of the FAIR principles (Findable, Accessible, Interoperable and Reusable).
Example of services offered:
- BAC provides formats and rules to collect and organize biological/chemical/physical data (e.g., species, temperature, current)
- BAC set up tools for sequence data to public databases (e.g.: nucleotide, genomics, SRA)
EDUCATION AND TRAINING
- “Introductory Course on Bioinformatics”, PhD Programme Course, 9-13 May 2022, Conference room, StazioneZoologica Anton Dohrn.
- “BLAST service at SZN – an example for TARA data”, 18 September 2020, StazioneZoologica Anton Dohrn
- “Data sharing and interoperability: a FAIR opportunity for SZN”, 16 July 2020, StazioneZoologica Anton Dohrn
- “Metabarcoding And Metagenomic Data Processing And Analyses”, 3-7 February 2020, StazioneZoologica Anton Dohrn, Assemble+ course (Co-funded by EMBRC)
- “Introduction to bioinformatics”, 10 January 2020, lesson to the students of the University of Rome “La Sapienza” visiting SZN, Conference Room, StazioneZoologica Anton Dohrn of Naples
- “Protein function and evolution: Databases and tools to predict and visualize protein structures”, PhD Programme Course, 9 December 2019, StazioneZoologica Anton Dohrn.
- “Basic course in Bioinformatics”, PhD Programme Course,15-18 July 2019, StazioneZoologica Anton Dohrn of Naples
- “Data Carpentry for Ecologist”, 6-7 February 2019, StazioneZoologica Anton Dohrn
- “BIOINforMA meets SZN”, 19 July 2018, StazioneZoologica Anton Dohrn of Naples