ACTIVITIES REPORT OF THE BIOINFORMATICS SERVICE

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Activities report of the Bioinformatics service – update at March 2019

BIOINforMA is taking care of implementing software, website and databases and maintaining HPC service for SZN people. The maintenance of the HPC began in May 2017. The bioinformatics services began in July 2018. Since then we received 45 official independent requests. 32 were successfully solve and 13 are in progress.

Activities and products:

Web based platforms:

  • Blast services for dedicated collection:
    • Currently available collections: TARA 16S and V9 rDNA metabarcoding
  • LTER web service. Status: in progress
  • Sea Turtles web service: Status: in progress
  • Microplastic website in collaboration with Christophe Brunet: Status: under planning (work not yet in progress)
  • GENOMA Query page. Status: ready

Genomics:

  • setting-up of a methodology to assess GFF based gene annotation quality. Status: done. Service: ready
  • setting-up of a methodology for GFF format based genome compositional analysis. Status: done

Transcriptomics:

  • setting-up of a methodology for RNA-seq analysis. Status: done. Service: ready
  • methodologies for dedicated semi-automated pipelines to increase service efficiency. Status: in progress

Proteomics:

  • setting-up of a semi-automated pipeline for functional annotations of entire proteomes. Status: done. Service: ready
  • full automation. Status: in progress
  • setting-up of a pipeline for three-dimensional modeling of protein structures. Status: done. Service: ready

Comparative genomics:

  • development of a methodology for genome comparison (“COMPARO”: COMparative genomics for PARalogs and Orthologs genes).
  • ortholog and paralog searches based on a multilevel approach (Ambrosino and Chiusano 2017; Ambrosino et al. 2018). Status: done. Service: ready
  • network of orthologs and paralogs construction (Ambrosino et al. 2018). Status: done. Service: ready
  • data quality assessment and method tuning : Status: in progress
  • stand-alone software release. Status: in progress
  • web applications release. Status: in progress. 
  • setting-up of a methodology for short conserved non-coding region (CNEs) prediction. Status: done. Service: ready.
  • setting-up of methodology service for sequence similarity searches against biological databases. Status: done. Service: ready

Metagenomics:

  • setting-up of a pipeline to identify recombinant sequences in a metagenomics analysis. Status: in progress. Service: available upon request
  • setting-up of shotgun and targeted metagenomics services. Status: done. Service: ready

System administration:

BIOINforMA is maintaining the following systems:

  • kraken: stable stage HPC cluster, 6 nodes
  • falkor: development stage HPC cluster (next-stable), 4 nodes
  • pan01: Panasas HPC parallel storage attached to clusters
  • servian: bioinformatic analysis and services workstation (located in the server room)
  • r2-d2: web and database services server, virtualized environments (located in the server room)

We are eventually helping on several general purpose systems on-demand by SIST (mostly LDAP authentication systems, mail  and antispam systems, network devices) and by single SZN users.

 

Bioinformatics service staff:

Chiusano, Maria Luisa

Associated researcher
Role in the scope of the bioinformatics unit:

  • Responsible of the Service

Activities:

  • Coordination, supervising of all the tasks to set up the Bioinformatics services.

Tangherlini, Michael

Researcher
Role in the scope of the bioinformatics service:

  • Contact person for shotgun and targeted metagenomics for prokaryotic and viral diversity.
  • Reference person for the implementation of shotgun and targeted metagenomics services for prokaryotic and viral diversity.

Activities:

  • Development of tools and web platforms:
    • Glossary (Tangherlini et al. 2018). Status: done
  • Analysis and retrieval of protein sequences from prokaryotic genomes and public databases for biotechnological applications. Status: done. Service: ready
  • Identification of state-of-the-art software suites and databases for facilitating shotgun metagenomic analyses
  • Reference for the organization of semi-automated dedicated metagenomics services Status: in progress
  • Ready to support the dedicated requests

Miralto, Marco

Staff Technician (CTER VI level)
Member of the Bioinformatics service since 08/05/2017 (ordinance n. 103 by General Director)
Role in the scope of the bioinformatics service:

  • Contact person for hardware and software HPC cluster systems and IT services for scientific computing
  • Contact person for High Performance networking
  • Contact person for IT technologies (programming languages, databases, tools)   

Activities:

  • Installation, configuration and tuning of IT systems:
    • installation, configuration and tuning of HPC systems (nodes and frontends)
    • installation, configuration and tuning of high performance network equipment
    • supported and implemented the installation and configuration of several general purpose IT internal services (ldap authentication systems, postfix mail server with dovecot LDA, antispam appliance, firewall and networking switches configuration)
  • Hardware bootstrap automation tools (based on Cobbler, Puppet, Ansible)
  • Deployment of IT services on bare metal and virtualized environments
  • Development of tools and web platforms:
    • BIOINforMA. Status: done
    • Glossary (Tangherlini et al.). Status: ready
    • Genoma Query page. Status: ready
    • Comparo: a tool for paralogs and orthologs gene network prediction. Status: in progress
  • IT technologies (hardware and software) assessment
  • System administration: a partial list of the systems managed is at the beginning of the document
  • development of parsers, databases and APIs to store and query the MEDA biogeochemical/pictures datasets. Status: in progress

Ambrosino, Luca

Research fellow
Role in the scope of the bioinformatics service:

  • contact person for evolutionary genomics:
    • sequence similarity searches, prediction of orthology and paralogy relationships
  • contact person for functional annotation analyses
  • contact person for structural analyses of proteins references and 3D-modeling.
  • Reference person for the implementation of the platform COMPARO

Activities:

  • development of a methodology for genome comparison (“COMPARO”: COMparative genomics for PARalogs and Orthologs genes).
  • ortholog and paralog searches based on a multilevel approach (Ambrosino and Chiusano 2017; Ambrosino et al. 2018). Status: done. Service: ready
  • network of orthologs and paralogs construction (Ambrosino et al. 2018). Status: done. Service: ready
  • stand-alone software release. Status: in progress
  • setting-up of a methodology for short conserved non-coding region (CNEs) prediction. Status: done. Service: ready.
  • setting-up of a semi-automated pipeline for functional annotations of entire proteomes. Status: done. Service: ready
  • full automation. Status: in progress
  • setting-up of a pipeline for three-dimensional modeling of protein structures. Status: done. Service: ready
  • setting-up of methodology service for sequence similarity searches against biological databases. Status: done. Service: ready

Colantuono, Chiara

Research fellow
Role in the scope of the bioinformatics service:

  • contact person for transcriptome analyses (RNA-seq);
  • contact person for genome analyses (genome assembly and masking, gene annotation).
  • reference person for the implementation of the GENOMA platform

Activities:

  • set-up of the GENOMA platform (GENOmes for MArine biology). Status: in progress.
  • BIOINforMA web pages set up and maintenance. Status: done.
  • AEO-aquatic web-page set up and maintenance. Status: in progress
  • setting-up of a pipeline to identify recombinant sequences in a metagenomics analysis. Status: in progress. Service: available upon request
  • contribution in the set-up of a gene annotation quality pipeline. Status: done. Service: ready
  • contribution in the set-up of a “compositional windows analysis” software. Status: done. Service: ready
  • contribution in the set-up of a pipeline for Differentially Expressed Genes (DEGs) calling in an RNA-seq analysis. Status: done. Service: ready
  • contribution in the set-up of a pipeline for transcriptome de novo assembly. Status: in progress

Sangiovanni, Mara

Research fellow
Role in the bioinformatics unit:

  • contact person for implementation of IT technologies: database and software development
  • contact person for machine learning approaches
  • reference person for the LTER website implementation

Activities:

  • setting-up of the GENOMA platform (GENOmes for MArine biology). Status: in progress
  • contribution in the development of the “COMPARO” (COMparative genomics for PARalogs and Orthologs genes) software.  Status: in progress
  • Design and development of a parser to load a MongoDB database for the LTER-Marechiara data (Biogeochemical, Fitoplancton, Mesozooplancton). Status: ready
  • Design and development of a web-based system to visualize and search the LTER-Marechiara data. Status: stopped
  • Development of parsers, databases and APIs to store and query the MEDA biogeochemical/pictures datasets. Status: in progress

Piredda, Roberta

Research fellow: part time contributing to the service (⅕)
RIMAR/EMI contratto protocollo n.1602/2018

Role in the scope of the bioinformatics unit:

  • contact person for DNA barcoding projects development
  • contact person for DNA metabarcoding development or downstream analysis in ecological and evolutionary framework
  • contact person for phylogenetic inferences using nucleotide or amino acid sequences
  • Reference person to implement dedicated semi automated services

Activities:

  • Retrieval and analysis of marine metabarcoding datasets from public repositories. Service: ready
  • Analysis of temporal metabarcoding data from LTER-Marechiara. Status: done

Paolillo, Pietro

Intern
Federico II Computer Science Bachelor thesis internship, November 2018 to February 2019
Tutors: M. Sangiovanni, M. Miralto

Activities:

  • Design of a managing system for the Centro di Recupero Tartarughe Marine (CRTM) Portici. Status: completed
  • Development of the designed system exploiting open-source, state-of-the art technologies and architectures (MongoDB, Flask, REST APIs): Status: almost completed.
  • Upload and harmonization of the legacy data. Status: completed

Esposito, Mauro

Intern
Voluntary study visit from May 2018 to July 2018

Activities:

  • development of a “compositional windows analysis” software. Status: ready
  • testing and results comparison of different short sequences alignment software.

Publications

  • Tangherlini M.*, Miralto M.*, Colantuono C., Sangiovanni M., Dell’Anno A., Corinaldesi C., Danovaro R., Chiusano ML. “GLOSSARY: the GLobal Ocean 16S Subunit web Accessible Resource”. BMC Bioinformatics 2018.
  • Ambrosino L., Ruggieri V., Bostan H., Miralto M., Vitulo N., Zouine M., Barone A., Bouzayen M., Frusciante L., Pezzotti M., Valle G., Chiusano M.L. “Multilevel Comparative Bioinformatics to Investigate Evolutionary Relationships and Specificities in Gene Annotations”. BMC Bioinformatics 2018.
  • Ambrosino L.*, Vassalli Q.A.*, D’Agostino Y., Cetrangolo V., Caputi L., Amoroso A., D’Aniello S., Chiusano M.L., Locascio A.“Functional conserved non-coding elements among tunicates and chordates”. Developmental Biology 2018.

Presentations

  • Ambrosino L., Colantuono C., Sangiovanni M., Monticolo F., Chiusano ML., “Parallel genome annotation versions: the need for data reconciliation in genomics”, 12th BBCC – Bioinformatics and Computational Biology International Conference, Naples, Italy, 18-20 December 2017 (oral presentation by Dr. Colantuono).
  • Ambrosino L., Colantuono C., Miralto M., Sangiovanni M, Chiusano ML. “A multilevel comparative genomics approach to check for inter and intra species relationships and gene predictions quality”, 12th BBCC – Bioinformatics and Computational Biology International Conference, Naples, Italy, 18-20 December 2017 (oral presentation by Dr. Ambrosino).
  • Colantuono C., Miralto M., Sangiovanni M., Ambrosino L., Chiusano ML. “GENOMA: a multilevel platform for marine biology”, BBCC2018 Meeting, Naples, 19 – 21 November 2018
  • Sangiovanni, R. Piredda, M. Miralto, M. Tangherlini , M.L. Chiusano. “Data sharing and interoperability from multi-source long term observations: challenges and opportunities in marine biology”, BBCC2018 Meeting, Naples, 19 – 21 November 2018

Poster

  • Colantuono C., Mazzoleni S., Chiusano ML., “Going deeper in deep sequencing: looking for recombinants molecules”, 12th BBCC – Bioinformatics and Computational Biology International Conference, Naples, Italy, 18-20 December 2017.
  • Tangherlini M., Esposito A., Danovaro R., Chiusano ML., “Metagenomic approaches to unravel the microbiome of deep-sea loriciferans”, 12th BBCC – Bioinformatics and Computational Biology International Conference, Naples, Italy, 18-20 December 2017.
  • Tangherlini M., Miralto M., Dell’Anno A., Corinaldesi C., Danovaro R., Chiusano ML., “GLOSSARY: the GLobal Ocean 16S Subunit web Accessible Resource”, 12th BBCC – Bioinformatics and Computational Biology International Conference, Naples, Italy, 18-20 December 2017.

Submitted / in preparation manuscripts

  • Vassalli Q.A., Colantuono C., Nittoli V., Ferraioli A., Fasano G., Aniello F., Chiusano M.L., Kelsh R., Sordino P., Locascio A. “Onecut genes in photoreceptors differentiation and their evolutionarily conserved role up to vertebrates” (manuscript in preparation)
  • “GENOMA: GENOmes for MArine biology” (manuscript in preparation)
  • “Ciona robusta: genomes and annotations reconciliation for the marine model organism” (manuscript in preparation)   
  • “COMPARO: COMparative for PARalogs and Orthologs genes” (manuscript in preparation)

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