Brief résumé (English)

Submitted by toniher on

Personal data

Toni Hermoso Pulido
Email address:
Code repositories: https://github.com/toniher
Slides and presentations: https://slides.com/similis

Profile

Bioinformatician (PhD, Biotechnology) who builds software and infrastructure for life-science research. Long-standing experience at the CRG maintaining data pipelines, biological databases and core-facility systems. A major contributor to the centre's training in reproducible research and Activity Lead in the ELIXIR Interoperability Platform, coordinating work across European institutions. Sits on the board of the Societat Catalana de Biologia and contributes to open science and open-source projects.

Professional experience

Specialised bioinformatician at the Bioinformatics Core Technologies Unit, CRG, 2009-present

Strategic and collaborative initiatives
Infrastructure and Core Services
  • Set-up of a Drupal website as a CMS for Bioinformatics scientific programme groups
  • Deployment and development of MediaWiki instances as Lab Information Management Systems (LIMS) in several units and laboratories at the CRG
  • Development and support of fee accounting and tracking solutions within the Scientific Core Technologies Units at the CRG
  • Deployment and survey design of the periodical assessment of user satisfaction of Scientific Core Technologies Units at the CRG
  • Maintenance and curation of the in-house mirroring of several popular biological resources used by the CRG community (NCBI, ENSEMBL, KEGG, etc.)
  • Support for scientific reproducibility approaches using Linux container technologies (Docker, Singularity) and CI/CD (Github Actions, Gitlab)
  • Deployment and support of in-house web services using containerization technologies (Docker, Podman, Docker compose) and software such as NGINX or Traefik
  • Set-up of data management and processing infrastructure for supporting massive PCR testing during the COVID-19 pandemic (reference)
  • Development of API-based data pipelines and web applications for supporting CRG Genomics Unit and Proteomics Unit workflows (e.g., Qsample)
Bioinformatics development
  • Development and/or support of Bioinformatics pipeline, in most of the cases using Nextflow software (e.g., FA-nf or ExOrthist)
  • Development and maintenance of biological databases websites (e.g., MyMPN or VastDB)
  • Support and deployment of genomics browser solutions (using UCSC Genome browser or IGV.js)
  • Development of novel web-based support applications (e.g., CRISPETA or Pergola) using web technologies based either in Python or NodeJS
Training and assessment
  • Design, teaching and/or support of training activities for either the CRG community or external partners. Courses mostly centred on scientific reproducibility techniques (more details...)
  • Deployment of cloud infrastructure based on AWS for online teaching activities (heavily used during the COVID-19 lockdowns)

New website development at Softcatalà, 2008

  • Sysadmin deployment on top of LXC (Linux containers)
  • Web development and design using the following frameworks:
    • Drupal
    • Mediawiki
    • Scripting (using PHP and Perl) for supporting different periodic tasks

Web developer at Careesma (Grupo Intercom, 2007-2008)

  • Study of Web 2.0 technologies applied to career recruiting and social networks
  • Web scraping
  • PHP programming
  • XML data interchange processing (e.g. with XPath)

Scholarship holder at Institut de Biotecnologia i Biomedicina (UAB), 2002-2007

  • Protein studies on phylogeny, taxonomy and classification of new protein families (metallocarboxypeptidases)
  • Creation of web applications for retrieving different biological data
  • Data mining and database management (MySQL)
  • Handling of existing biological APIs (e.g., ENSEMBL) for gathering new and pre-existing data
  • Usage and managing of several Bioinformatics Linux applications
  • Perl programming and scripting (e.g. with BioPerl)

Education

  • B.Sc. Biochemistry, UAB (2002)
  • M.Sc. Biotechnology, UAB (2005)
  • PhD. Biotechnology, UAB (2015)

Other

Research stays

  • Laboratories of Molecular Biophysics, Rockefeller University, New York - USA (2002)
  • Andrej Sali Lab. Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, UCSF, San Francisco - USA (2004)

Additional details

Skills

  • Programming languages: Bash, Perl, Python (Pandas, Scikit-learn), PHP, Javascript (NodeJS, jQuery), Java
  • DBMS: MariaDB/MySQL, PostgreSQL, SQLite. CouchDB/PouchDB, Redis. Neo4j
  • Web frameworks: Express (NodeJs), MediaWiki (PHP), Flask (Python), Django (Python)
  • Version control systems: RCS, Subversion, Git (GitHub, Gitlab)
  • CI/CD: GitHub Actions, GitLab CI
  • Containerization: LXC, Docker, Podman, Docker Compose, Singularity/Apptainer
  • Web serving / reverse proxy: NGINX, Traefik
  • Orchestrators: Nextflow
  • Cloud: AWS (deployment with Terraform)
  • Big data: AWS Glue, Spark/Hadoop

Languages

  • Catalan (Native)
  • Spanish (Native)
  • English (Full Professional Proficiency) - Certificat d'Aptitud d'Anglès EOI (1999)
  • Romanian (Elementary Proficiency)

Open source and community

  • Software localization.

    Translation into Catalan of widely used software such as MediaWiki and Zotero, and previously Firefox.

  • Open science.

    Promotion of open-science practices within scientific organizations (e.g., the FOSTER project).

  • Bioinformatics pipelines.

    Contribution to nf-core, the community effort for reproducible Nextflow pipelines.

  • Mozilla and the open web.
    • Contribution to open web standards and Mozilla principles
    • Localization and documentation of applications (e.g., Firefox, Thunderbird)
    • Language-support tools for end users (e.g., dictionaries)
  • Wikimedia and wiki projects.

Membership

  • Softcatalà
    • Software localization, sysadmin tasks and writing of policy documentation
  • Societat Catalana de Biologia (currently in organization's board)
    • Biological Sciences' promotion activities, support to web initiatives and interaction with third-party providers