Brief résumé (English)

Submitted by toniher on

Personal data

Toni Hermoso Pulido
Birth: Granollers, September 11, 1980
Residency: Barcelona
Email address: toniher@cau.cat
LinkedIn: https://www.linkedin.com/in/toniher
Publications / ORCID: https://orcid.org/0000-0003-2016-6465
Code repositories: https://github.com/toniher
Slides and presentations: https://slides.com/similis

Professional experience

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

  • Setup 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 (reference)
  • 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.)
  • 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
  • Development and/or support of Bioinformatics pipeline, in most of the cases using Nextflow software (e.g., FA-nf)
  • Support for scientific reproducibility approaches using Linux container technologies (Docker, Singularity) and CI/CD (Github Actions, Gitlab)
  • 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 and support of in-house web services using containerization technologies (Docker, Podman, Docker compose) and software such as NGINX or Traefik
  • Deployment of cloud infrastructure based on AWS for online teaching activities (heavily used during COVID-19 lockdowns)
  • Set-up of data management and processing infrastructure for supporting massive PCR testing during COVID-19 pandemics (reference)
  • Development of API-based data pipelines and web applications for supporting CRG Genomics Unit workflows
  • Participation at CRG Research Data Management Committee. Support to users with Data Management Plan writing requests

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.com (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)
  • Containeirization: LXC, Docker, Podman, Singularity/Apptainer
  • 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)

Interests

  • Software Localization.

    Translation into Catalan of several widely used software such as MediaWiki or Zotero and, in the past, also popular applications such as Firefox browser

  • Open Science.

    Promotion activities focused on the benefits of open science within scientific organizations and for the future of research. (e.g., within FOSTER project)

  • Open Knowledge and Open Source.

    Mozilla

    • Engagement in activities about Open Web standards and Mozilla principles
    • Localization and documentation of several applications (e.g., Firefox or Thunderbird)
    • Provision of language support tools for final users (e.g., dictionaries)

    Long-time involved in Wikimedia and wiki-related projects

Membership

  • Softcatalà
    • Software localization, sysdamin 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

Others

  • B Spanish Driving Licence