Mark McDowall
Head of Dataops @Elsevier Scibite
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WORK HISTORY
Head of Dataops @Elsevier Scibite
EDUCATION
University of Dundee
PhD, Prediction of Protein-Protein Interaction
University of York
MRes, Bioinformatics
Durham University
BSc, Molecular Biology and Biochemistry
SKILLS
ABOUT MARK MCDOWALL
I lead a team of specialists in pipeline and infrastructure development solving scaling and automation issues for curation and data science teams.Specialities- Bioinformatics, Statistics, Next Generation Sequence (NGS) analysis, Ontologies, NER/NLP, HPCProgramming Languages- Python: 2005 to present. Developing APIs and pipelines for the Multiscale Complex Genomics project. Have also contributed to the Luigi Python module, on GitHub, extending it to run jobs in LSF- R: 2005 to 2010 regularly, as required ever since- Java: 2006 to 2010. Used it during the PhD for predicting protein-protein interaction using a naive Bayesian model- Perl: 2010 to 2019. Creating pipelines to import data from the PomBase project into Ensembl Fungi along with processing pipelines for PomBase, and various projects as part of Ensembl Core.Data Storage- MySQL: 2005 till present. Heavy use for the storage or large datasets. Worked on the optimisation of databases for use in web servers for efficient indexing and querying. Still enjoy the challenge makingqueries run faster - PostgreSQL: 2010 till 2019. Developed pipelines for importing curation data from Chado scheme into Ensembl- HDF5: 2016 till present. Development of storage mechanisms for several data types including for predicted 3D genomes and indexing of genomic data- Cassandra: 2016. Experimenting with data structures for storing 3D data.Webserver development- Drupal: 2010 till 2017. Developed the PomBase website using Drupal 6. Including numerous extra modules for caching and displaying data. Also assisted others with the development of Phytopath and Ensembl Genomes web servers- PHP, JavaScript: 2010 till 2017. Linked with the Drupal experience for the develpment of web services and interfaces- Java/JSP 2007 till 2010. The PIPs web server for the presentation of predicted protien-protein interactionsOperating Systems- Linux: 2005 till present. Use as my standard work and home operating system- Windows user platforms.
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