Hire

Martin Fitzpatrick, Ph.D
Utrecht, the Netherlands
e: martin@mfitzp.io

Freelance software developer and data scientist using Python for machine learning, visualisation and application development. A big fan of optimisation and automation, I like to simplify the process of getting useful information out of data.

I am currently available for remote work. Have an interesting opportunity? Get in touch.

Services

  • Product feasibility consulting and platform advice.
  • Rapid Minimum Viable Product development — Django, Flask, PyQt.
  • Custom data analysis and visualisation — numpy, scipy, matplotlib, d3.js.
  • Machine learning, predictive models and insights — scikit-learn, scikit-image.
  • Automated workflow/pipeline construction for reproducible analyses.
  • Web application development — Django, Flask, JQuery, AngularJS.
  • Desktop application development — PyQt, wxWidgets.

History

A self-taught programmer with over 25 years experience dating back to the days of the ZX Spectrum and Sam Coupé. After dabbling in IT, I took a 7 year detour into biology, completing a Medical Science (BMedSc) degree, masters (MRes) and PhD in the metabolomics of inflammatory diseases, where I found myself using code to solve analysis problems. I had unexpectedly become a “bioinformatician”. Following a 2 year post-doctorate in bioinformatics and proteomics, I moved out of academic research to focus full-time on software development.

I code most happily in Python but remain familiar with a long list of languages that I learnt along the way including C, MATLAB, Pascal, Perl, PHP, Prolog, R, Sam BASIC and z80 ASM.

I write Python tutorials and books, and provide one-to-one code tutoring.

Software

  • biocyc - a Python package interface to the biocyc.org service, providing a caching API with support for user-friendly representations of data in Jupyter notebooks.
  • PaDuA - a Python package supporting scriptable and interactive (via Jupyter notebooks) processing and analysis of proteomic data. Visualizations via matplotlib and statistical modelling via scikit-learn.
  • Pathomx - a workflow-based GUI application for the analysis of complex datasets. Built using PyQt, numpy+scipy, with IPython (Jupyter) kernel, matplotlib visualisation and scikit-learn data analysis.
  • pyqtconfig - a configuration manager for PyQt applications, providing a simple Pythonic way to access, save and reload values of Qt widgets (as a Python dict). Supports automatic syncing of multiple linked widgets.
  • Wooey - automatically create Web UIs (WUI) from Python scripts. Django-based with celery job scheduling. Automatic generation of Django forms from argparse, click and docopt command lines. (See also: clinto for command line parsing).

For a complete list of developed software and libraries see apps and libs.

Academic Publications

Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. Martin A. Fitzpatrick, Catherine M. McGrath, Stephen P. Young. BMC Bioinformatics pmid:25490956 doi:10.1186/s12859-014-0396-9 (October 2014)

Metabolic profiling predicts response to anti-TNFα therapy in patients with rheumatoid arthritis. Sabrina R Kapoor, Andrew Filer, Martin A Fitzpatrick, Benjamin A Fisher, Peter C Taylor, Christopher D Buckley, Iain B McInnes, Karim Raza, Stephen P Young Arthritis & Rheumatism pmid:23460124 doi:10.1002/art.37921 (March 2013)

Metabolomics – a novel window into inflammatory disease. Martin A. Fitzpatrick, Stephen P. Young Swiss medical weekly pmid:23348753 doi:10.4414/smw.2013.13743 (January 2013)

Metabolomics in the Analysis of Inflammatory Diseases Sabrina Kapoor, Martin Fitzpatrick, Elizabeth Clay, Rachel Bayley, Graham R. Wallace, Stephen P. Young InTech ISBN:978-953-51-0046-1 (February 2012)

A complete list of publications, absracts and theses are available here.

Career

Oct 2016-Present Software Developer & Data Scientist
Freelance/contractor
Short and long-term contract projects primarily focused on using the scientific Python stack, matplotlib and pandas for data analysis, machine learning and visualisation. Experienced in user interface development and design, both on web (Django/Flask) and desktop (PyQt).

If you have an interesting project you would like to discuss please feel free to get in touch.

Oct 2014-Oct 2016 Postdoctoral Researcher (Bioinformatics)
University of Utrecht, Utrecht, Netherlands
Proteomic data analysis. Using the scientific Python stack, matplotlib and pandas to perform routine analyses and develop automatable workflows.

Skills

  • Web Site development (Django, Flask, Pelican) and front-end UI (HTML, CSS, JQuery).
  • APIs RESTful API design and development (Django rest framework, Flask)
  • Databases Relational database design and management (Postgres, MySQL) including ORM methods (Django, SQLAlchemy) and search platforms (Lucene/Solr)
  • Data Data processing and handling (pandas, numpy, scipy)
  • Visualisation Plotting figures and interactive dashboards (matplotlib, d3.js)
  • Statistics Standard parametric and non-parametric statistical tests (numpy, scipy)
  • Machine Learning linear models (PCA, PLS), decision trees and clustering algorithms (scikit-learn, scipy, Eigenvector PLS Toolkit)
  • GUI Graphical interface development (PyQt, PySide, wxWidgets)
  • Collaboration Experience working with international groups, both locally and remotely to successfully complete projects. Frequently collaborate with other programmers on open-source projects via Github.
  • Revision Control Git (preferred), SVN
  • Coding Style Adherence to PEP8 (pylint, pyflakes, PyCharm)
  • CI & Testing Experience using Jenkins CI on open-source projects
  • Documentation Pandoc (and readthedocs.org), asciidoc, markdown

Education

2011-2016 PhD.
School of Immunity & Infection, University of Birmingham, Birmingham, United Kingdom
Metabolic profiles of differentiated human macrophages and their influence in chronic inflammatory disease (Wellcome Trust Combined Training Programme)

2012-2014 Dutch Entry Stage 1
Brasshhouse Language Centre, Birmingham, United Kingdom

2010-2011 MRes. Biomedical Research
School of Immunity & Infection, University of Birmingham, Birmingham, United Kingdom
The Immune System in Health & Disease (Wellcome Trust Combined Training Programme). Consisting of two short research projects: “Tracking viral entry into target cells by virological and immunological methods” and “Do differentiated macrophages display distinct metabolic phenotypes reflecting their different functions?”

2007-2010 BMedSc. (Hons) Medical Science (Cellular and Molecular Pathology) (1st)
University of Birmingham, Birmingham, United Kingdom
Dissertation topic: “What is the impact of vaccination on the development of adaptive immunity to Non-typhoidal Salmonella?”

2001-2002 Certificate of HE - Psychology, Artificial Intelligence & Linguistics
University of Edinburgh, Edinburgh, United Kingdom

FE Qualifications Chemistry (Scottish Higher; 2006), Computer Science, Biology, Communication Studies, General Studies (A Level; 2000) at Grade A.