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Bertrand Caron Software Engineer | Data Scientist

Brisbane, Australia


Former PhD Student in Computational Biochemistry with 4 year experience in Software Engineering, DevOps and Data Science looking for challenging opportunities in the Tech sector.


PhD Student (Supervisor: Prof. Alan E. Mark)

Brisbane, Australia
The University of Queensland
April 2015 - Now
During my PhD, I have developped the following skills:
  • Software Engineering I have written code for more than 30 projects, some of them open source and available on my Github. They total tens of thousands of lines of code and span areas ranging from graph matching to combinatorial optimisation.
  • Communication I have presented my PhD work at conferences in multiple countries: Germany, The Netherlands, Switzerland.
  • Project Management and Collaboration I have led multiple international collaborative projects: Bennion Brian (LLNL, USA), Engler Martin (HHU, Germany).
  • Writing I have co-authored multiple scientific papers and wrote a thesis (120 pages and counting).
  • Data Analysis I have analysed large datasets in search of patterns.

Research Assistant (Supervisor: Prof. Alan E. Mark)

Brisbane, Australia
The University of Queensland
Jan 2015 – Mar 2015
The Automated topology Builder and Repository is a python-CGI website backed up by an MySQL database and sitting on an Apache server. It totals 180,000 submitted molecules, more than 6,500 users and up to 2,000 page views per day. My contributions involved:
  • Database Refactoring: Shrinking the database by 95% by moving files from the database to the file system.
  • MVC Refactoring: Refactoring of the code to comply to the Model - View - Controller paradigm. Heavy use of Jinja2 templates
  • Implementation of a RESTful API: Both as a way to integrate new features as well as standardising old ones.
  • Search Engine Optimisation (SEO): Implementation of a SEO strategy with Google Analytics, tracking of download and topology generations with custom-labeled events

Experimentally-guided coarse-grained RNA folding (Supervisor: Prof. Samuela Pasquali)

Paris (France)
Laboratoire de Biochimie Theorique (LBT), Institut de Biologie Physico-Chimique (IBPC)
Feb-July 2014
  • Development of SAXS-CG, an Ab-Initio Small-Angle X-ray Scattering (SAXS) profile prediction tool written in Fortran

Properties of Model Regnum-Specific Lipid Bilayers (Supervisor: Dr. David Poger)

Brisbane (Australia)
School of Chemistry and Molecular Biosciences, The University of Queensland
Feb-July 2013
  • Advanced shell scripting (awk) and data visualisation (gnuplot), Python programming (Quantum Mechanical output text parser)

Introduction to Protein Dynamics (Supervisor: Dr. Sophie Barbe)

Toulouse (France)
Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP)
June-July 2012
  • Discovery and use of scientific software: Unix Environment, Shell Scripting (Bash, Zsh)


PhD (Doctor of Philosophy) in Computational Biochemistry

Brisbane (Australia)
The University of Queensland
April 2015 - Now
  • Thesis title: "Improving Automated Force Field Parametrisation for Molecular Simulation: A Graph Approach" (Link)
  • Funded by a UQI scholarship.
  • Submitted (October 2018), currently under review.
My thesis focused on the use of graph-based approaches to develop new automated parametrisation paradigms which can exploit large data sets to simultaneously develop and assign parameters for empirical force field used in Biomolecular simulations. Many of the tools developed as part of this thesis have been open-sourced on Github ( and have been made available to the scientific community.

Master of Science and Technology in Analytical, Physical and Theoretical Chemistry

Paris (France)
École Normale Supérieure (ENS) - University Pierre and Marie Curie (UPMC)
2012 - 2014
Relevant courses: Multi-scale modelling of complex systems, Modelling principles and methods of molecular properties, Molecular modelling: applications, Elementary processes in chemical reactivity: from simple to complex systems.

Bachelor of Science and Technology in Chemistry

Paris (France)
École Normale Supérieure (ENS) - University Pierre and Marie Curie (UPMC)
2011 - 2012
Relevant courses: Cell Molecular Biology, Chemical Kinetic and Reactivity, Intermolecular Bonding.

"Classe Préparatoire aux Grandes Écoles" in Physics, Chemistry and Engineering Sciences

Paris (France)
Lycée Henri IV
2009 - 2011
Two-year intensive Chemistry (12 hours/week), Mathematics (12 hours/week) and Physics (10 hours/week) courses to prepare for a two-month national examination. Received at the École Normale Supérieure ULM.

"Baccalauréat Scientifique", English European Section, magna cum laude ("Mention Très Bien")

Amiens (France)
Lycée Louis Thuillier
2008 - 2009


Computer Languages


Lambda functions, major libraries (subprocess, sciPy, numPy), module development


Development of modules, derived types, operator overloading


Ruby on Rails Framework


Functional programming in bash, development of large libraries (2k+ lines), multithreaded scripts


Common libraries (jQuery, flot.js), simple web interfaces (AJAX requests, callbacks)


Basic functional programming: static typing, currying, pattern matching, guards


Cocoa framework, XCode

Markup - Typesetting - Data Visualisation

Data Visualisation

Advanced scientific plotting experience: matplotlib (Python), flot.js (Javascript)


Experience with advanced Markup: Google's structured data, templating


Experience with popular libraries (Bootstrap) and icons (Font Awesome)


Typesetting large, complex documents with a robust, programmable and version-controlled approach


MySQL - MariaDB - SQLite

Experience with large tables (millions of rows), table refactoring, query optimisation


Basic usage (implementing a functional cache)

Workflow Tools


Advanced git worklow: branching, merging, rebasing, submodules


Mouse-free productivity, most advanced features : syntax highlighting, code folding, key mapping


Automated data-driven workflows

Programming Paradigms

DRY (Don't Repeat Yourself)

Extensive eperience with refactoring large, legacy codebases

Functional Programming (FP)

Haskell, Functional Python (no control flow statement, writing pure functions)

Test Driven Development (TDD)

Testing libraries: unittest (Python), cucumber (Ruby); code coverage

Object-Oriented Programming (OOP)

Python Classes, Inheritance

Continuous Integration

Experience with Gitlab CI, continuous deployment with git submodules

Coding Techniques

Code Optimization

Experience with profiling tools: Apple's Instruments, GDB, Python's PDB

Code Parallelization

Experience with both OpenMP and MPI


Linux Distributions

Experience with Ubuntu (14.04, 16.04), CentOS (6, 7), Darwin; package managers

Hosting - Web Servers

DNS Records, Apache, NGINX, CGI (uwsgi, Flask), HTTP/HTTPS

Cloud Computing

Amazon Web Services (AWS) EC2 (t2.micro), Nectar Research Cloud, HPC


The molecular origin of anisotropic emission in an organic light-emitting diode

Nano Letters (2017)
T. Lee, B. Caron, M. Stroet, D.M. Huang, P.L. Burn, A.E. Mark

Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light‐Emitting Diode Films

Angewandte Chemie (2017)
C. Tonnelé, M. Stroet, B. Caron, A.J. Clulow, R.C.R. Nagiri, A.K. Malde, P.L. Burn, I. R. Gentle, A.E. Mark, B.J. Powell

Validating lipid force fields against experimental data: Progress, challenges and perspectives

BBA - Biomembranes (2016)
D. Poger, B. Caron, A. E. Mark

Some Like It Hot: The Relative Effect of Membrane Composition on Lipid Ordering

J. Phys. Chem. Lett. (2014)
B. Caron, A.E. Mark, D. Poger

Effect of Methyl-Branched Fatty Acids on the Structure of Lipid Bilayers

J. Phys. Chem. B (2014)
D. Poger, B. Caron, A.E. Mark



Brisbane (Australia)
The University of Queensland
August 2015 - November 2017
  • CHEM3011: Advanced Physical Chemistry Semester 2, 2015-2017: 16-45 students, 3 hours per week
  • SCIE2100: Introduction to Bioinformatics Semester 1, 2016-2017: 52-55 students, 3-6 hours per week (2016: received tutor award)

Tutor - Oral Examiner (2 hours/week, groups of 3-4 students, class of 40+)

Paris (France)
Lycée Henri IV
August 2015 - November 2017
Oral examiner for students in first year of 'Classe Préparatoire aux Grandes Écoles' in Physics, Chemistry and Engineering Sciences.


HealthHack BNE (3rd place)

November 2017
Andra: A robot conversation with patients to encourage healthy lifestyle choices
November 2017

Tutor Award – School of Chemistry and Molecular Biosciences (SCMB)

October 2016
Awarded to top 10% tutors
October 2016

Shortlisted for the 2015 Lush Prize (Young Researcher Category)

August 2015
August 2015

2015 CTCMS Symposium Poster Prize

May 2015
Awarded first prize for 'Insights Into the Structure and Order of Bacterial Membranes'
May 2015

UQ International Scholarship (UQI)

April 2015
Scholarships awarded competitively, based on merit, to outstanding international students undertaking a research higher degree.
April 2015

XXVth French Chemistry Olympiads (2nd)

Medaled by the French Academy of Science for ranking Second.


Prof. Alan E. Mark

VC Senior Research Fellow, School of Chemistry and Molecular Biosciences, The University of Queensland (Australia)

Assoc. Prof. Mikael Boden

Course Supervisor (SCIE2100), Assoc. Prof. of Bioinformatics, The University of Queensland (Australia)