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Lucas Sinclair, Python Developer in Milan, Metropolitan City of Milan, Italy
Lucas Sinclair

Python Developer in Milan, Metropolitan City of Milan, Italy

Member since July 17, 2018
Lucas has a master's degree from the Swiss Institute of Technology (EPFL) and a PhD in bioinformatics from Uppsala University. He specializes in data analysis, mining, and visualization as well as GUIs and teaching; he often deals with biologically-related data but not always. He can automate things and create custom data processing pipelines with his eight years of experience in the field. Give Lucas any kind of IT problem and he'll solve it.
Lucas is now available for hire

Portfolio

Experience

  • Bioinformatics, 8 years
  • Python, 8 years
  • System Administration, 7 years
  • Data Visualization, 7 years
  • Statistical Analysis, 6 years
  • University Teaching, 6 years
  • User Interface (UI), 4 years
  • Data Mining, 4 years
Milan, Metropolitan City of Milan, Italy

Availability

Part-time

Preferred Environment

Sublime Text, PyCharm, Git CLI, macOS, LaTeX

The most amazing...

...and longest-running project I’ve built was an app that would automate the analysis of high-throughput DNA sequencing data from ecological samples.

Employment

  • Freelance Consultant in Data Science, Biology, Education, and IT

    2016 - 2018
    Sinclair.Bio
    • Consulted on various projects for different partners across Europe.
    • Developed online platforms.
    • Built custom pipelines.
    • Conducted ecological analyses of microbial communities.
    • Worked on other projects that are under NDAs.
    Technologies: Python, C, Git, LaTeX, Django, Flask, ML, System Administration
  • Post-doctoral Fellow

    2017 - 2017
    University of Geneva
    • Enrolled in the laboratory of Molecular Systematics & Environmental Genomics.
    • Performed ecological studies on microbial communities using high-throughput DNA sequencing.
    • Wrote scientific articles for publication.
    • Collaborated with over-seas scientific partners.
    Technologies: Python, LaTeX, Git, Excel, PyCharm
  • Lead Teacher for Graduate Python Course

    2016 - 2016
    Uppsala University
    • Designed and obtained funding for a Python course aimed at data analysis in STEM fields.
    • Taught up to 20 PhDs students at a time.
    • Taught theory, provided exercises, and graded personal projects during the course.
    Technologies: Python, Git, Big Data
  • Scientific Assistant in the Bioinformatics Core Facility

    2010 - 2012
    École Polytechnique Fédérale de Lausanne
    • Collaborated as a consultant with different laboratories within the university on research projects.
    • Helped, in a team, develop and use novel tools for processing and analyzing genomic high-throughput sequencing data catering to their scientific questions.
    • Developed longer lasting software and online platforms designed to be used by our scientific partners in research. One major project was an interactive genome browser.
    Technologies: Python, JavaScript, Ruby, Git, SVN, UX

Experience

  • Linking Sequences to Environments Through Text Mining (Development)
    https://peerj.com/articles/2690/

    A first-author publication in which we analyzed high-throughput sequencing data in novel ways, in particular with text mining.

    We performed similarity searches of short DNA sequences against publicly available nucleotide database and proceeded to apply text-mining on the associated metadata of every hit.

    Classifying the resulting vocabulary in a hierarchical-ontology method, enabled us to better contextualize the results of microbial ecology experiments through comparative statistics and quantitative descriptions.

  • Python Library for Easy IO with Genomic Tracks (Development)
    https://github.com/xapple/track

    One of the routine operations in medical bioinformatics is to read and write results from "genomic track" files. These files come in a wide variety of formats but all represent either a series of intervals along a one-dimensional genome or a discrete signal varying along the genome.

    This library enables easy IO operations in Python in a fashion that is independent of the underlying format.

  • Python Course for PhDs in STEM Fields (Other amazing things)
    https://sinclair.bio/pdf/python_syllabus.pdf

    In this project, I designed, obtained funding for, and led a Python course aimed at teaching data analysis to graduate students at the University of Uppsala.

    The course fit 20 PhDs students at a time (from all the STEM fields) and included theory, exercises, and a personal project.

    It focused on writing programs to process, filter, clean, analyze, and visualize scientific data as well as the ability to automate the computational tasks that are used in day-to-day research.

  • Development of an Online Platform for Data Distribution (Development)
    http://anaerodynamics.com

    In this project, I planned, developed, and deployed a Python web server acting as a public data repository. The results contained in the repository concern microbial community analyses from industrial digesters producing biogas.

  • Pipeline for Automation of Microbial Community Analyses (Development)
    https://sinclair.bio/pdf/cluster_report.pdf

    In this project, I designed and developed a Python pipeline that automates the cleaning, processing, analysis, and visualization of the data obtained from sequencing a series of microbial communities.

    The program takes as input N files containing the raw output of the DNA sequencer and outputs a PDF report (example shown below) summarizing the salient characteristics of each sample as well as biodiversity indicators and a comprehensive comparison.

  • Publication: Bacterial Diversity Along a 2,600-kilometer River (Development)
    https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.12886

    In this publication, I was tasked with performing the required bioinformatics and biostatistics on the ~100 samples sequenced as part of a comprehensive study of the Danube's microbial communities.

    My tasks also included producing the various figures that the article needed.

Skills

  • Languages

    Bash, Python, LiveCode, R, AppleScript, SQL, JavaScript, C, Java
  • Libraries/APIs

    Pandas, NumPy, Scikit-learn, Node.js, HDF5
  • Tools

    PyCharm, LaTeX, Biopython, Adobe Illustrator, Microsoft Excel, MATLAB, Adobe Photoshop
  • Platforms

    Linux, MacOS, Heroku, Windows, Docker
  • Other

    University Teaching, Bioinformatics, Data Visualization, Test Case Development, Molecular Biology, Genetics, User Interface (UI), System Administration, Statistical Analysis, Data Mining, Image Processing, Ecology, Dash
  • Paradigms

    Pipeline programming, Agile Software Development, Functional Programming
  • Storage

    SQLite, PostgreSQL, MongoDB
  • Frameworks

    Django, Flask, Machine Learning

Education

  • Doctor of Philosophy (PhD) degree in Bioinformatics, Genetics, and Aquatic Microbial Ecology
    2012 - 2016
    Uppsala University - Uppsala, Sweden
  • Master of Science degree in Life Sciences and Technologies
    2008 - 2010
    École Polytechnique Fédérale de Lausanne - Lausanne, Switzerland
  • Bachelor of Science degree in Life Sciences and Technologies
    2005 - 2008
    École Polytechnique Fédérale de Lausanne - Lausanne, Switzerland
  • Swiss high school diploma in Specialization: Physics and Applied Mathematics
    2002 - 2005
    Collège de Saussure - Geneva, Switzerland
Certifications
  • Academic Teacher Training
    JANUARY 2016 - PRESENT
    Uppsala University
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