Computational biology PhD researcher. Interested in science, software development, and machine learning. I write about medical research at BioSky.co and contribute content to a variety of additional publications.CVAbout
Computational Biology PhD 2017
2014-2017 | Graduate Researcher | Australian National University
- Developed a new methodology using computer vision to quantify honeybee behaviour.
- My research experience has developed my ability to understand extremely technical research papers and synthesise their key findings into my own technical reports.
- I wrote my image analysis software in C++ and used machine learning to train the computer to distinguish different patterns in the tags I used on the bees.
- Developed a MySQL database in order to analyse large datasets using Python.
2013-2016 | Course Tutor | Australian National University
- Delivered tutorials to classes of up to thirty students for courses in molecular biology and software development.
2013-2014 | Researcher | CSIRO
- Developed a workflow for analysing count data from the Human Microbiome Project
- Built an interactive visualisation program using R
2013 | Researcher | CSIRO & Australian National University
- My research documented the genetic and morphological diversity of a parasitic mite representing a significant threat to the honeybee industry.
- My analysis of the data I collected provides a foundational understanding of the baseline diversity of this species.
2012 | Researcher | University of the Sunshine Coast & Kanazawa University
- Wrote Python scripts to identify conserved regions within viral genomes over the summer break. My program identified regions of viral genomes that were unique to different types of virus.
- Worked on a project where I learned how to elicit the proboscis extension reflex of the honeybee. Project involved weeks of work requiring intense concentration where I trained the bees to associate a scent with a sucrose reward.
2011-2012 | Web Developer | University of the Sunshine Coast
- Converted course content into HTML/CSS mark-up
- Undertook an upgrade of the university’s journalism website, involving the conversion of their video player from Flash to HTML5, transferring the website across to a new server and updated site layout
- I also designed websites in Photoshop and developed their HTML/CSS front-end for the Office of Learning and Teaching.
2011 | Web Developer | Pumpmaster
- Raised the Google page rank of the website by integrating social media into the site and adding regular content.
2015-2017 | Co-founder | Recomeal
- Finalist in the 2015 Innovation ACT business competition.
- My team worked on developing a business plan for a healthy meal planning app for university students. We surveyed over 200 students at self-catered colleges and interviewed key stakeholders within the university system including the heads of colleges and researchers who specialised in diet and nutrition.
- After the initial research phase, my role has been to develop the technical capabilities of the company. This has involved me setting up a MySQL database and developing a RESTful API in Python.
2016-2017 | Co-founder | BioSky
- Established BioSky as a site dedicated to making research papers, clinical trials and biological concepts accessible to people without a scientific background.
- Have written and edited multiple articles which are available at biosky.co/author/jacksimpson.
2015-2017 | Co-convener | COMBINE
- Organised programming, bioinformatics and machine learning workshops and training events for researchers at institutions within Canberra, including ANU, CSIRO and UC.
- The project management experience gained from planning and teaching at these events taught me a lot about coordinating with stakeholders including university admin, researchers, students and external contractors such as catering companies.
- Taught multiple workshops to scientists on Python and R.
- I developed a machine learning workshop to introduce programmers to core concepts in machine learning like splitting training and testing datasets, visualizing your data and using techniques like SVM to train a classifier.
- Some of my friends from Software Carpentry were able to teach a workshop with these materials at PyCon this year
2016 | Consulting Competition | ANU Consulting Society
- Entered a consulting competition organised by PwC and the ANU Consulting Society to learn more about the consulting industry.
- The team I was in collaborated closely to write a case report and give a presentation to PwC staff which resulted in us being amongst the top 4 teams selected to present to the PwC partners from more than 80 teams.
2016 | Participant | GovHack
- Image Analysis & OpenCV
- Machine Learning
- Databases & SQL
- HTML & CSS
Research & Analysis
- Research & Problem Solving
- Project management
- Communicating technical information in an accessible way.
- Data analysis and statistics
- Research and the ability to write technical reports
- Presentation skills