I am a passionate learner with an M.Sc. in Biochemistry, and over extensive experience in academic and industry research facilities.
I became proficient with Python using online courses, and started using programming as way to analyze large datasets. As I learnt more Python, I found a new love from programming. It reminded me of building with LEGO where each block is a piece of code. The goal being to build something complex that works together.
I have built my own small projects, and websites. I have taken University level courses in my spare-time, including bioinformatics, data structures, and machine learning (2022).
I now code in Python, Linux, Java, HTML, CSS, and Javascript and hope to add more to this list in the future. Below are some of my interesting projects
Currently constructing a RNA-seq pipeline to process raw sequencing data on HPC cluster (slurm), and return enrichment results of specific genes based on sample treatment. The pipeline is controlled by a Python script that calls Shell scripts onto HPC nodes to process data using fastp, multiqc, STAR, htseq, and deseq2 (R programming language).
Branch containing RNA-seq pipeline
Website coded using Python (Dash, Pandas, Plotly, Biopython). Recursively calculates all primers that match design guidelines for modification of nucleotides in a provided gene. Interactive primer design
In the future I plan to add ability to recognize gene IDs and directly import, as well as user control over design guidelines.
I built a simple game where the goal was to switch nucleotides (A, T, C, G) within a gameboard to try and match for provided codon. The goal of the game would be to complete the entire nucleotide sequence. It is a fun challenge in OOP programming, path-finding algorithms, and interactivity.
In the future I plan to add a GUI interface, give users the option to provide genes, and track a leaderboard.
As I am learning to code, I am always looking for new challenges. Advent of Code provides daily challenges in December (and remains posted afterwards) for people to solve. They also have a supportive community to help provide feedback and show the best answers for any giving problem. This is an incredible resource to practice my skills, especially when learning a new language.
Python-2019 -- Python-2020 -- Java-2020
From an early age, I've always loved solving puzzles. Science became the perfect outlet for that curiousity. I've since worked on developing clinical diagnostic tests, mapping protein-protein interaction changes in metabolic diseases, and characterizing mouse models of human genetic diseases. This work has led to international recognition and publications.
I am currently responsible the designing and carrying-out a wide range of sequencing projects. This includes advising on the overall approach, carrying out the bench-work, and running/maintaining the sequencing equipment itself.