PyFlatten: A package for flattening nested data structures

Yesterday, I released PyFlatten to PyPI – it’s a utility that can flatten nested data structures (e.g. list of lists; dictionaries of lists of tuples) into a single 1-by-N vector, while also returning an ‘unflattener’ function that can restore the original data structure from the flattened version. The source code are available on GitHub, where I […]

Recent Papers

Finally, after ~2 years of learning, working, collaborating and writing, there’s been a slew of papers from our research lab going out. Really happy to have finally contributed to our collective scientific knowledge, both through my own efforts and through working with others. Here’s the list of papers, and I’m absolutely thrilled to have contributed […]

Webinar

Today, I gave a webinar to the IRD and ViPR technical and advisory board meeting. There were a number of challenges to giving a webinar that I want to reflect on here, as a note to my future self and others who may read this entry. In contrast to my previous entry, I’m choosing to […]

Flask, Jinja2, bootstrap.css – and thoughts on being a maker

I recently built a front-end GUI for one of my projects, which is a primer calculator for doing Gibson assembly with influenza segments. (small detour) The back-drop to this is that 7 years after the invention of the Gibson assembly method in the synthetic biology world (where I used to be), influenza researchers are still […]

Chalk Talk

Yesterday, I presented my work on influenza ecology and evolution at the Infectious Disease Program seminar series at the Broad Institute. Most of the talks I’ve seen there were Keynote or PowerPoint slide deck talks, and so this time round, I thought I might shake things up and do a chalk talk (or whiteboard talk) […]

Reticulate Evolution and Microbial Ecology

I am happy to announce that, with my advisor’s (Jon Runstadler, MIT) approval, I’ve uploaded my first 1st-author paper to BioRXiv. This may sound surprising, to document and write about the paper pre-peer review, rather than after being formally accepted after peer-preview in a journal. This choice is borne out of two desires. Firstly, I […]

Software Engineering Skills for Data Analytics

When you think about software engineering skills, you probably don’t think about the analytics types, or data scientist (DS) teams. This is a reasonable thought. Data scientists aren’t in the business of building software, they’re in the business of using software to analyze data. That said, I think it’s still important for a data scientist […]