A Coffee with CompBio

As our first season comes to an end, we would like to wish all of our listeners a very happy holiday season . But wait! We also have some presents for our listeners. In this episode of “A Coffee with Compbio”, Lorena Pantano and Alex Bartlett present 12 cool things in bioinformatics.  From a tool that will rescue you out of Python dependency hell to the one that can generate a functional genome, t...

What really happens when a wet lab scientist and a computational biologist sit down to plan an experiment? Spoiler: it's not always smooth sailing. In this episode of 'A Coffee with Compbio,' Lorena Pantano and Alex Bartlett chat with Amulya about the real talk nobody tells you about scientific collaborations. They break down the three make-or-break moments of any project: that first meeting where...

In this episode of A Coffee with Comp Bio , hosts Alex Bartlett and Lorena Pantano sit down with Saranya Canchi, a computational biologist specializing in neuroscience. Together, they explore how to thrive as a self-directed learner in bioinformatics—tackling early challenges, learning through projects, and building problem-solving resilience. Saranya shares her journey as a self-taught bioinforma...

Grab your coffee and join us for another episode of Coffee with CompBio !  This time, we kick things off with Amulya, a PhD student at Boston University and co-chair of Boston Women in Bioinformatics, who introduces us to llmr — a new Tidyverse-friendly tool for connecting with LLMs like ChatGPT, Gemini, and more. Think structured outputs, agent workflows, and even building your own chatbot in R....

In this episode, Alex and Lorena tackle the computational challenges of spatial transcriptomics. Learn how BPCells can help you work with millions of cells without needing terabytes of RAM, discover how Banksy's neighborhood-aware clustering reveals tissue architecture, and explore RCTD's approach to cell type deconvolution in spatially-resolved data. Plus, Lorena reviews Positron, the new R-frien...

Alex Barlett and Lorena Pantano welcome Katie Hughes, their first guest, to discuss her career transition from bioinformatics to product management. Katie shares her journey from studying genetics, working in wet labs, and discovering a passion for bioinformatics, to eventually earning a master's degree in the field. She details her experience at various biotech companies, including Harvard Medica...

Alex and I dig into the tricks and tips that'll actually make your R code work better. We're talking about ditching those old habits we all picked up and switching to code that works better in 2025. We cover over 10 solid habits that'll seriously boost your R game - everything from how you're reading and storing files, making plots that are publish-ready, theming, data manipulation, and setting up...

In this episode, we journey through the real-life challenges of building interactive single cell spatial data visualizations for large projects. Lorena shares her recent adventure turning mountains of data into a web app using tools like Python, R, and the (tricky-to-pronounce) single-cell viewer Vitessce . She discusses the hurdles of image cropping, memory limits, Python-R crossovers, and why “j...

Alex and Lorena discuss a large bulk RNA-seq project that yielded lasting changes to their group’s everyday bioinformatics practices via the creation of parameterized R Markdown code templates. In the “ Quick Sip ” segment, they discuss reticulate for managing python environments in an R context, and in “ Brewing Up Answers ”, they reflect on the differences between industry and academia bioinform...

In this episode of A Coffee with CompBio , Lorena and Alex share the twists and turns of realizing their methylation data wasn’t what it seemed. From puzzlingly low mapping rates to unexpected cloud costs caused by unoptimized compute jobs—thankfully caught just in time thanks to cost alarms—they highlight how essential clear communication and bioinformatics-aware experimental design are to any su...

In our first episode, Alex and Lorena dive into the messy reality of processing single-cell RNA-seq data. What started as a simple QC project turned into a week-long journey across compute environments, mysterious pipeline errors, and zero-cell outputs. Along the way, we troubleshoot issues with Cell Ranger, uncover strange sequencing artifacts, and reflect on lessons in data handling, pipeline re...

In the introductory episode, Lorena and Alex introduce themselves and share how they got started in computational biology. They talk about their career paths, what drew them to bioinformatics, and some of the challenges and surprises they’ve encountered along the way. They also give a preview of the kinds of topics and practical issues they’ll be covering on the podcast, from workflow basics to tr...