a coffee with compbio by Lorena Pantano
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.
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.
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 bioinformatician, highlighting the importance of mastering the field’s unique language and embracing failure as part of growth. Whether you’re just starting out or looking to strengthen your learning approach, this conversation offers practical insights and inspiration for your bioinformatics journey.
Grab your coffee and join us for another episode of Coffee with CompBio!
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-friendly IDE that's catching attention in the bioinformatics community.
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 Medical School, Moderna, Sonata Therapeutics, and Generate Biomedicines. Katie emphasizes the importance of curiosity, adaptability, and soft skills in making career transitions. She explains what a product manager does, differentiates it from similar roles, and outlines the skills and experiences that helped her succeed. The discussion also covers the day-to-day responsibilities of a product manager, the collaborative nature of the role, and advice for those interested in making a similar career shift.
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 environments so your code works when you come back to it later. If you want to up your R skills, this one's got practical stuff you can start using right away.
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 “just putting it online” isn’t as easy as it sounds—especially when it comes to privacy, deployment, and avoiding surprise cloud bills.If you’ve ever had a collaborator say, “Can you just build me an app I can play with?”, this episode is for you.
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 bioinformatics.
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 successful project.
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 reproducibility, and client communication.
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 troubleshooting analysis hiccups.
