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, they discuss some really innovative tools that have been rolled out this year. Tune in to listen to these 12 tools and how you might use them! And find out about the exciting announcement we have at the end!Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7Thanks to Amulya Shastryfor editing and management support.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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 you're figuring out if single-cell sequencing on mouse eyes is actually the move (hint: maybe start simpler), the data processing stage where quality issues rear their ugly head, and those uncomfortable conversations when results don't pan out.What you'll learn:How to redirect overambitious project plans without shutting people downSmart ways to communicate technology limitations earlyWhat to say when pilot data quality is... not greatWhy being adaptable beats being rigid every single timeIf you want to level up your collaboration game and avoid common pitfalls, grab your coffee and tune in.Thanks to Amulya Shastryfor editing and management support.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here:https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.https://s-canchi.github.io/Thanks to Amulya Shastry for editing and management support.Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7Please get in touch if you or your business would like to help support this podcast.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.Then we sit down with Lina Faller, a veteran in bioinformatics with nearly two decades of experience bridging software engineering, research, and pharma. Lina shares why she started blogging about sustainable data systems, leadership in tech, and the very human side of computational biology. We dive into one of her favorite topics: why computational biologists should keep lab notebooks (yes, even if your “lab” is just a laptop). From reproducibility to institutional memory to the art of “forensic bioinformatics,” Lina brings stories and advice that will be useful to anyone working with data.If you’ve ever forgotten what you coded six months ago (we’ve all been there), or wondered how AI might fit into documentation and knowledge-sharing, this episode is for you.Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7https://ellmer.tidyverse.org/articles/ellmer.htmlhttps://lfaller.github.io/Thanks to Amulya Shastry for editing and management support.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.https://github.com/bnprks/BPCellshttps://github.com/prabhakarlab/Banksyhttps://github.com/dmcable/spacexrhttps://github.com/bcbio/spatial-reportshttps://github.com/seandavi/awesome-single-cellhttps://positron.posit.co/Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/Thanks to Amulya Shastry for editing and management support.If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.Marty Cagan How I AI podcastSend us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7Please get in touch if you or your business would like to help support this podcast.Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.Send us your comments, questions, and suggestions using this form: https://forms.gle/ncwo6HZeN4uA9gPg7Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.In the “Quick Sips” segment, Alex and Lorena share tips on automating code linting with GitHub Actions. Finally, in our “Brewing Up Answers” segment, we chat about managing people in academia vs. industry, and why it’s a very different ballgame on each side of the fence.Send us your comments, questions, and suggestions using this form: https://forms.gle/ncwo6HZeN4uA9gPg7Also, we are looking for sponsors! Please get in touch if you or your business would like to help support this podcast .Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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. Thanks to our 300+ listeners of past episodes!Send us your comments, questions, and suggestions using this form: https://forms.gle/ncwo6HZeN4uA9gPg7Also, we are looking for sponsors! Please get in touch if you or your business would like to help support this podcast.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1Hosted on Ausha. See ausha.co/privacy-policy for more information.

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 new segments, Quick Sips and Brewing Up for Answers, we talk about PIXI for managing software environments and dig into the ever-present challenge of staying organized across complex projects.Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7Also, we are looking for sponsors 💰! Please get in touch if you or your business would like to help support this podcast 🙏.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1.Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/If you enjoyed the episode, please subscribe and leave us a review.Hosted on Ausha. See ausha.co/privacy-policy for more information.

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.Hosted on Ausha. See ausha.co/privacy-policy for more information.