A Coffee with CompBio

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.

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.

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.

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.

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 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.