A Coffee with CompBio

• Collaboration Survival Guide for 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.

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• A coffee with Saranya Canchi - Fail, learn, repeat, the bioinformatics way!

  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.

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• (Dry) Lab Notebooks: The Importance of Recordkeeping in CompBio

  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.

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• The Spatial Transcriptomics Toolkit: Memory, Clustering, and Deconvolution

  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.

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• A coffee with Katie Hughes - First hand experience on transitioning to a Product Manager role

  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.

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