The Spatial Transcriptomics Toolkit: Memory, Clustering, and Deconvolution

A Comp-bio holiday calendar: 12 tools and tips to make this holiday season a fantastic one!

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/ncwo6HZeN4uA9gPg7 [https://forms.gle/ncwo6HZeN4uA9gPg7] Thanks to Amulya Shastry [https://www.linkedin.com/in/amulya-shastry/]for editing and management support. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ [https://www.linkedin.com/in/lpantano/] and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ [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 [https://podcast.ausha.co/a-coffee-with-compbio?s=1] Hosted on Ausha. See ausha.co/privacy-policy [https://ausha.co/privacy-policy] for more information.

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 down * Smart ways to communicate technology limitations early * What to say when pilot data quality is... not great * Why being adaptable beats being rigid every single time If you want to level up your collaboration game and avoid common pitfalls, grab your coffee and tune in. Thanks to Amulya Shastry [https://www.linkedin.com/in/amulya-shastry/]for editing and management support. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ [https://www.linkedin.com/in/lpantano/] and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ [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 [https://podcast.ausha.co/a-coffee-with-compbio?s=1] Hosted on Ausha. See ausha.co/privacy-policy [https://ausha.co/privacy-policy] for more information.

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/ [https://s-canchi.github.io/] Thanks to Amulya Shastry [https://www.linkedin.com/in/amulya-shastry/]for editing and management support. Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 [https://forms.gle/ncwo6HZeN4uA9gPg7] 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/ [https://www.linkedin.com/in/lpantano/] and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ [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 [https://podcast.ausha.co/a-coffee-with-compbio?s=1] Hosted on Ausha. See ausha.co/privacy-policy [https://ausha.co/privacy-policy] for more information.

(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/ncwo6HZeN4uA9gPg7 [https://forms.gle/ncwo6HZeN4uA9gPg7] https://ellmer.tidyverse.org/articles/ellmer.html [https://ellmer.tidyverse.org/articles/ellmer.html] https://lfaller.github.io/ [https://lfaller.github.io/] Thanks to Amulya Shastry [https://www.linkedin.com/in/amulya-shastry/]for editing and management support. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ [https://www.linkedin.com/in/lpantano/] and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ [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 [https://podcast.ausha.co/a-coffee-with-compbio?s=1] Hosted on Ausha. See ausha.co/privacy-policy [https://ausha.co/privacy-policy] for more information.

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/BPCells [https://github.com/bnprks/BPCells] https://github.com/prabhakarlab/Banksy [https://github.com/prabhakarlab/Banksy] https://github.com/dmcable/spacexr [https://github.com/dmcable/spacexr] https://github.com/bcbio/spatial-reports [https://github.com/bcbio/spatial-reports] https://github.com/seandavi/awesome-single-cell [https://github.com/seandavi/awesome-single-cell] https://positron.posit.co/ [https://positron.posit.co/] Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 [https://forms.gle/ncwo6HZeN4uA9gPg7] Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ [https://www.linkedin.com/in/lpantano/] and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ [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=1 [https://podcast.ausha.co/a-coffee-with-compbio?s=1] Hosted on Ausha. See ausha.co/privacy-policy [https://ausha.co/privacy-policy] for more information.