A Coffee with CompBio

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

16min | 09/23/2025

Description

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://ellmer.tidyverse.org/articles/ellmer.html

https://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=1

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

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

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

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

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

Description

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://ellmer.tidyverse.org/articles/ellmer.html

https://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=1

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

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

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

About A Coffee with CompBio

Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode, they break down complicated analyses, demystify big data approaches, and share real-world stories from their own bioinformatics research adventures. Whether you’re a seasoned bioinformatician or just bio-curious, Alex and Lorena's engaging banter, expert interviews, and practical tips will guide you through the fascinating process of turning raw biological data into meaningful scientific discoveries. Join them as they make computation in the life sciences accessible—and even a little bit fun!

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

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