OMGenomics Podcast

Valerie de Crissy-Lagard, a seasoned scientist specializing in enzyme function prediction, and Rachel Thomas, co-founder of Fast AI and an AI expert pursuing a PhD in immunology, discuss the promising yet precarious role of AI in biological research. They delve into a case where AI's enzyme predictions fell short and emphasize the dire need for collaboration between machine learning experts and biologists. With insights on automation bias and the intricacies of genomic annotation, they highlight the importance of a multidisciplinary approach to enhance research quality.

We talked about what scientists do with their lives after their PhD. Ashley is a PhD student herself who created PhDPaths by interviewing hundreds of PhD graduates about their career paths outside academia. Join the discussion in the comments on YouTube: https://youtu.be/rU8EAT1RJYY Where to find us online: https://omgenomics.com

We discuss our experiences with rewriting software, why it's nearly always a bad idea, and the ONE situation where it's justified anyway. Join the discussion in the comments on YouTube: https://youtu.be/5JDhydALi8c Where to find us online: https://omgenomics.com

Academic software has a bad reputation for being poorly maintained. We discuss our experiences maintaining our own bioinformatics tools and the systemic issues that influence the quality of academic software. Topics * Lessons we've learned from maintaining our 8+ year old tools: Ginkgo, Assemblytics, SplitThreader, Ribbon. * Discussing career implications and systemic incentives of maintaining academic software. * How we build bioinformatics web apps today versus when we first started out. * Supporting users when you're not even in that field anymore. * Lots of embarrassing stories of bad software engineering in bioinformatics tools. Join the discussion in the comments on YouTube: https://youtu.be/eyd7Cb7ueNg * For academics, do any other metrics get considered for your tools other than citations? * How do you cite tools you used that you didn't mention in the methods, e.g. samtools, parallel, IGV. * Do any programs match up volunteer experienced software engineers with scientists writing software? Where to find us online: https://omgenomics.com

In the last episode of the season, we discuss Cal Newport's book "So Good They Can't Ignore You" and our experience applying those ideas to bioinformatics. Topics: * Why "follow your passion" is bad advice, especially in science. * Career capital: acquiring rare and valuable skills to craft a career you'll love. * How your personality affects which skills you might pursue. * Deliberate practice and deep work. Where to find us online: https://omgenomics.com

We interview Kaja Wasik, co-founder of Variant Bio, whose goal is to develop new therapies by studying the genetics of communities with exceptional health traits. Topics: * Kaja's circuitous journey in the biotech startup industry. * How Variant Bio ethically collects genetic data from more than 20 populations worldwide. * Their unique approach to benefit sharing with the communities they work with. Show notes: * Kaja's fundraiser for Life Science Cares: https://www.justgiving.com/fundraising/kaja-wasik1 * Twitter: Twitter: https://twitter.com/kajawasik * LinkedIn: https://linkedin.com/in/kaja-wasik-8a8aa26b/ * Variant Bio's work in French Polynesia: https://vimeo.com/683490754 * Variant Bio's work in the Faroe Islands: https://vimeo.com/705567729 Where to find us online: https://omgenomics.com

Nils Homer, co-founder of Fulcrum Genomics, brings his bioinformatics expertise to the table. He shares insights on launching a consulting business driven by the desire for flexibility and growth. Discover why he views 'working hard' and 'lifestyle business' as compatible concepts. Nils discusses the importance of embracing open-source technology and fostering genuine client relationships. He also delves into the future of bioinformatics collaboration and the crucial role of transparency and equity in hiring practices.

Our guest Steve Osazuwa helps us answer the PhD question (namely, should you do one?). Since we both have PhDs, we are bringing on our friend Steve who has been successful in bioinformatics without a PhD to add his perspectives. Topics: * How Steve ended up in bioinformatics. * Starting a PhD after working in industry. * What Steve's barber thinks about his colleagues' advice. * Would we do a PhD again? * The opportunity cost of doing a PhD instead of going directly to industry. Where to find us online: https://omgenomics.com

Inspired by opinions seen on Twitter, we discuss whether people should stay much more than 1 year per company to avoid being judged by future employers as a job-hopper, and whether companies should be discriminating this way. Topics: * Benefits of job hopping, early versus late in your career. * A debatable statement by chatGPT. * Is it ethically okay? disloyal? greedy? * Being loyal to a corporate entity that may have no feelings for you. * How can employers/teams deal with the reality of short stints. * The bus/lottery factor. * But isn't this different for biotech than tech? Where to find us online: https://omgenomics.com

Accepting that we're all imposters in bioinformatics, we tell stories from our own careers. Topics: * Robert's grad school experience in a biology program coming from a computer engineering background. * Maria's experience interviewing at grad schools. * "You can't just go around being like, I'm an idiot. Even if you feel like an idiot, that's just not helpful." Where to find us online: https://omgenomics.com