Episodes
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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
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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
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Episodes manquant?
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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
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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
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We interview Nils Homer, the co-founder of Fulcrum Genomics, a thriving bioinformatics consulting business.
Topics:
* Why Nils decided to start a consulting business in the bioinformatics space.
* Embracing open-source.
* Finding customers is the easy part.
* Scoping and pricing in science when figuring out what work is possible or necessary is a huge part of the work itself.
* Why Nils believes "working hard" and "lifestyle business" are not conflicting concepts.
* Exploring the possibilities of productizing services in the custom-driven world of bioinformatics.
* Nils' thoughts on selling software to scientists.
Show notes:
* Nils' Twitter: https://twitter.com/nilshomer
* Fulcrum Genomics is hiring! https://fulcrumgenomics.com/careers/
Where to find us online:
https://omgenomics.com
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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
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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
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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
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We discuss our experiences with unofficial industry sabbaticals, aka taking time between jobs for our own projects.
Topics:
* Funemployment versus sabbatical
* Robert's 2021 sabbatical building sandbox.bio learning platform and 42basepairs genomics cloud platform
* Maria's 2017 OMGenomics entrepreneurship experience, building Circa visualization software and a YouTube channel
* Sabbatical projects helping you get the next job
* Satisfaction and meaning from personal projects
Links:
* Ask us a question!: omgenomics.com/podcast
* 42basepairs.com (Robert's genomics cloud platform)
* sandbox.bio (Robert's bioinformatics learning platform)
* omgenomics.com/circa (Maria's visualization tool)
* youtube.com/omgenomics (Maria's YouTube channel)
* OMGenomics Q&A episode featuring Robert: https://www.youtube.com/watch?v=4SfDHheyKBU&ab_channel=OMGenomics
Where to find us online:
https://omgenomics.com
