OMGenomics Podcast

We visit Plasmidsaurus and spoke with CEO Mark Budde about why they are offering sequencing for so cheap, what surprises came up when their customers first got whole plasmid sequencing, and how sequencers are like bread machines.

Join the discussion in the comments on YouTube: https://youtu.be/Ss8H6VUQBGo

Where to find us online:
https://omgenomics.com

We talk about the promise and the perils of AI and dive into a particular case where AI was used to predict enzyme function and gave results that looked really promising, but were not quite right.

Learn more about the online Master of Science program from the University of Florida Department of Microbiology and Cell Science: https://microbiologyonline.ifas.ufl.edu/?utm_source=youtube&utm_medium=social-paid&utm_campaign=omgenomics&utm_term=ms&utm_content=

Join the discussion in the comments on YouTube: https://youtu.be/o097zC7CM5I

Where to find us online:
https://omgenomics.com

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