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10 years of building software in industry taught me that rewriting software is nearly always a bad idea. Here's why I'm doing it anyway 😁 omgenomics.com/podcast

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 a...

The 3 core skills to start with. Where to focus your learning depending on your level of biology expertise.

Talking about the book "So good they can't ignore you" by Cal Newport and how it relates to bioinformatics with some random stories from our own lives.

In this episode, our guest Kaja Wasik, co-founder of two genomics biotech companies, including Variant Bio, shares her journey in the biotech startup industry. We delve into how Kaja has managed to ethically collect genetic data from more than 20 intriguing populations worldwide. We explore her unique approach to conducting genetic research within diverse communities, discuss specific studies u...

We interview Nils Homer, the co-founder of Fulcrum Genomics, a thriving bioinformatics consulting business. Highlights: * 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 bel...

Using Circa to make a circos plot of differential gene expression results from DESeq2. * 0:00 Loading data into Circa * 3:13 Fixing problematic data using Google Sheets * 9:47 Styling the plot with neon color scheme Buy Circa: omgenomics.com/circa Data from this paper: www.mdpi.com/2072-6694/13/17/4485#B24-cancers-13-04485 - thank you Vikas!

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 industry 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. * Would we do a PhD again? * The oppor...

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 corpo...

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."

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 CZcams channel * Sabbatical projec...

Basics of GNU parallel, how to use it to run scripts and functions, all the way to using parallel to orchestrate launching jobs with different parameters like we often do in bioinformatics. You can find all the code from this video here: omgenomics.com/parallel

In bioinformatics, we often find ourselves editing scripts while ssh-ing into a remote server, which means using command-line editors instead of our favorite GUI editor like VSCode.

3 systems I use to keep myself organized when doing bioinformatics work. These are lightweight, flexible systems built on top of git, basic text files, and a single Google Doc no to-do list apps here :) 0:00 Introduction 1:07 The lab notebook 5:05 The journal 11:17 The logs

How DeepConsensus works

Trends in genomics I'm most excited about

How to land bioinformatics jobs in industry? Answering your questions!

Genes and geography a bioinformatics project

Test-driving GitHub copilot for bioinformatics algorithms

Bioinformatics project ideas

5 genomics file formats you must know

Answering your bioinformatics questions

Mint spending analysis with Pandas and Altair

DeepVariant 1.0 (conference talk)

5 tips for better bioinformatics software

Maria Nattestad interviewed on The Genomics Life podcast

Should you do a PhD?

Going from CS to bioinformatics

Five steps for getting started with bioinformatics