Category Archives: Bioinformatics

Public Health Big Data: The Wages of Privatization

I spent a significant part of my career in and around these kinds of data, and I think the article below, while very good in terms of description of the failures of COVID-19 data collection, misses the larger picture: this … Continue reading

Posted in Bioinformatics, COVID-19, Funding, Public Health, We're Really Fucked

Biologists Should Not Learn How to Code

Update added here OK, that’s a little extreme, but over the Thanksgiving weekend, I came across some advice which essentially amounted to biologists should learn how to code. I’m not sure that’s great advice. Since I’m in the genomics bidness, … Continue reading

Posted in Bioinformatics, Computers, Statistics | 5 Comments

The Mad Biologist’s Rules of Bioinformatics

Just some random observations, most of them snarky, that I’ve made over the last decade: 1. The server will always go down when you need it the most. Pretty self-explanatory. 2. The documentation is always no more than 95 percent … Continue reading

Posted in Bioinformatics | 4 Comments

The Phrase That Makes Bioinformaticians Grind Their Teeth: Another Short-Read Genome Assembler

Michael Barton laments the state of bioinformatics software: Grants are harder and harder to obtain, yet we fund the current attrition of moving bioinformatics software forward one reinvention at a time. Where else is it acceptable to reinvent a tool … Continue reading

Posted in Bioinformatics, Genomics

Why Should Publishers Organize Science?

We do need to rethink project and data management, communication networks, and so on. But I’ll be damned if I let a publisher be involved from the outset.
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Posted in Bioinformatics, Publishing | 3 Comments

Sequencing Technology Adoption and the Power of Informatic ‘Lock In’

Data output legacy effects matter.
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Posted in Bioinformatics, Genomics | 3 Comments

Genome Annotation: There’s Too Much Crap in GenBank

Polluted databases slow down genomics.
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Posted in Bioinformatics, Genomics | 17 Comments

What Is a Bioinformaticist?

What do you think?
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Posted in Bioinformatics | 9 Comments

The Double Standard of Genomic Data Release and the Role of Incentives

Should any data, not just genomic data, be held hostage by the grant award process?
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Posted in Bioinformatics, Funding, Genomics | 1 Comment

The Future of Sequencing at NHGRI Report: The Human Microbiome

Some good suggestions for NHGRI’s role in microbiome research.
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Posted in Bioinformatics, Funding, Genomics, Meetings, Microbiome, NIH | 2 Comments