Mark Schreiber, PhD
@genometron.bsky.social
Reposted by Mark Schreiber, PhD
1/ Bioinformaticians, I’ll say it loud:
Never blindly trust the data you're given.
Not from collaborators. Not from vendors. Not even from “reliable” sources.
Here’s why:
Never blindly trust the data you're given.
Not from collaborators. Not from vendors. Not even from “reliable” sources.
Here’s why:
September 25, 2025 at 1:15 PM
1/ Bioinformaticians, I’ll say it loud:
Never blindly trust the data you're given.
Not from collaborators. Not from vendors. Not even from “reliable” sources.
Here’s why:
Never blindly trust the data you're given.
Not from collaborators. Not from vendors. Not even from “reliable” sources.
Here’s why:
Reposted by Mark Schreiber, PhD
It’s often said that solar isn’t a reliable energy source. Yet it has reliably powered our entire ecosystem for several billion years.
a man in a suit and tie is standing next to a woman in a black dress .
ALT: a man in a suit and tie is standing next to a woman in a black dress .
media.tenor.com
September 25, 2025 at 12:23 PM
It’s often said that solar isn’t a reliable energy source. Yet it has reliably powered our entire ecosystem for several billion years.
Do we need an excuse for firing lasers at things?
September 13, 2025 at 2:31 PM
Do we need an excuse for firing lasers at things?
Top tip, cooking spray is a trap. It contains a protein based emulsifier to make it easier to spray. When heated it forms a glue like substance that sticks to everything including non stick pans. 🤨
August 30, 2025 at 1:35 PM
Top tip, cooking spray is a trap. It contains a protein based emulsifier to make it easier to spray. When heated it forms a glue like substance that sticks to everything including non stick pans. 🤨
🚀 This is big! AWS HealthOmics now supports ECR pull through caches and remaps image URIs. Now you can use workflows that use containers from public repos without having to change all the image URIs. And you get all the reliability and security benefits of using ECR!
#genomics #wdl #cwl #nextflow
#genomics #wdl #cwl #nextflow
What's New at AWS - Cloud Innovation & News
aws.amazon.com
August 29, 2025 at 5:31 PM
Incredible engineering youtu.be/h_zgURwr6nA?...
Unveiling High NA EUV | ASML
YouTube video by ASML
youtu.be
August 26, 2025 at 6:27 PM
Incredible engineering youtu.be/h_zgURwr6nA?...
So true. In 2025, do everyone a favor and ask an LLM to update your README.md with comprehensive documentation.
1/ I’ve reviewed hundreds of bioinformatics GitHub repos in my career.
Here’s the brutal truth: most tool documentation fails the people it’s meant to help.
And it’s not because the algorithms are bad.
Here’s the brutal truth: most tool documentation fails the people it’s meant to help.
And it’s not because the algorithms are bad.
August 14, 2025 at 1:19 PM
So true. In 2025, do everyone a favor and ask an LLM to update your README.md with comprehensive documentation.
Dear software developers.
A useful error message contains: 1. The specific error, 2. The likely cause, 3. Potential actions a user can take to prevent the error.
A useful error message contains: 1. The specific error, 2. The likely cause, 3. Potential actions a user can take to prevent the error.
August 11, 2025 at 2:05 PM
Dear software developers.
A useful error message contains: 1. The specific error, 2. The likely cause, 3. Potential actions a user can take to prevent the error.
A useful error message contains: 1. The specific error, 2. The likely cause, 3. Potential actions a user can take to prevent the error.
Reposted by Mark Schreiber, PhD
1/ 8 Books for you to learn bioinformatics🧵
August 11, 2025 at 1:45 PM
1/ 8 Books for you to learn bioinformatics🧵
The thing people seem to miss about gerrymandering is that it doesn’t just disenfranchise voters from one party it disenfranchises everyone in the district. By making a district uncompetitive the representative no longer needs to care about any of their constituents. All voters loose. The party wins
August 9, 2025 at 6:57 PM
The thing people seem to miss about gerrymandering is that it doesn’t just disenfranchise voters from one party it disenfranchises everyone in the district. By making a district uncompetitive the representative no longer needs to care about any of their constituents. All voters loose. The party wins
Time for another coffee!
August 5, 2025 at 12:59 PM
Time for another coffee!
Definitely not how it looked in my biology textbooks. The reality is so much cooler!
Forget how your biology textbooks depicted the endoplasmic reticulum.
@hhmijanelia.bsky.social scientist Andrew Moore used our open graphics tool AGAVE to create this image showing the ER's outer membrane. The tool borrows animation studio techniques to create realistic light sources.
@hhmijanelia.bsky.social scientist Andrew Moore used our open graphics tool AGAVE to create this image showing the ER's outer membrane. The tool borrows animation studio techniques to create realistic light sources.
July 2, 2025 at 12:58 PM
Definitely not how it looked in my biology textbooks. The reality is so much cooler!
One of The Oatmeal’s best so far.
June 25, 2025 at 9:17 PM
One of The Oatmeal’s best so far.
Reposted by Mark Schreiber, PhD
Boost your HPC performance and efficiency on AWS with the newly updated Well-Architected HPC Lens! The new guidance consolidates years of AWS expertise into structured best practices for running HPC workloads on AWS. Read more about it at aws.amazon.com/blogs/hpc/op...
Optimize HPC Workloads with the Updated AWS Well-Architected Lens | Amazon Web Services
Today, we're announcing an update to the AWS Well-Architected High Performance Computing (HPC) Lens, providing you with comprehensive architectural guidance in a single, authoritative resource. This n...
aws.amazon.com
June 24, 2025 at 2:48 PM
Boost your HPC performance and efficiency on AWS with the newly updated Well-Architected HPC Lens! The new guidance consolidates years of AWS expertise into structured best practices for running HPC workloads on AWS. Read more about it at aws.amazon.com/blogs/hpc/op...
Reposted by Mark Schreiber, PhD
dev.to/aws-builders...
Many examples use hardcoded credentials. These should never really be used. The good news is that in almost all cases there is a better way. When working with services like GitHub Actions and workflows you can use Open ID Connect (OIDC) for auth to AWS. (1️⃣/3️⃣)
🧵
Many examples use hardcoded credentials. These should never really be used. The good news is that in almost all cases there is a better way. When working with services like GitHub Actions and workflows you can use Open ID Connect (OIDC) for auth to AWS. (1️⃣/3️⃣)
🧵
Step-by-Step Guide to Setting OIDC With Terraform for GitHub Actions Workflows with AWS
Your GitHub Actions Secrets Are the Weakest Link in Your AWS Security Chain Are you still using...
dev.to
June 22, 2025 at 2:42 PM
dev.to/aws-builders...
Many examples use hardcoded credentials. These should never really be used. The good news is that in almost all cases there is a better way. When working with services like GitHub Actions and workflows you can use Open ID Connect (OIDC) for auth to AWS. (1️⃣/3️⃣)
🧵
Many examples use hardcoded credentials. These should never really be used. The good news is that in almost all cases there is a better way. When working with services like GitHub Actions and workflows you can use Open ID Connect (OIDC) for auth to AWS. (1️⃣/3️⃣)
🧵
Eggatha don’t care!
June 21, 2025 at 5:29 PM
Eggatha don’t care!
🧬🚀 Happy to announce linter rules for Nextflow v0.1.2. Featuring some fixes, improved testing, improved docs and better tooling. Also added the CICD friendly option to fail on lint violations. github.com/awslabs/lint...
Release v0.1.2 · awslabs/linter-rules-for-nextflow
Release v0.1.2
Release Date: 2025-06-20
Changes
chore: bump version to 0.1.2 (728467f)
feat: add comprehensive release automation (59b94ce)
Installation
JAR Files
linter-rules-0.1.2.jar
ast-echo...
github.com
June 20, 2025 at 4:55 PM
🧬🚀 Happy to announce linter rules for Nextflow v0.1.2. Featuring some fixes, improved testing, improved docs and better tooling. Also added the CICD friendly option to fail on lint violations. github.com/awslabs/lint...
🇳🇿🇦🇺🇬🇧🇸🇪🇸🇬🇮🇩🇲🇾🇹🇭🇷🇺🇨🇺🇵🇭🇩🇪🇨🇭🇨🇳🇹🇼🇿🇦🇮🇹🇳🇱🇨🇿🇮🇳🇯🇵🇧🇷🇲🇽🇺🇸
What’s your flag count?
What’s your flag count?
June 18, 2025 at 11:47 PM
🇳🇿🇦🇺🇬🇧🇸🇪🇸🇬🇮🇩🇲🇾🇹🇭🇷🇺🇨🇺🇵🇭🇩🇪🇨🇭🇨🇳🇹🇼🇿🇦🇮🇹🇳🇱🇨🇿🇮🇳🇯🇵🇧🇷🇲🇽🇺🇸
What’s your flag count?
What’s your flag count?
AWS HealthOmics Run Analyzer can help you optimize your resource allocations for production workflows.
aws.amazon.com/blogs/indust...
aws.amazon.com/blogs/indust...
Reduce Genomic Discovery Time and Costs with AWS HealthOmics Run Analyzer | Amazon Web Services
Bioinformatics researchers running production genomic workflows face a critical challenge: ensuring computational resources are properly allocated to maximize cost efficiency without sacrificing perfo...
aws.amazon.com
June 9, 2025 at 2:59 PM
AWS HealthOmics Run Analyzer can help you optimize your resource allocations for production workflows.
aws.amazon.com/blogs/indust...
aws.amazon.com/blogs/indust...
77F and humid at 9am. It’s gonna be scorchio! 🥵☀️
June 5, 2025 at 12:51 PM
77F and humid at 9am. It’s gonna be scorchio! 🥵☀️
In a new tutorial I explain how to use Amazon Q Developer CLI's natural language and agentic AI capabilities to rapidly create, run, debug and analyze genomics workflows in AWS HealthOmics. What used to take bioinformatics experts days can now be achieved by any scientist in under an hour.
github.com
May 16, 2025 at 3:57 PM
In a new tutorial I explain how to use Amazon Q Developer CLI's natural language and agentic AI capabilities to rapidly create, run, debug and analyze genomics workflows in AWS HealthOmics. What used to take bioinformatics experts days can now be achieved by any scientist in under an hour.