Show threadPeter CockMar 2

Seems the recent #GenerativeAI #slop pull requests that I've looked at for #Biopython have preferentially targeted the "Good First Issues". We really wanted those to be onboarding ramps for new #OpenSource contributors - and not for padding anyone's GitHub profile or whatever the motivation here is.

So I think any formal policy will want to say explicitly #NoAI on those issues at the very least.

Peter CockFeb 27

The #GenerativeAI #slop pull requests to #Biopython seem to be on the rise - https://github.com/biopython/biopython/pull/5171 might help?

Failing to use the PR template is definitely a red flag 🚩

Stress importance of the PR template by peterjc · Pull Request #5171 · biopython/biopython

There have been several PRs recently not following the template - some using generative AI even, if not done by a software agent. In either case, this adds to the burden of review (we don't wan...

GitHub
KemalJan 24

How I Built a Machine Learning Tool to Predict Drug Manufacturing Failures

A bioprocess engineer's journey into machine learning and why the pharmaceutical industry desperately needs this bridge When I tell people I work in bioprocess engineering, I usually get blank stares. When I explain that I help manufacture proteins in giant tanks for therapeutic use, the response is often: "Oh, like brewing beer?" Not quite. But close enough. What I don't usually mention is that I've been teaching myself machine learning on nights and weekends. Not because it's trendy, but […]

https://kemal.yaylali.uk/from-bioreactors-to-ai-how-i-built-a-machine-learning-tool-to-predict-drug-manufacturing-failures/

How I Built a Machine Learning Tool to Predict Drug Manufacturing Failures – Kemal's

BioResireJan 12

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Show threadPeter CockDec 8
@sethmlarson we use the library-specific not-silent-by-default warning in #Biopython and it still catches people out when stuff is removed 🤷 https://github.com/biopython/biopython/blob/biopython-186/Bio/__init__.py#L77
biopython/Bio/__init__.py at biopython-186 · biopython/biopython

Official git repository for Biopython (originally converted from CVS) - biopython/biopython

GitHub
Peter CockNov 24
I blogged my thoughts on receiving generative AI contributions as an Open Source project maintainer https://blastedbio.blogspot.com/2025/11/thoughts-on-generative-ai-contributions.html - seen with #Bioinformatics and #Biopython in particular in mind, but most of these issues are generic to #OpenSource development. It worries me #GenAI
Thoughts on generative AI contributions as an Open Source project maintainer

To be clear up front, these are my personal opinions right now, and while they will influence any future policy I have a hand in writing, th...

Open Bioinformatics FoundationOct 28
#Biopython 1.86 released on PyPI https://pypi.org/project/biopython/1.86/ - see the NEWS file for changes https://github.com/biopython/biopython/blob/biopython-186/NEWS.rst
Client Challenge

Peter CockJul 22, 2025

I got approached today at #ISMBECCB2025 #BOSC2025 with “Are you the pyANI guy?” (Re https://github.com/pyani-plus/pyani-plus - and yes, one of them).

Confusing as I’m more used to being called the “#Biopython guy” 🤣

GitHub - pyani-plus/pyani-plus: Development repo for pyani-plus (the next iteration of pyani)

Development repo for pyani-plus (the next iteration of pyani) - pyani-plus/pyani-plus

GitHub
Peter CockJul 21, 2025
The first #biopython mention I’ve caught at #ISMBECCB2025, in the context of pyJASPAR for accessing JASPAR motifs in Python - “JASPAR-Suite: An open toolkit for accessing TF binding motifs” by Aziz Khan #BOSC2025 🧬🐍👍
Peter CockJun 18, 2025
Asking for #Biopython, but are #GitHubPages sites generally currently #GeoBlocked from #Argentina - see https://github.com/biopython/biopython.github.io/issues/207 and https://biopython.org
Possible IP geoblocking: biopython.org unreachable from Argentina · Issue #207 · biopython/biopython.github.io

Hello Biopython team, I'm writing to report that the main Biopython website (https://biopython.org) appears to be inaccessible from Argentina. I consistently get a "connection timed out" error from...

GitHub