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

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

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@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

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

#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

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” 🤣

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 🧬🐍👍

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

@OpenBio only noticed the typo now: it is available on PyPI, but I meant we test running #Biopython under the #PyPy implementation of Python

@OpenBio The next commit/pull request will put the #Biopython git repository’s default branch at over 16,000 commits!

#Biopython 1.85 released, supports Python 3.9 through 3.13 and PyPI. https://biopython.org/

Pre-compiled wheels available on PyPI https://pypi.org/project/biopython/1.85/ with #CondaForge to follow soon https://anaconda.org/conda-forge/biopython

Big city life - triaging #Biopython bug reports while finishing my latte in a trendy cafe in Glasgow.

@gedankenstuecke @gravitystorm @openstreetmap The OSM number of contributors looks several magnitudes higher than for #biopython (not surprising), but we’ve not finished our relicensing effort yet 😅

#Biopython 1.84 has been released, see https://www.open-bio.org/2024/06/28/biopython-1-84-released/ or https://mailman.open-bio.org/pipermail/biopython/2024-June/017055.html - or https://github.com/biopython/biopython/blob/biopython-184/NEWS.rst for the change-log. Thank you to everyone who contributed.

@python_discussions PS: There is also #biopython

@Edent Python has a tradition of functional testing of doctests in docstrings (code snippets within the API docs), and I use a generalised version of this for our main docs in #Biopython.

However that doesn’t solve this use case of testing installation instructions - which seems doable in principle but complex to orchestrate. I wonder if there’s something off the shelf which covers the basics (in Python in particular)? …

@mjgardner @Edwardsmoon @BobOHara @bduncan It is a step backwards, likely explained by people migrating to #bioconductor (in #rstats) or #biopython and wanting to break from clean from #perl. However neither R nor python provided the facilities that perl has to deal with features in text and flat text files.

#Biopython 1.83 has been released, see https://www.open-bio.org/2024/01/10/biopython-1-83-released/ or https://mailman.open-bio.org/pipermail/biopython-announce/2024-January/000190.html - this is to address an unintended legacy API break in Biopython 1.82

Years in the execution, the #Biopython Tutorial has just switched from #LaTeX with HTML output via hevea http://biopython.org/DIST/docs/tutorial/Tutorial-1.82.html to #reStructuredText #RST output with #Sphinx https://biopython.org/docs/dev/Tutorial/index.html

#Biopython 1.82 has been released, see https://www.open-bio.org/2023/12/22/biopython-1-82-released/ or https://mailman.open-bio.org/pipermail/biopython-announce/2023-December/000186.html for more details. Thanks everyone who contributed!