#biopython — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #biopython, aggregated by home.social.
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@dalke thank you Andrew for your thoughtful reply (and past contributions to #Biopython and #BOSC which is also still going strong): https://mailman.open-bio.org/pipermail/biopython/2026-April/017116.html
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I've started an email thread "Generative AI policy for contributions to Biopython" which I hope will lead to a pull request laying out some guidelines for acceptance of AI assisted contributions (personally I'd like to just reject them, but doubt that stance is universally held with the current pool of maintainers, we'll see): https://mailman.open-bio.org/pipermail/biopython/2026-April/017113.html #Biopython
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That's #Biopython 1.87 released today https://mailman.open-bio.org/pipermail/biopython-announce/2026-March/000195.html - files on PyPI etc https://pypi.org/project/biopython/1.87/
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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.
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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 🚩
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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 […] -
From Bioreactors to AI: 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. The $50 Million Problem Nobody Talks About What I don't usually mention is that I've been teaching myself machine learning […] -
From Bioreactors to AI: 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. The $50 Million Problem Nobody Talks About What I don't usually mention is that I've been teaching myself machine learning […] -
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🚀 Unlock top bioinformatics tools like BLAST, Galaxy & Biopython! Master life sciences analysis with BioResire. Enroll now! 🔬💻 www.bioresire.in
#BioinformaticsTools #BioResire #Bioinformatics #BLAST #Galaxy #Biopython #BiotechEducation #BioinformaticsTraining #LifeSciences #NGS #Genomics #BioResireBio #BioinformaticsSoftware #TopBioTools
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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
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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
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#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
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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” 🤣
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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” 🤣
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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” 🤣
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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” 🤣
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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” 🤣
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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 🧬🐍👍
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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
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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
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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
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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
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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
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@OpenBio only noticed the typo now: it is available on PyPI, but I meant we test running #Biopython under the #PyPy implementation of Python
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@OpenBio The next commit/pull request will put the #Biopython git repository’s default branch at over 16,000 commits!
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#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
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Big city life - triaging #Biopython bug reports while finishing my latte in a trendy cafe in Glasgow.
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@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 😅
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#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.
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@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)? …
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#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
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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
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#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!
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There are now pre-compiled #Python wheel files for Python 3.12 (recently released) on PyPI for #Biopython https://mailman.open-bio.org/pipermail/biopython/2023-October/016987.html https://pypi.org/project/biopython/1.81/#files
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Studium General #bioinformatics -Pascasarjana Universitas Amikom. Saya membahas "Biopython for Structural Bioinformatics " #biopython #python https://youtube.com/live/-Cn2dk7G3uU?si=pOPj8sLKT0Okcb4_ @indonesia #indonesia
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@pjacock #BioPython has 114 open pull requests? That seems excessive.
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Also, does #Biopython need to be on Mastodon (we have/had an account on Twitter)?
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We’ll be working on releasing #Biopython 1.82 fairly soon https://mailman.open-bio.org/pipermail/biopython/2023-May/016975.html - if you’ve got a favourite issue or pull request which you think should go in, please speak up now.
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Way overdue, but #Biopython 1.80 is out https://pypi.org/project/biopython/1.80/ - expect formal announcement later https://mailman.open-bio.org/pipermail/biopython/2022-November/016950.html - conda packages soon too! Thank you to all the contributors