@Biopython

Open-source bioinformatics libraries in Python

 Worldwide
biopython.org
Joined March 2009
  • Tweets837
  • Following47
  • Followers4.4K
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We don't have a dedicated Mastodon account, for now keep an eye on genomic.social/@OpenBio and #Biopython

Open Bioinformatics Foundation (@[email protected])

70 Posts, 17 Following, 642 Followers · The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run organization that supports #OpenSource #bioinformatics. Our member projects include...

genomic.social
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We're following the OBF lead and not using Twitter anymore, see open-bio.org/2023/11/20/leav… And Biopython 1.82 has just been released, see open-bio.org/2023/12/22/biop…

OBF and BOSC leaving Twitter/X

As of November 21, 2023, the Open Bioinformatics Foundation and BOSC will no longer post on Twitter/X. Although in the past it was a useful social medium, it is no longer compatible with our values, …

open-bio.org
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Way overdue, but Biopython 1.80 is out pypi.org/project/biopython/1… - expect formal announcement later mailman.open-bio.org/piperma… - conda packages soon too! Thank you to all the contributors /Peter

biopython

Freely available tools for computational molecular biology.

pypi.org
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Replying to @webflags1 @NCBI
Sounds like a planned change - and quite likely the NCBI did make an announcement somewhere (I’m not familiar with that particular DB) /Peter
Replying to @webflags1 @NCBI
You’ll have to ask the NCBI - I’d suggest sharing the URL itself, the handle from Bio.Entrez has a .url attribute you can look at. You can also try debugging the URL in your browser (e.g. try other format/mode combinations). /Peter
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Biopython Project retweeted
Peter Cock@pjacock12 Jul 2022
Just ordered a pair of free 2FA keys courtesy Google Open Source Security Team for use with PyPI where a few of my projects are now deemed “critical” (plus @Biopython) pypi.org/security-key-giveaw…

PyPI 2FA Security Key Giveaway

PyPI is implementing a 2FA requirement for critical projects, and distributing security keys to critical maintainers.

pypi.org
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Biopython Project retweeted
Martin Larralde@althonos10 May 2022
55 lines of #Python code to build a Multiple Sequence Alignment viewer for the terminal with the #Rich library (from @textualizeio) #bioinformatics
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We’re deprecating the older Bio.pairwise2 in the next release.
Replying to @pjacock @tomeraltman
Logged as github.com/biopython/biopyth…

Define SeqFeature __sub__ for integer offset · Issue #3831 · biopython/biopython

See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and __add__, need to do the same specifically for integer offsets. Workaround feature + (-5) instead of feature - 5, see htt...

github.com
Replying to @chasewnelson @ThePSF
Not really a Biopython thing, does feel like something the #Python #Pandas community could help with though? /Peter
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Replying to @NWaglechner @kaiblin
This was due to a change in GenBank files without an actual sequence are represented as of Biopython 1.79, see also deprecation of the UnknownSeq object open-bio.org/2021/06/03/biop… /Peter

Biopython 1.79 released!

Biopython 1.79 has been released and is available from our website and PyPI. This is the final release supporting Python version 3.6. It also supports Python versions 3.7, 3.8, and 3.9, as well as …

open-bio.org
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Replying to @KarenFlemingPhD
Yes please - pull request via the “Edit on GitHub” link top left of that page would be most welcome. /Peter
Replying to @mglerner @KarenFlemingPhD @Python
Commit github.com/biopython/biopyth… should fix the doctest formatting on biopython.org/docs/dev/api/B… (next time the HTML gets updated). If you spot anymore, please open an issue. Thanks /Peter

Line break before >>> docstring · biopython/biopython@e16f46e

[ci skip]

github.com
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Replying to @kaiblin
This will be the replacement for the UnknownSeq object I think? Could you log an issue please /Peter @pjacock
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Biopython Project retweeted
Yu Kitago@uKitago14 Apr 2021
#Biopython can handle #snapgene file! Using this feature, it's possible to easily convert many snapgene files into #genbank format files!!
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NumPy has dropped Python 3.6 support, Biopython plans to soon. Any objections? github.com/biopython/biopyth… mailman.open-bio.org/piperma…

Deprecating Python 3.6 support; one more release... by peterjc · Pull Request #3426 · biopython/b...

I hereby agree to dual licence this and any previous contributions under both the Biopython License Agreement AND the BSD 3-Clause License. I have read the CONTRIBUTING.rst file, have run pre-co...

github.com
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Biopython Project retweeted
SonarCloud
@SonarCloud10 Nov 2020
Our #Python bug hunt in popular, well-maintained projects (@TensorFlow, numpy, salt, sentry and @Biopython) turned up interesting stuff like undefined var reference, unreachable code, and more. blog.sonarsource.com/sonarcl…
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Replying to @BiomedIsaac @numpy_team @ProjectJupyter
No, you need to star them on GitHub too ;) More seriously, have a look at the issue trackers for beginner or newcomer friendly issues if you want to contribute directly. /Peter
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Replying to @DownToAby
Glad you solved it. Yes, KeyError is expected when the key isn’t in the dictionary.
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Biopython Project retweeted
Vini Salazar@vinisalazar_16 Sep 2020
Very happy to have my first contribution to @Biopython merged today! Hope to contribute more in the future. Shoutout to @pjacock for the patience in reviewing my PR. #opensource #python #bioinformatics
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