@Biopython

Open-source bioinformatics libraries in Python

 Worldwide
biopython.org
Joined March 2009
  • Tweets837
  • Following47
  • Followers4.4K
6Media
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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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, 640 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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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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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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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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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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Biopython 1.78 has been released open-bio.org/2020/09/04/biop… - please note the Bio.Alphabet removal biopython.org/wiki/Alphabet

Biopython 1.78 released

Biopython 1.78 has been released and is available from our website and PyPI. The main change is that Bio.Alphabet is no longer used. In some cases you will now have to specify expected letters, …

open-bio.org
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Biopython Project retweeted
Peter Cock@pjacock29 Jul 2020
No more Bio.Alphabet in Biopython 1.78, we’re collecting some examples of changes needed here:github.com/biopython/biopyth… Are we missing your use case?

Bio.Alphabet to molecule type transition for file output · Issue #3156 · biopython/biopython

Cross reference #2046, we are removing Bio.Alphabet. There are relatively few use-cases where it is needed, one being working with file formats which track DNA vs RNA vs protein. For example, the S...

github.com
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Read or listen to the “Biopython Project Update 2020” 5 minute talk given at #BCC2020 #BOSC2020 f1000research.com/slides/9-7… bcc2020.sched.com/event/coLV…
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Biopython Project retweeted
João Vitor Cavalcante@jvcavv26 Jul 2020
Great work by all the volunteers, I'm glad I was able to contribute, it was fun and I ended up learning a lot. 🎉🎉
Biopython Project@Biopython25 Jul 2020
One outcome of the #BCC2020 CoFest - we now enforce the black #Python formatting style for all of Biopython 🎊
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One outcome of the #BCC2020 CoFest - we now enforce the black #Python formatting style for all of Biopython 🎊
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We have several people already active on Biopython projects at the #BCC2020 CoFest - with pull requests merged and issues closed. Thank you - and please join us! bcc2020.github.io/cofest/

CollaborationFest

BCC2020 brings together the Galaxy Community Conference and Bioinformatics Open Source Conference to meet jointly online.

bcc2020.github.io
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Biopython 1.77 is belatedly up on conda-forge anaconda.org/conda-forge/bio… - the glitch holding up the package update turned out to be frustratingly simple in the end. Enjoy! /Peter
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Technical discussions are hard; a few tips gael-varoquaux.info/programm… Some thoughts and advice on better communications in technical projects, in particular open source
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Biopython 1.77 is now out open-bio.org/2020/05/25/biop… - available from PyPI for “pip install --upgrade biopython”

Biopython 1.77 released

Biopython 1.77 has been released and is available from our website and PyPI. This is the first release since we dropped support for Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us...

open-bio.org
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Biopython Project retweeted
Chris Rands@c_rands24 Mar 2020
New #Jupyter Notebook tutorial for @Biopython - illustrates some simple #bioinformatics analysis to characterise small sequences like a #coronavirus genome github.com/chris-rands/biopy…

GitHub - chris-rands/biopython-coronavirus: Biopython Jupyter Notebook tutorial to characterize a...

Biopython Jupyter Notebook tutorial to characterize a small genome - chris-rands/biopython-coronavirus

github.com
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Biopython Project retweeted
Debian upload@DebianUpload20 Dec 2019
New upload: python-biopython 1.76+dfsg-1 by Michael R. Crusoe into unstable... deb.li/i7CPG
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