Blogroll

Biopython 1.84 has been released and is available from our website and PyPI. This contains about 5 months worth of updates, so the change-log in the news file is longer than usual. There have also been a few deprecations, most noteworthy this may be our last release with Python 3.9 support. Many thanks to the Biopython developers and community for making this release possible, especially the following contributors: Anil Tuncel (first contribution) David Cain Fabio Zanini (first contribution) Joao Rodrigues Judith Bernett (first contribution) Luca Monari (first contribution) Meridia Jane Bryant (first contribution) Manuel Lera-Ramirez Michael M. [Read More]

We’re sharing some important news with you regarding our mailing lists. From early on, we’ve maintained a self-hosted Mailman server for any OBF project that needs a mailing list, including our member roster list. After careful consideration, we have decided we need a solution that keeps track more reliably with current and emerging spam-fighting technologies and standards, and that simultaneously requires much less administration time and know-how. Specifically, we are planning to migrate the lists to paid hosting, possibly Mailchimp. [Read More]

On March 14, 2023, we held a webinar (hosted by ISCBacademy) about “Re-Thinking the Patient’s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative” presented by Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative. See the webinar announcement for a full description. BOSC organizing committee member Monica Munoz-Torres introduced Ms. Wei and fielded a lively Q&A session. The webinar recording is available on YouTube at https://youtu. [Read More]

As previously described, during the November 2021 public Board meeting, the OBF announced two new initiatives to be voted on by the OBF membership. Both of these received a large majority of votes: OBF Community Support Sponsorship (53 for, 3 against, 2 abstaining) OBF Code of Conduct (54 for, 2 against, 1 abstaining) The work to set up the new Community Support Sponsorship is underway. The new Code of Conduct is now available on the OBF website. [Read More]

Date & Time: Tuesday, February 22, 2022, 15:00 UTC / 11am EDT Location: online webinar hosted by ISCB Speaker: Yo Yehudi, Open Life Science (former OBF board member and Google Summer of Code admin & mentor) Topic: Growing open source communities with internships The ISCB, which runs the annual ISMB conference, is offering a series of ISCBacademy webinars hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are free to ISCB members. [Read More]

The OBF has two sets of domain names available for adoption by a non-profit or open source project: biows.org, biows.com, biows.net and biocpp.org, biocpp.com, biocpp.net These domains were registered and donated to us with bio-web-services (biows) and bio-c-plus-plus (BioC++ or BioCPP) in mind, but we’ve failed to find a good home for them. Please note that this is like adopting a free puppy - we’ll transfer them at no cost, but domain names come with annual renewal charges which the recipient organisation would be responsible for paying. [Read More]

OBF was accepted as a mentoring organisation for Google Summer of Code this year. It was another good year for OBF, with Kai Blin, Michael R. Crusoe, Sarthak Sehgal, and Yo Yehudi as administrators. We hosted eight students all of which successfully completed their work: Srijan Verma (mentors: Dmitry Petrov, Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers Himanshi Mathur (mentors: Jun Aruga, Evan Nemerson, Michael R. [Read More]

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, molecule type (DNA, RNA, protein), or gap character explicitly. Please consult the updated Tutorial and API documentation for guidance. This simplification has sped up many Seq object methods. See https://biopython.org/wiki/Alphabet for more information. Bio.SeqIO.parse() is faster with “fastq” format due to small improvements in the Bio. [Read More]

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 take advantage of new functionality and syntax, and simplify our code base and testing. This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been tested on PyPy3.6.1 v7.1.1. pairwise2 now allows the input of parameters with keywords and returns the alignments as a list of namedtuples. [Read More]

Biopython 1.76 has been released and is available from our website and PyPI. Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a focus hereafter on Python 3. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing. [Read More]