Open-Source

This is a guest blog post from Aziz Khan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the ISMB/ECCB and BOSC 2019 meeting in Basel, July 2019. The OBF’s Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Find more information here.

Computational tools and software are now becoming the core of scientific discovery, and making it open source and sharing it freely with the community helps to take scientific discoveries to the next level. We live in an era where international and interdisciplinary collaborations become very central to answer big scientific questions. Given science is becoming more collaborative and data-intensive, we need intelligent and robust computational algorithms to help us to understand and interpret such big-data.

If you’d like the opportunity to present your work at BOSC 2019 (which will take place in Basel, Switzerland, on July 24-25, the last two days of ISMB/ECCB 2019), now’s your chance! The late round of abstract submission is open, and we will be choosing a few abstracts for “Late-Breaking Lightning Talks” as well as posters.

BOSC welcomes submissions about all aspects of open source bioinformatics, open science and open data. More information, and a link to the EasyChair submission portal, can be found at /events/bosc/submit/ .

Dear Biopythoneers,

I’m writing this in Portland at the GCC BOSC 2018 conference, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI:

https://biopython.org/wiki/Download https://pypi.python.org/pypi/biopython/1.72

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and SeqIO.write (especially when used in a for loop).

BioJava 5.0.0 was released on the 23rd of March 2018. This represents a major milestone that brings more consolidation and reorganisation of modules. This is the first release to be based on Java 8, bring in your lambdas and stream API calls!

The release represents work done in the last 2 years, alpha releases were available for quite some time and now this makes all the changes officially public.

Some major refactoring occurred in the biojava-structure module. The data model to deal with macromolecular structures has been adapted to be closer to the mmCIF data model. Other improvements in biojava-structure are support for MMTF format and improved symmetry detection code.

Dear Biopythoneers,

Source distributions of Biopython 1.71 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI) including pre-compiled Wheel Packages for Linux, Mac OS X and Windows.

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now dropped support for Python 3.3). It has also been tested on PyPy2.7 v5.10.0 and PyPy3.5 v5.10.1.

Python 3 is the primary development platform for Biopython. We will drop support for Python 2.7 no later than 2020, in line with the end-of-life or sunset date for Python 2.7 itself.

Podcast.__init__ describes itself as “The Podcast About Python and the People Who Make It Great”, and the most recent episode is " Biopython with Peter Cock, Wibowo Arindrarto, and Tiago Antão (Episode 125)".

Listening to the finished podcast, interviewer Tobias Macey did a great job. There are things I would have liked to have said - but it turned out pretty well. I hope you’ll agree:

Its worth looking back over the podcast archives, here are a few that caught my eye:

Dear Biopythoneers,

Source distributions of Biopython 1.70 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI). Windows installers and/or wheels should be available later. ( Update: Compiled wheel packages now available for Linux, Mac OS X and Windows).

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now dropped support for Python 3.3). It has also been tested on PyPy v5.7, PyPy3.5 v5.8 beta, and Jython 2.7 (although we are deprecating support for Jython).

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.69 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure.

Source distributions and Windows installers for Biopython 1.67 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but support for Python 2.6 is considered to be deprecated. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.65 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.

The most visible change is that the Biopython sequence objects now use string comparison, rather than Python’s object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).