The color of bioinformatics: what is it and how can it be modified?
Posted on August 29, 2018
| tendai
This is a guest blog post from Tendai Mutangadura, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the GCCBOSC 2018 meeting in Portland, June 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of three awards from our April 2018 travel fellowships call. Our August call recently closed, the current call closes 15 December 2018, you might want to apply?
[Read More]Taking Turns
Posted on August 2, 2018
| nlharris
BOSC 2019 will be part of ISMB 2019 Every year until 2018, BOSC was part of the annual ISMB conference as a community of special interest (COSI, formerly known as a SIG, Special Interest Group). As part of our continuing quest to broaden and deepen the BOSC community, we decided to perform an experiment this year by partnering with the Galaxy Community Conference rather than with ISMB. As we reported, the experiment was a success–participants were overwhelmingly positive about the experience, and the conference did attract a somewhat different mix of attendees than in past years.
[Read More]GCCBOSC 2018 post-meeting report
Posted on July 27, 2018
| nlharris
This year, the Galaxy Community Conference (GCC) and the Bioinformatics Community Conference (BOSC) met together to form the first Bioinformatics Community Conference. At GCCBOSC 2018, participants were able to meet and collaborate with a broad community of bioinformatics developers and users who focus on open, interoperable software tools and libraries that facilitate scientific research.
Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC attracted nearly 300 participants from around the world.
[Read More]Following up from BOSC's OBF Birds of a Feather meeting
Posted on July 9, 2018
| yo
It was really great to meet so many of you at GCCBOSC this year! We will soon have a couple of Travel Fellowship blog posts talking about the conference, so we won’t provide too much of a general overview at this point, but we would like to share a little more about one of the Bird of Feather (BoF) events we ran - specifically the OBF community BoF. The aim of this BoF was to engage anyone who was:
[Read More]Biopython 1.72 released
Posted on June 27, 2018
| peterc
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 .
[Read More]OBF Birds of a Feather at GCCBOSC 2018
Posted on June 14, 2018
| nlharris
If you’re going to GCCBOSC 2018, we invite you to join us at the OBF Birds of a Feather on Wednesday, June 27, from 5:40-7:40pm. Come and chat over dinner! Everyone is invited, whether you’re a longtime OBF member or someone who’s never even heard of the OBF. (By the way, anyone who is involved in open source or open science is welcome to join the OBF, and there is no membership fee.
[Read More]Travel award recipients for April 2018
Posted on May 25, 2018
| peterc
We had another great round of applications for the OBF Travel Fellowship this spring. After reviewing the applications, the OBF Board selected three recipients, who have all accepted the award.
Congratulations to our spring 2018 recipients:
Anisha Keshavan – attended the eLife Innovation Sprint. Anisha is a postdoctoral fellow at the University of Washington, where she develops open source code, including citizen scientist platforms for image quality classification and image segmentation ( update - see blog post).
[Read More]Saving science from itself: A review of the 2018 eLife Innovation Sprint
Posted on May 22, 2018
| akeshavan
This is a guest blog post from Anisha Keshavan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the 2018 eLife Innovation Sprint in Cambridge, May 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of three awards from our April 2018 travel fellowships call. The current call closes 15 August 2018, you might want to apply? It is hard for me to put into words the thrill, excitement, and inspiration I’m feeling after attending the 2 day eLife Innovation sprint on May 10th and 11th. The
#eLifeSprint (
https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018) in Cambridge, UK, brought together software developers, researchers, designers, and anyone who was passionate about leveraging web technology to advance open scientific communication. The goal: to save science from itself!
[Read More] Welcome to our Google Summer of Code 2018 students
Posted on April 24, 2018
| kblin
The Open Bioinformatics Foundation is again participating in the Google Summer of Code program this year. Last Monday the selected students were announced. Congratulations to all of you, and a heartfelt welcome. I also want to use this opportunity to thank all students who applied. Resources were limited, we did not get all the slots that we asked for, and so we had to make some tough choices. We wish you all the best for your future endeavours, and hope to be able to work with you in future.
[Read More]BioJava 5.0.0 is out
Posted on April 9, 2018
| josemduarte
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.
[Read More]
