H3ABionet’s Introduction to Bioinformatics Training (IBT) 2020: a report of the first iteration hosted in Cameroon
Posted on September 24, 2020
| armando_djiyou
The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Armando Blondel DJIYOU DJEUDA, a researcher from University of Douala, Cameroon, set up and host H3ABioNet‘s Introduction to Bioinformatics course (IBT), supported by this fellowship granted to him in application round 1 of 2020.
Due to the rich biodiversity of sub-Saharan African countries, bioinformatics and data management are crucial in helping to advance biomedical research.
[Read More]Biopython 1.78 released
Posted on September 4, 2020
| chebizarro
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]Planning an online vs. an in-person conference: which is harder?
Posted on September 1, 2020
| nlharris
Online. By at least a factor of two. Our recent article entitled Lessons learnt from organizing a virtual conference discusses some of our technology choices and how we leveraged them to put on a successful online meeting. That article touches briefly on some of the challenges we faced, but it doesn’t fully convey how much work it was–both in advance and during the event.
Before we go any further, who are you?
[Read More]Smart computational imaging: a report from CLEO 2020
Posted on August 25, 2020
| pengfeifan
The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Pengfei Fan, a researcher from Queen Mary University of London, was supported to participate in CLEO 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.
During the last two decades, we are witnessing a fascinating growth of computational imaging (CI) methods, e.
[Read More]Call for applications for OBF Event Fellowship, Round 2 of 2020
Posted on August 22, 2020
| malvikasharan
We are glad to announce that the call for applications for the OBF Event Fellowship is now open. The deadline for this round is 1 October 2020. Applications should be submitted via this Google Form.
Renaming from “OBF Travel Fellowship” to “OBF Event Fellowship” One of the goals of the OBF fellowship is to increase the participation of members from traditionally underrepresented groups at events or communities that promote Open Source software development and/or open science practices in the biological sciences.
[Read More]Getting introduced to Bioinformatics and Open Science through BCC 2020
Posted on August 19, 2020
| gigikenneth7
The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Gigi Kenneth, a biochemistry undergrad and a bioinformatics enthusiast from Nigeria, was supported to participate in Bioinformatics Community Conference 2020 by this fellowship granted to her in the application round-1 of 2020. Find more information here.
I’m a biochemistry undergraduate, in my final year from the University of Port Harcourt, Nigeria.
[Read More]A Software Engineer's Experience at BCC 2020
Posted on August 16, 2020
| edidiongmichael08
The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Edidiong Etuk (Eddie), an open-source lover and a software engineer from Nigeria, was supported to take part in Bioinformatics Open Source Conference 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.
TL;DR This post is about my experience at Bioinformatics Community Conference 2020.
[Read More]Lessons learned from organizing a virtual conference (BCC2020)
Posted on August 13, 2020
| nlharris
BCC2020 (the collaborative BOSC + GCC meeting) was held online, with over 800 people registered for some part of the meeting. We used Remo.co as the technology platform, along with Discord for chat. Read about why we chose those, how it worked out, and our tips for others who are organizing virtual conferences here.
“Table view” in Remo during BCC2020
BCC2020 pre-conference open house
Posted on July 8, 2020
| nlharris
After much discussion, the BCC2020 organizing committee has decided to hold the meeting on Remo.co, which is similar to Zoom but offers a more conference-like experience, with “floors” and “tables” where you can mingle with other attendees. It has great small group and presentation support, including for posters and demos. It’s also more fun than most online conference platforms.
Because Remo is not familiar to most BCC participants, we are holding two open houses, one in each hemisphere, the day before BCC training starts.
[Read More]Biopython 1.77 released
Posted on May 25, 2020
| chebizarro
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]
