[Bosc-announce] Open Bioinformatics Foundation Newsletter January 2019

Tue Jan 8 22:08:13 UTC 2019

[Quick note, 8 January: I'm re-sending as this mail as it failed to send to
bosc-announce last time. Apologies if you receive it twice.]

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OBF Newsletter Jan 2019 OBF News OBF Founder named Commander of the British
Empire

Ewan Birney, one of the founders of the OBF and OBF President until 2005,
has been awarded the title "Commander of the British Empire" (CBE) in
service to genomics and the life sciences. Read the EMBL-EBI press release
<https://www.ebi.ac.uk/about/news/press-releases/ewan-birney-CBE>.
We have a new logo!

[image: OBF logo - unlocked padlock surrounded by a circular DNA helix]
<https://raw.githubusercontent.com/OBF/obf-docs/master/logos/obf_logo_text_circle.png>
OBF redesigns Logo

In the first issue of our newsletter
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md>, we
encouraged you to vote in the OBF logo redesign competition. The winning
logo, designed by Aleix Lafita <https://github.com/lafita>, is shown above.
Website

During late 2018 and early 2019, our Outreachy <https://www.outreachy.org/>
intern Deepashree Deshmukh <https://github.com/kushinauwu> will be
redesigning the OBF website, with the goal of creating a unified community
hub for the OBF. More on our blog
<https://news.open-bio.org/2018/11/19/updates-are-coming/>.
GCCBOSC 2018 Videos

Videos from GCCBOSC 2018 are now up! The BOSC videos can be found on YouTube
<https://www.youtube.com/playlist?list=PLir-OOQiOhXaHvCY_KYshsOMULuXDqvh7>.
OBF Travel Fellowships

The OBF travel fellowships
<https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> offer
up to $1000 USD for conference travel and accommodation. Awardees from the
last round Anisha Keshevan <https://github.com/akeshavan>, Tendai
Mutangadura
<https://news.open-bio.org/2018/08/29/the-color-of-bioinformatics/>, and Farah
Zaib Khan
<https://news.open-bio.org/2018/08/18/city-of-roses-they-call-it-portland-oregon-usa/>
shared their experiences as fellowship recipients on the OBF blog.

We're particularly keen to offer these fellowships to people from
underrepresented groups, including applicants outside Europe and the USA -
please share with friends and acquaintances. The* next deadline to apply
<https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> is the
15th of April*.
BOSC 2019 will be in Basel, Switzerland with ISMB

After 2018's great success combining BOSC with the Galaxy Community
Conference
<https://news.open-bio.org/2018/07/27/gccbosc-2018-post-meeting-report/>,
we're hoping to alternate years
<https://news.open-bio.org/2018/08/02/taking-turns/> between ISMB
<https://www.iscb.org/ismbeccb2019> and GCC. In 2019, BOSC
<https://www.open-bio.org/wiki/BOSC_2019> will be held at ISMB in Basel,
Switzerland on the 24th and 25th of July (with the Codefest the following
days).
Google Summer of Code

The Google Summer of Code (GSoC) is a three-month paid internship
opportunity for students around the globe to learn about contributing to
open source. The OBF typically acts as an umbrella organisation, allowing
member projects and affiliated projects to take on GSoC students.

In 2018, students worked on projects for BioJS, BioNode, CobraPy, NextFlow,
and OpenMS
<https://news.open-bio.org/2018/04/24/welcome-to-our-google-summer-of-code-2018-students/>
.

If you have an open source project idea, consider mentoring as part of the
OBF! It's a great two-way exchange - students get paid to get open source
experience, while projects get three months of dedicated work. If you're
interested, visit the OBF GSoC site to learn more
<https://obf.github.io/GSoC/> - project ideas are due in late January, so
now's the time to start thinking!

Tweet - OBF mentors at the 2018 GSoC mentor summit
<https://twitter.com/thejmazz/status/1053037514037088257>
Community updates

   - People who use NextFlow workflows might be interested in nf-core
   <https://nf-co.re/> - a curated set of high-quality re-usable analysis
   pipelines with good documentation.
   - Do you edit common biological file formats like fasta, sam, or pdb?
   BioSyntax <https://github.com/bioSyntax/bioSyntax> is an open source
   plugin that provides syntax highlighting for multiple file formats
   <https://biosyntax.org/man#supported-file-formats> in vim, less, gedit,
   & sublime.

Galaxy Training CoFest

The Galaxy Training Network has developed an infrastructure to deliver
interactive training based on Galaxy: one central place (
https://training.galaxyproject.org) to aggregate training materials
covering many current research topics. Each topic is supported by tutorials
developed and maintained by the community via a GitHub repository:
https://github.com/galaxyproject/training-material.

To support the community and this project, the Galaxy Training Network is
organizing regular online CoFests (Collaboration/Contribution Fests) once
every 3 months on the 3rd Thursday for a day of the collaborative work on
the training content. The last one was on the 15th of November and the next
one will be on the *21st of February*. More information can found on GitHub
<https://github.com/galaxyproject/training-material/issues/1152>.
Interesting links

   - Have you ever had cause to feel unsafe online as a researcher who
   works openly? The GitBook Digital Safety for Open Researchers
   <https://digital-safety-for-open-research.gitbook.io/project/introduction/untitled>
   might be worth a read.
   - Do you support credit for academic code authors, code review for
   scientific software, and open peer review? The Journal of Open Source
   Software (JOSS <https://joss.theoj.org/>) has an open call for editors
   <http://blog.joss.theoj.org/2018/12/call-for-editors> (apply by Jan
   18th), and/or sign up to review software in your area of expertise
   <http://joss.theoj.org/reviewer-signup.html> (sign up anytime).
   - Do you present training webinars? Ten simple rules for delivering live
   distance training in bioinformatics across the globe using webinars
   <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006419>
   is both interesting and informative!

Your content needed for the next issue!

Tell us about the things that catch your attention in the open source
bioinformatics world! If you have an exciting project update, request for
feedback, or interesting link, feel free to share it with us on GitHub
<https://github.com/OBF/newsletter/issues/8>, or discuss it offline if
you're not sure whether or not your content is suitable - we're looking for
content that's primarily open source / science related.
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