[Open-bio-l] Open Bioinformatics Foundation Newsletter July 2018

[Yo Yehudi]

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*OBF Newsletter July 2018Hi everyone and welcome to the Open Bioinformatics
Foundation Newsletter. At GCCBOSC this year we had a fantastic Birds of a
Feather meeting discussing ways to improve community year-round for the OBF
<https://news.open-bio.org/2018/07/09/following-up-from-boscs-obf-birds-of-a-feather-meeting/>.
One of the ideas was to create a newsletter, with the aim of allowing
community members to provide updates on the open bioinformatics related
projects they're working on or aware of. Right now this is very
experimental, so we'd welcome feedback of any kind.
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#obf-news>OBF
news
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#gccbosc>GCCBOSCIf
you couldn't make it this year (and maybe even if you could) you can read
the official report (coming soon), enjoy the brilliant photos taken by
Berenice Batut
<https://www.flickr.com/photos/134305289@N03/sets/72157695693844792/>,
or fill out the GCCBOSC feedback survey
<https://docs.google.com/forms/d/e/1FAIpQLSckB5ckoxvXf8UoheO9qOiGuWYsMRXWoOu_HkQ0RATzXmQZQA/viewform>
-
particularly if you didn't attend![image: CoFest at GCCBOSC 2018]
<https://github.com/OBF/newsletter/blob/master/newsletters/images/2018-07/collabfest.jpg>Figure
1. Participants at the GCCBOSC CoFest (photo by Bérénice Batut
<https://www.flickr.com/photos/134305289@N03/albums/72157695693844792/page3>under
a CC-BY-SA license
<https://creativecommons.org/licenses/by-sa/2.0/>)[image: Figure 2.
Participants at the OBF BoF]
<https://github.com/OBF/newsletter/blob/master/newsletters/images/2018-07/obf-bof.jpg>Figure
2. Participants at the OBF BoF
<https://news.open-bio.org/2018/07/09/following-up-from-boscs-obf-birds-of-a-feather-meeting/>
at
GCCBOSC, led by Yo Yehudi. (Photo by Nomi Harris)
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#obf-logo-redesign>OBF
logo redesignVoting on the OBF's new logo is now open!
<https://goo.gl/forms/9cR0aqYNBpIDZ14K2> Three volunteers have created
drafts of what could soon be the new logo for the OBF. Vote now
<https://goo.gl/forms/9cR0aqYNBpIDZ14K2> to have your say - and special
thanks to Sarah Thursby, Chuck McCallum, and Aleix Lafita for their design
efforts![image: Three candidates for the new OBF logo, designed by
community members]
<https://github.com/OBF/newsletter/blob/master/newsletters/images/2018-07/potential-logos.png>Figure
3. Three candidates for the new OBF logo, designed by community members.
Vote for your favorite here
<https://docs.google.com/forms/d/e/1FAIpQLSexizXWITDKLoH5NIQNyf_V3k846RpOCaeBpMOjFVhBmJN0fQ/viewform?fbzx=2434550998028402000>!
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#community-updates>Community
updates
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#mirtop>miRTop[image:
new miRTop logo]
<https://github.com/OBF/newsletter/blob/master/newsletters/images/2018-07/mirtop-logo.png>Lorena
Pantano presented miRTop at GCCBOSC
<https://gccbosc2018.sched.com/event/EiuN/mirtop-an-open-source-community-project-for-the-development-of-a-unified-format-file-for-mirna-data>
this
year, and already has some great updates, including an official page for
the miRNA annotation format,  <https://github.com/miRTop/mirGFF3>a
brand-new listing on FAIRsharing <https://fairsharing.org/bsg-s001218/>,
and a winner for their logo competition
<https://github.com/miRTop/mirtop/issues/29>!
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#what-is-a-pathway-anyway>What
is a pathway, anyway?Lluís Revilla is looking for feedback on a personal
project that aims to help standardize what a pathway is, or at least to
compare the different database definitions and see their implications
further down on the enrichment analysis tools using them. The GSEAdv
package <http://github.com/llrs/GSEAdv> analyses the properties of pathways
of any database and will be released in Bioconductor when finished.
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#interesting-links>Interesting
links - Mozilla Open Leaders
<https://foundation.mozilla.org/opportunity/mozilla-open-leaders/> - Are
you interested in learning how to work openly, or already work openly but
want to boost your project and learn how to create a community around it?
The Mozilla Open Leaders program is accepting applications until the end of
the month
<https://foundation.mozilla.org/opportunity/mozilla-open-leaders/apply/> and
is a great way to increase your project's openness, quality, and
visibility.- PLOS open source toolkit
<https://channels.plos.org/open-source-toolkit>, a curated set of articles
that focuses on good quality open source tools and alternates between
hardware and software. Many OBF projects could be highlighted here. Submit
an article
<https://channels.plos.org/open-source-toolkit/open-source-toolkit-submit>
(even
non-PLOS) anytime.- Mozilla Festival, especially the openness space
<https://mozillafestival.org/spaces#Openness> - proposals for sessions at
this internet-health oriented festival in London are open until the end of
the month.- Opencon <https://www.opencon2018.org/> - Applications to this
open-oriented conference are now closed, but you can still register to
attend remotely <https://www.opencon2018.org/opencon_2018_live#intro>.-
Free biology icons from Reactome, available freely under CC-BY.
<https://reactome.org/icon-lib>
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#future-editions>Future
editions
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#what-format>What
format?This is the first edition of this newsletter but we hope it won't be
the last! We're still working out the details and have some questions we
haven't ironed out yet. Should we accept content from any source, or only
members and perhaps BOSC attendees or presenters? We don't want to
overburden the newsletter curators. How often should the newsletter be?
Monthly seems maybe too often - perhaps quarterly? If you have any thoughts
we'd love to hear from you - or if you love writing and would like to help
curate the newsletter, please let us know!
<https://github.com/OBF/newsletter/blob/master/newsletters/2018-07.md#your-content-needed-for-the-next-issue>Your
content needed for the next issue!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/3>, 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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