BOSC 2022 dates: July 13-14, as part of ISMB 2022
Location: Madison, WI, USA, and virtual
BOSC announcements mailing list:
Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2022
April 21, 2022: Deadline for submitting talk/poster abstracts
May 12: Talk/poster acceptance notifications
May 19: Late poster (and Late-Breaking Lightning Talk) submission
May 26: Late poster / LBLT acceptance notifications
July 13-14: BOSC 2022 <https://www.open-bio.org/events/bosc-2022/>
July 15-16: CollaborationFest (CoFest)
The Bioinformatics Open Source Conference promotes and facilitates the open
source development of bioinformatics tools and open science. Since 2000,
BOSC has provided a forum for developers and users to interact and share
research results and ideas in open source bioinformatics and open science.
BOSC’s broad spectrum of topics includes practical techniques for solving
bioinformatics problems; software development practices; standards and
ontologies; approaches that promote open science and sharing of data,
results and software; and ways to grow open source communities while
promoting diversity within them.
As usual, BOSC will include keynote talks, longer and shorter (lightning)
talks from submitted abstracts, posters, Birds of a Feather, and more!
New this year: Joint session with Bio-Ontologies
We are excited to announce that BOSC and Bio-Ontologies
<https://www.bio-ontologies.org.uk/ismb-annual-meeting> will join forces
for part of a day at ISMB 2022. The joint session will feature keynote
speaker Melissa Haendel as well as talks chosen from abstracts submitted to
BOSC or Bio-Ontologies.
Keynote Speakers <https://open-bio.org/events/bosc-2022/bosc-2022-keynotes>
Melissa Haendel is the Chief Research Informatics Officer at University of
Colorado Anschutz Medical Campus, and Director of the Center for Data to
Health (CD2H). With expertise in molecular genetics and developmental
biology as well as translational informatics, Dr. Haendel focuses on open
science and data integration to improve rare-disease diagnosis and
mechanism discovery. She is a leader in ontologies and standards for data
Lior Pachter is the Bren professor of computational biology at Caltech. He
is a Fellow of the International Society of Computational Biology
<https://www.iscb.org/iscb-fellows> and has been awarded a National Science
Foundation CAREER award, a Sloan Research Fellowship His research interests
span the mathematical and biological sciences, including algorithms,
combinatorics, comparative genomics, algebraic statistics, molecular
biology and evolution. Dr. Pachter is known as a vociferous advocate of
open and accountable science.
A third keynote speaker will be announced soon!
We encourage you to submit abstracts
<https://www.open-bio.org/events/bosc-2022/submit/> (due April 21 – sorry,
no extensions) on any topic relevant to open source bioinformatics or open
science. After review, some abstracts will be selected for lightning talks,
longer talks, or posters. Abstracts that are not chosen for talks will
automatically be considered for posters.
Abstract submission will be via ISMB’s EasyChair. Note that ISMB/ECCB
requires a short (200-word) text-only abstract for all submissions (talk or
poster), plus a “long abstract” (PDF, 2 pages max) if you want to be
considered for a talk. A second, later round of submissions will end May
19. Abstracts submitted in the late round will be considered only for
posters and a limited number of “late-breaking lightning talk” slots; they
are not eligible for longer talks.
Registration fee assistance
We realize that the cost of ISMB may be prohibitive for some. If you are
submitting an abstract to BOSC and would have difficulty covering the cost
of registration, you can request a registration fee waiver right on the
abstract submission form (which will not be seen by reviewers). Those who
are not submitting abstracts can apply for an OBF Event Fellowship
<https://www.open-bio.org/event-awards/> (deadline April 1, 2022).
BOSC topics include (but are not limited to):
Ontologies: Open Source Tools and Approaches (new this year – joint
session with Bio-Ontologies COSI <http://www.bio-ontologies.org.uk/>)
Open Science and Reproducible Research
Open Biomedical Data
Standards and Interoperability
Open Approaches to Translational Bioinformatics
Open Science for Global Health
Developer Tools and Libraries
Inclusion, Outreach and Training
Bioinformatics Open Source Project Reports (about new or existing
Open and interoperable ontologies (joint session with Bio-Ontologies
We look forward to reading your abstract and seeing you (in person or
virtually) at BOSC 2022!
BOSC 2022 Organizing Committee: Nomi Harris, Karsten Hokamp, Hervé Ménager,
Monica Munoz-Torres, Deepak Unni, Nicole Vasilevsky, Jason Williams
The Galaxy Committers team is pleased to announce the release of Galaxy
- Developer and admin release announcement
- User release announcement
A few release highlights are:
New Colour Selector
Do you use tools which require colour inputs, like Circos? Previously, we
had a very restricted colour input which gave you a very limited palette.
Now, you have complete freedom of choice with the modern colour selector.
Improved File Export
If you've been exporting files from Galaxy lately, you've probably seen the
amazing new remote file source export, which allows you to export files to
FTP, Dropbox, and other locations.
Improved File Uploads
Previously, Galaxy servers used a variety of methods to let you upload
large files easily, including some servers which required FTP for large
files. We have replaced this with a new upload method, which will be
enabled on all usegalaxy servers soon. This will make file uploads
significantly smoother, and will be more tolerant of network failures and
interruptions! You do not need to make any changes.
Beta History: Collection Improvements
If you've been trying out the beta history (which will be the default
history in the next release!), it has been updated to indicate whether
collections are homogeneous or heterogeneous. This will help you see more
easily if you've accidentally included an incorrect dataset.
Galaxy starts as a FastAPI application by default
Starting Galaxy via run.sh will use the new gravity process manager
<https://github.com/galaxyproject/gravity>. The new configuration uses
Gunicorn <https://gunicorn.org/> and FastAPI <https://fastapi.tiangolo.com/> to
drive Galaxy's web process, and starts job handler and Celery
<https://docs.celeryproject.org/> processes automatically. For more details
and instructions, please consult the Migrating to Gunicorn documentation
User Preferences can be encrypted in Galaxy Vault
Galaxy can now be configured to store secrets in an external vault, which
is useful for secure handling and centralization of secrets management. In
particular, information fields in the "Manage information" section of the
user profile, such as dropbox keys, can be configured to be encrypted at
rest in a vault (Hashicorp, Custos or database) instead of being stored as
plain text in the user preferences table. For detailed information on
configuration, refer to the vault section
the admin documentation.
Please see the full release notes
a lot more details and instructions for upgrading your Galaxy installation.
Thanks for using Galaxy!