The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for <https://summerofcode.withgoogle.com/> Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). Among this list of projects are Reactome and GMOD and its software projects -- JBrowse; Galaxy; WormBase; and others.
Call for 2021 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, and Scott Cain (emails above).
You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2021>.
For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC><http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 19th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.
Please forward this to others who might be interested in taking part.
If you have any questions please let us know.
Robin, Marc, and Scott.
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:
Tool Panel Views
We now have "Tool Panel Views"! These are different views into the same
toolbox and might help make it easier to find the tools you want. In the
future, there are plans to create user-customisable toolboxes, but until
then go explore the new EDAM Ontology-based toolboxes which organise tools
around scientific areas or processes. For example, a category like
"Filtering" might have tools like "select lines" or "filter bam by
quality", both doing the same process of filtering, despite their different
file types and formats.
Unfortunately, not all tools are fully annotated yet, and while we also
pull terms from bio.tools, this still doesn't get us full coverage and many
tools will still appear under a large section "Uncategorized". Hopefully,
this will improve as users and tool developers annotate these tools with
the appropriate terms that help everyone find them.
Collections (Beta History Updates)
Did you ever create *a collection with the wrong dbkey or datatype*? Well,
in the Beta History you can now change collections' datatypes and dbkeys!
This should save a lot of time for everyone working with large datasets (Pull
Request 11799 <https://github.com/galaxyproject/galaxy/pull/11799/>).
Additionally, did a *collection ever fail* for you? And you wondered why?
Now you can find out with the view details button for collections (Pull
Request 12261 <https://github.com/galaxyproject/galaxy/pull/12261>)!
Selecting datasets from the Remote Files view has gotten easier! Now, you
can select folders and files and import at once all of the datasets
recursively in those folders. Previously, you could only select files
within a folder, so this is a huge improvement in the usability of such a
key new feature of Galaxy (Pull Request 12310
<https://github.com/galaxyproject/galaxy/pull/12310>). But with great power
comes great responsibility, be careful not to import the entirety of NCBI!
Report components used to automatically arrange themselves in a smart way,
but due to some issues with the floating of components, these will now be
full width until we can figure out a good way to provide a similar
Request 12085 <https://github.com/galaxyproject/galaxy/pull/12085>).
Enhancements for Working with Remote Data and Distributed Computing
Many fixes and enhancements were made to improve how Galaxy can import and
write to remote data using the configured file source plugins. In addition
to the History Export functionality, which can write to remote locations,
we have added an Export datasets Tool for exporting individual Datasets and
Dataset collections to configured remote locations. The Tool will
automatically maintain the name and structure of Datasets and Dataset
Collections. We have added the possibility to import entire folders of
remote data and made the data selection dialog more intuitive. We also
added numerous improvements and fixes to the extended metadata collection
strategy and Pulsar <https://github.com/galaxyproject/pulsar>, so that many
more tools are able to run in Pulsar
<https://github.com/galaxyproject/pulsar> and write data back to storage
without passing through Galaxy first.
Migration to FastAPI and Extended Documentation of API Routes
We have modernized and migrated many more API routes to FastAPI and have
extended the documentation and validation of these routes.
Migration to SQLAlchemy 1.4 and Declarative Mapping
Galaxy is now using SQLAlchemy <https://www.sqlalchemy.org/> version 1.4,
which is a prerequisite for asynchronously interacting with the database.
We also modernized the way our database models are defined to the more
commonly used Declarative Mapping approach, which is more concise and
Modernization of Tool Form Interface
The tool form interface has been almost completely migrated from Backbone
<https://backbonejs.org/> to Vue <https://vuejs.org/>. This improves the
reactivity of parameter validation and enables the migration of tool
parameters to Vue, which will also allow us to add many more types of tool
parameters. We further migrated the tool form variant for the Workflow
Editor, the Workflow run form and the Show Dataset Parameter page to Vue.
New User Welcome Page
We have added a page that new users will be directed to after creating a
new Galaxy account.
Please see the full release notes
a lot more details and instructions for upgrading your Galaxy installation.
Thanks for using Galaxy!