Dear Sarah and Gabry,
I would like to confirm that the Galaxy Training Network is interested in
participating in, and would like to send one or more people to this
hackathon in April. We don't know who yet, but metagenomics is a key
concern for the Galaxy community. (And we are holding a Metagenomics tools
and workflows hack next week.)
Do you need anything else from us at this time?
On Mon, Nov 23, 2015 at 2:58 AM, Gabriella Rustici <gr231(a)cam.ac.uk> wrote:
> Dear all,
> You are invited to participate to the ‘GOBLET/Elixir thematic hackaton for
> metagenomics training materials re-use’ that will take place in Copenhagen,
> on 6-8 April 2016.
> The aim of this workshop is to bring together trainers and researchers
> working in the field of metagenomics from within Europe and beyond, to
> enhance the training network within this field.
> The workshop will focus on the curation of training materials in the area
> of metagenomics data analysis, encompassing appropriate high-throughput
> sequencing workflows (genome assembly, annotation and analysis) and related
> subjects, such as phylogenetics and comparative genomics.
> Participants are expected to bring to the workshop the training materials
> that they have developed in the domain of metagenomics data analysis.
> During the workshop we aim to:
> - Develop a collection of metagenomics training materials that are
> consistently described, to enable sharing and re-use of such materials
> across the training community;
> - Define an approach for the curation of training materials for re-use
> through training portals and repositories such as TeSS and the GOBLET
> portal; and
> - Link training materials to databases and standards in the BioSharing
> registry and tools in the ELIXIR Tools & Data Services Registry.
> Funding is available for attendees that are not Elixir funded.
> Save the date and drop us an email to confirm your participation.
> Additional information will follow shortly.
> Looking forward to see you in Copenhagen!
> Best regards,
> Sarah & Gabry
> Gabriella Rustici, PhD
> Bioinformatics Training Manager
> Department of Genetics
> University of Cambridge
> Downing Street
> Cambridge CB2 3EH
> United Kingdom
> Email: gr231(a)cam.ac.uk
> Tel: +44 (0)1223 333614
> URL: http://training.csx.cam.ac.uk/bioinformatics/Event-timetable
Hello Fourie, Terri, Michelle, and Peter, (and the Galaxy training
The Galaxy training community has discussed what we would like to see in
GOBLET in the coming year. I initially floated several ideas on the
galaxy-training mailing list, and these were then modified and extended by
This email lists those items and includes some suggestions for implementing
Fourie, we're handing these to you for presenting to the larger group.
Peter van Heusden of SANBI will also be in attendance and can also speak
from his experience within the Galaxy community.
Many thanks for Hans-Rudolf Hotz and Björn Grüning for starting this
conversation and contributing to it, and to Fourie for agreeing to
If anyone has anything to add to the items below, please do so in the next
Thanks, and have a great meeting,
Dave C on behalf of the Galaxy Training Network
*Five items we would like to see discussed are:*
*1. Enable/Host online discussion about bioinformatics training.*
We'd like GOBLET to host a mailing list or online forum for discussion of
bioinformatics training issues. GOBLET has an announcements mailing list,
but it would be a huge win if GOBLET hosted *the* place to discuss
training issues. We argue this place list/forum be open to anyone, not
just GOBLET members.
Galaxy has had significant success with a Biostar based forum (but a
mailing list would be great too.)
*2. Either start sending a regular newsletter, or stop saying we have one.*
Our preference is to start sending a regular newsletter, but that is effort
and the payoff is uncertain. Having a newsletter does increase GOBLET's
visibility and it also great for newcomers to see what is going on. (And
having a better welcome for new GOBLETeers is one of our goals.)
I prepare the monthly Galaxy Newsletters and this takes a little over a day
of my time, every month. (But when I suggested to the Galaxy training list,
that this might not be worth my time, I got pushback that it was worth my
*3. Should GOBLET offer a bioinformatics trainer certification?*
GTN is in favor of a GOBLET Trainer badge as a way of both promoting GOBLET
and as a way of saying "I've participated in GOBLET training" or "I'm
Perhaps attendees at the just finished best practices workshop would be the
*4. Make it easier to publish, share, and refine training material.*
(I'm channeling Björn Grüning here. Björn, please correct me if I go
Software and Data Carpentry's model for training material is to use GitHub
for version control, and to use Github's branching and merging capabilities
to enable community editing of that training material.
Right now GOBLET's (and GTN's) training material sharing is purely
upload/download. It might be worth considering taking a hard look at how
Carpentry does this and then support a similar model. Embracing this might
lead to an explosion of collaboration on training material. It has been
very successful for Software Carpentry
The danger here is that the upload/download model is simple to use and easy
to implement, and a Github based system would be a lot of work up front,
and might not ever catch on.
*5. Shared Training Datasets are Precious!*
(Also channeling Björn here, although he never used the word "precious.")
Given the difficulty and time required to create good datasets for
training, it might be worthwhile for GOBLET to create a central repository
for training datasets. This increases their visibility and usefulness, and
also increases the visibility of the training dataset creators.
Right now people can upload datasets of up to 50MB, which is good, but it
would be great if there were some way to identify just training datasets,
or training resources that include datasets.
In the wake of the Carpentry TTT workshop not being scheduled for GCC2016,
Mo Heydarian (CC'd here) suggested that perhaps we have a much
lighter-weight session during GCC2016 training that covers best practices
and resources for training with Galaxy. Mo and I scrambled our brains
together and came up with this nomination:
We would love to have feedback on this proposal, both specific and big
picture. The text of the nomination can easily be updated any time between
now and next Monday, when voting opens.
This is an opportunity to gather best practices into a single place, and
would be a friendly place to bring new trainers into the fold.
Also, please let me know if you'd be interested in helping teach this.
Thanks, and many thanks to Mo for making this happen,