Hi Myhanh
Will you please write to Andreas cc'ing debian-med (in cc) in answer to his
question?
Thanks
Jon
> Hi Jon and Kristoffer,
>
> could you please confirm my guess that the hotel is just booked for the
> sprint members?
>
> Kind regards
>
>Andreas.
>
> On Tue, Nov 03, 2015 at 1
Thanks both
J:)
> Hi Jon,
>
> I switched the discussion where it belongs and should be done.
>
> On Tue, Nov 17, 2015 at 06:45:11PM +0100, Steffen M�ller wrote:
>> Am 17/11/15 um 17:50 schrieb ji...@cbs.dtu.dk:
>> > Quick question. Do you have any stats on the number of downloads,
>> installat
Folks
The link to OLS was to a deprecated ontology browser running an ancient version
of EDAM.
Please use this one instead (it's in beta, so go steady):
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM
Alternatively you can use this:
http://bioportal.bioontology.org/ontologies/EDAM/
:)
Still recovering from massive backlog of urgent things, we will get to it!
(and pick up on all other threads)
J:)
> On Wed, Feb 10, 2016 at 11:14:00PM +0700, Matus Kalas wrote:
>> This is absolutely amazing Andreas! Thank you very much to everybody who
>> contributed!
>
> I admit I would sl
Thanks Fabian
Not sure if I replied already about this. Anyway, the link to OLS you mention
is horribly out of date. Please use one of
these (the 1st is more reliable, the 2nd is good but in beta):
http://www.ebi.ac.uk/ols/beta/ontologies/edam
http://bioportal.bioontology.org/ontologies/EDAM?p
Thanks Fabian
Not sure if I replied already about this. Anyway, the link to OLS you mention
is horribly out of date. Please use one of
these (the 1st is more reliable, the 2nd is good but in beta):
http://www.ebi.ac.uk/ols/beta/ontologies/edam
http://bioportal.bioontology.org/ontologies/EDAM?p
Evening all
A few thoughts:
Perhaps something to check the EDAM annotations are valid wrt the latest EDAM ?
Something to check package description for export (to bio.tools) has not become
out of synch with what's in bio.tools
And I wonder about the relationship between the "EDAM metadata files
On behalf of ELIXIR / DTU I'd like to say thanks to the Debian guys, had a real
blast and it's a pleasure with such hard
working people.
A slight clarification (this is often mixed up): EDAM is a simple controlled
vocabulary (for bio-topics, operations data
and data formats). It is used to des
Yes - you can register your workflows at bio.tools. A workflow can, after all,
be considered just a tool with an input and
output. Noone asked until now, though, so there may be some workflow-specific
metadata that we don't currently capture
(but can extend biotoolsXSD for it).
As for serving
Thanks for this work, folks.
The ELIXIR bods have been swamped since the sprint; March is also horrendous:
this situation will improve in April! Watch
this space ... :)
Cheers
Jon
> On Wed, Mar 09, 2016 at 06:55:44PM +0100, Steffen M�ller wrote:
>>
>> I have now also prepared a more detailed
Hi Steffen
To get the EDAM annotations, it could be much more straightforward to wait
until the SEQwiki tools imported into bio.tools
(this right now is the #1 content priority) and then export to DebianMed of the
descriptions from there (using the
format/tool that Hervé was leading discussions
Excellent. We have a bio.tools issue for this, and I've assigned it to you to
lead, Matus (forgive my rude presumption :)
https://biotools.sifterapp.com/issues/32
As for schema - please fire away! But that's a discussion probably for
registry-core list (do you want in, by the way
Steffen? See
Hi folks
I second all of Steffen's comments here!
As for a Debian-themed COST action; this could be good and I'd certainly
support it, in so far as it complements the work
of bio.tools & EDAM specifically and ELIXIR-DK generally, including e.g.
benchmarking angles. ELIXIR-DK will likely be
inv
Hi Steffen
I like very much the "extra day" idea following the template at the last
Sprint, i.e. a day focused essentially on outreach
to a specific community, project, application etc. beyond Debian. I think that
could help Debian Med in various ways. But
someone else should pay for it (ideal
Hi folks
Forgive the very naive question, but do you maintain a list of links to
packages (source, binary) currently available in
the Debian distro ?
I want to support linking to Debian packages from named tools in bio.tools.
If not a link, I guess I could just support package names; in this ca
Hey Steffen
> Now, being cited in a Nature Reviews Genetics paper is something that I
> presume we all appreciate. This other gang of four (the one first
congrats!
> upcoming description of ours, but I presume we all agree there should be
> an upgrade and we should aim at some higher impact fact
Hey Steffen
The plan* is indeed to annotate such "training workflows" (steps within them,
and the overall thing) with EDAM, and thus
provide a way to link to bio.tools from the diagrams, via the API (i.e. tool
for this step in the workflow). It could
provide a nice visual way to navigate conten
Exactly
Abstract workflows with primary value (at least IMO) for teaching, and also for
navigating TeSS and bio.tools content.
Cheers
J:)
> My understanding from talking with the TESS team is that these are abstract
> workflows and not meant to be directly executable, so no competition for
> C
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