Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

[Charles Plessy]

Le Fri, Jun 17, 2016 at 11:04:33PM +0200, Steffen Möller a écrit :
> 
> Eh, we have Charles at RIKEN, who is badly overdue to join - here or there.

Hi Steffen and everybody,

it would be great to have a meeting somewhere near Japan's timezone.  Currently
I am still in a state of constant tiredness with all the productivity loss that
it induces (and when I hear my colleagues say that week-end is great to write
papers, I wonder if I should laugh or cry: don't they know that kindergartens
are closed on week-ends ??).  Altogether, fear of jet lag and work backlog made
me avoid the Debian Sprints.  But things are getting better and better.

There are fundraising schemes to organise international workshops in Japan,
this is an option that I have not explored very well at the moment...

Have a nice week-end,

Charles

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

[Steffen Möller]

Hi Afif,

On 16/06/16 09:43, Afif Elghraoui wrote:
> Hi, all,
>
> على الأربعاء 15 حزيران 2016 ‫05:01، كتب Sascha Steinbiss:
>>> Should there possibly a second Debian Med meeting on another
 continent than Europe? 
>> Sure, if there is enough interest -- especially for newcomers from
>> overseas :) For now there have only been a handful of people traveling
>> that far. Not sure if more would come if there was an event closer to them.
>> However, I myself would probably only be able to make it if the travel
>> costs are moderate as my employer won't cover that.
>>
> I'm located on the USA west coast and this is precisely the reason I
> haven't been to these events. The travel costs are just too much for me
> to justify for a volunteer-work trip.
We have the developers of AutoDock close to you at Scripps as DebianMed
associates,
and indeed it would be nice to meet up over there. There was a Debian
special
interest group once http://scd.debian.net/ and if they are still
existing it may
be somewhat fruitful to get them on board.

Since California does not have a Winter, we need another theme for you,
too ;)
The ones I proposed for Sascha seem to fit. More seriously, I would very
much
like to have another event when the earth is on the other end of the sun
(you
all also follow Debian Astro, right?), let alone for how many activities
that last
meeting has spawned. If we think about giving meetings a special touch, then
this also defines a bit who shall be present and travel costs lose a bit
of their
importance since the meeting turns relevant for work. And we shift from
getting software into Debian towards getting workflows into Debian, which
should also attract more people. So we could for instance keep the Winter
meetings for the more Debian Med infrastructure bits (at the seaside,
please)
and the summer meetings for workshops on workflows (WoW, google that)
I propose to keep next to large scientific institutions. The Debian Med
Infrastructure meeting would be of continued core Debian interest, the
application side should have someone else or nobody to finance, I suggest.

Sascha's first meeting could be: Workflows for prokaryotic genome
annotation,
and I propose to team up with DebianMed-friendly EagleGenomics for that,
and if the genome campus is booked, consider to even have it at Babraham.
Afif's first meeting could be: In silico workflows for reducing clinical
drug
resistance. Actually, we yesterday discussed preparing (pre-preparing)
a workshop on semantics controlling expression data analysis for drug
screening
to be held in Budapest and we could make that a Debian event, too. Maybe
we find another organisation than Debian to co-host and co-organise it all.
Given that fortune that big pharma spends on sending their folks around for
training, there should be some possibilities to raise some interest.

Steffen

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

[Steffen Möller]

Hi Sascha,

On 15/06/16 14:01, Sascha Steinbiss wrote:
> Hi Steffen and all,
>
>> I was peeking into the one or other scientific collaboration of mine to
>> invite them to our next Debian Med sprint. But I could not really tell
>> much about it, yet. Besides deciding where to convene next (which to my
>> recollection is decided by someone saying loudly that he/she wants to
>> host us ... hello?) 
> FYI as a side note: I have reached out to informatics people here at
> Sanger during the regular campus-wide Informatics Group Meetings by
> giving a brief talk about Debian Med and the history of the sprints and
> also trying to get an idea of who would support such an event in-house.
> In the discussion afterwards indeed some upstream developers agreed that
> this would be a good idea and would benefit the institute. However,
> there was little initiative from any particular group to approach me
> afterwards and find out how to make it work together; it was merely
> suggested to contact the Genome Campus conference centre (which might be
> on the more expensive side compared to our previous venues).
> I can try to poke some people to bring the topic back to the table.
Fantastic campus, fantastic people, just that carp-loaded bit of water does
not really qualify. Why don't you start a second theme and have it during
the summer, one that could more easily then start migrating abroad. It
could for instance be "attached to upstream" both in the sense of data
providers and possibly a conference for those traveling from far?
Also "automate big clinical chemical data" (ABCCD) comes to mind :o)
>> we should possibly also lean back a bit and decide if we want to
>> change the one or other thing. This could start with the name. In my
>> perception what we are having is not so much a problem-focused
>> Sprint.
> Yes, I agree in principle.
>> So, what do you all think?  Would it help to officially come up with 
>> some extended Sprint format? What would you change? Nothing? More
>> talks? More time?
> If the number of participants supports this, maybe some pre-allocated
> time for custom break-out sessions, to allow for some in-depth mentoring
> or bug squashing without missing group discussions or talks?
> What do you think?
Most of us seem to be professional bioinformaticians. If we want to do
bug squashing we can basically do that any time via skype and github.
I sense particular value in learning whom to actively contact for help when
something is difficult to track down if this is not upstream. It would be
very nice for all the infrastructure bits, though, especially for the CI
additions that you in particular I have seen to contribute much for.

What if what you referred to as "bug squashing" we apply on data processing,
i.e. workflows for best biological insights? Particularly for a large
data site like
yours it may be very nice to have something intertwining Debian with CWL
for education, documentation and production.
>> Should there possibly a second Debian Med meeting on another
>> continent than Europe? 
> Sure, if there is enough interest -- especially for newcomers from
> overseas :) For now there have only been a handful of people traveling
> that far. Not sure if more would come if there was an event closer to them.
> However, I myself would probably only be able to make it if the travel
> costs are moderate as my employer won't cover that.
We could have Sanger this year, and maybe The Cancer Genome Atlas
in the next? Maybe we could find some way to report a bit more on what
we talked about, i.e. the things that are not in papers: problems in not
always homogeneous biological big data and how to spot or circumvent
them. We may find quite an audience also outside of Debian for such
extra level of confidence. Eh, we have Charles at RIKEN, who is badly
overdue to join - here or there.
>> With the same focus? Or more medical?
> Personally I probably wouldn't be too interested in medical or research
> applications as I tend to focus more on the technical/infrastructure
> aspect. But that's just me, YMMV. I can imagine that it might make sense
> to attract the non-core-Debian crowd as well.
>
I fell out of the Debian GSoC after the organisers killed accepted projects
of mine since they felt it was not close enough to Debian. I am still
furious
thinking about it. If we start paying people to travel overseas so that we
can help biomedical research to avoid false positive/negative findings
because of erroneous data handling, then tend to think that this indeed
beyond the scope of core Debian and we should find other ways to
finance ourselves - as much as we today want to avoid any such split
from Debian. We are so few that even charging for the participation to
allow someone to travel would not help so much and break a bit of how
we interact so far.

Best,

Steffen

Re: Hmmer,Hmmer2 autopkgtests [GSOC]

[Canberk Koç]

Hello all,

I upload packages.Thank you for your help.

Best Regards

Canberk Koç
www.about.me/canberkkoc
16 Haz 2016 19:23 tarihinde "Canberk Koç"  yazdı:

> Hello Afif,
>
> Thanks for your help . I'll commit packages tonight.
>
> Best Regards
>
>
>
> Canberk Koç
> [image: https://]about.me/canberkkoc
>
> 
>
> 2016-06-15 10:55 GMT+03:00 Afif Elghraoui :
>
>> Hi, Canberk,
>>
>> على الإثنين 13 حزيران 2016 ‫14:51، كتب Canberk Koç:
>> > I am waiting for these packages to transfer git . Thanks for your help.
>>
>> Done.
>>
>> ssh://git.debian.org/git/debian-med/hmmer.git
>> ssh://git.debian.org/git/debian-med/hmmer2.git
>>
>> Many thanks and regards
>> Afif
>>
>> --
>> Afif Elghraoui | عفيف الغراوي
>> http://afif.ghraoui.name
>>
>>
>

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

[jison]

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 (ideally with extras) to bring your costs down.  
And making the case for that support is a
good validation of Debian Med's relevance.  Importantly though - it should be 
done in a way that doesn't detract from your
actual sprints!  My experience from EDAM & bio.tools is that, going the extra 
mile on outreach is at the expense of
targeted sprints to get essential technical work done.  Not good.  So a balance 
is needed between hackathon, sprint and
outreach dimensions.

Just my two-penneth

Happy hacking!

J:)



> Hello,
>
> I was peeking into the one or other scientific collaboration of mine to
> invite them to our next Debian Med sprint. But I could not really tell
> much about it, yet. Besides deciding where to convene next (which to my
> recollection is decided by someone saying loudly that he/she wants to
> host us ... hello?) we should possibly also lean back a bit and decide
> if we want to change the one or other thing. This could start with the
> name. In my perception what we are having is not so much a
> problem-focused Sprint. It is more like many Sprints held at the same
> time, spiked with educational bits and team building. This year had this
> twofold. It had it externally to Debian with the ELIXIR folks and it had
> it internally to Debian with the promotion of continuous integration
> tests. Well done! I also liked this year's clear-cut extra day.
>
> So, what do you all think?  Would it help to officially come up with
> some extended Sprint format? What would you change? Nothing? More talks?
> More time? Should there possibly a second Debian Med meeting on another
> continent than Europe? With the same focus? Or more medical?
>
> Is there something else we could do to ease the waiting time for the
> next winter? With EU projects one has (too many) virtual meetings. But
> maybe this would not be too bad after all.
>
> Many greetings
>
> Steffen
>
>
>