Codefest logistics for July 13th and 14th

[Brad Chapman]

Hello all;
I'm excited about all of the interest in Codefest and it'll be
great to catch up with everyone next week. All of the fun will take
place at the MetaLab thanks to their generous hosting:

http://metalab.at/wiki/English

The coding kicks off at 10am on July 13th. Peter Cock will be
helping with the organizing and is the person to look for when you
arrive at the MetaLab. I am flying in on the redeye and getting
there early on the 13th, so may not have made it out from the
airport yet. Lars is our contact at MetaLab, so if you can't find
Peter you can ask for him as well.

There are lots of great project ideas already listed on the shared
Google Doc and please feel free to add more:

https://docs.google.com/document/d/1EFe9YszL5Lp5FjZjJLFhWepsto1jhC6oASWcG4Wlnds/edit?hl=en

Ask away if you have any questions or concerns. Looking forward to a
fun time,
Brad

[Hilmar Lapp]

Just FYI, it turns out that I can only fly out on July 13th (NSF grant
submission deadline on the 12th), so I'll arrive straight off the
plane on Thursday morning, probably around 10am. (Brad are there any
other flights than redeyes from the East Coast?). Sorry for having to
miss the Wednesday, I was looking forward to it. Hoping the Thu will
still be enough fun ...

-hilmar

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--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Brad Chapman]

Hilmar;
Thanks for the heads up; it'll be great to see you on Thursday. The
flights from the east coast just aren't convenient times. On the way
over you are stuck with redeyes, then on the way back everything is
in the morning. For some reason, everyone won't get on board with
the idea that they should structure the world to accommodate my needs.

Looking forward to Vienna,
Brad

[Raoul Bonnal]

I'll be there with my colleague on July 14th, no way to get 13 :-/

I'd like to explore the possibility to include BioNGS into BioLinux
after its official release
https://github.com/helios/bioruby-ngs

> > >https://docs.google.com/document/d/1EFe9YszL5Lp5FjZjJLFhWepsto1jhC6oA...

[Brad Chapman]

Raoul;

> I'll be there with my colleague on July 14th, no way to get 13 :-/

Sounds great. Looking forward to seeing you again on the 14th.

> I'd like to explore the possibility to include BioNGS into BioLinux
> after its official release
> https://github.com/helios/bioruby-ngs

Yes, please. Once this is available from the gem repository it is no
problem to add it into the CloudBioLinux build. We already install
fastx toolkit and gnuplot so the dependencies are fine.
The gem name just needs to go into:

https://github.com/chapmanb/cloudbiolinux/blob/master/config/ruby-libs.yaml

In general it would be great to get feedback from ruby folks on the
installed libraries and environment. I've tried to make it
reasonable but don't do a lot of ruby work so may be missing some
gems that would be nice to have.

Brad

[Raoul Bonnal]

Hi Brad,

On Jul 7, 2:19 pm, Brad Chapman <chapm...@50mail.com> wrote:
> Raoul;
>
> > I'll be there with my colleague on July 14th, no way to get 13 :-/
>
> Sounds great. Looking forward to seeing you again on the 14th.

:-)

>
> > I'd like to explore the possibility to include BioNGS into BioLinux
> > after its official release
> >https://github.com/helios/bioruby-ngs
>
> Yes, please. Once this is available from the gem repository it is no
> problem to add it into the CloudBioLinux build. We already install
> fastx toolkit and gnuplot so the dependencies are fine.
> The gem name just needs to go into:
>

> https://github.com/chapmanb/cloudbiolinux/blob/master/config/ruby-lib...

>
> In general it would be great to get feedback from ruby folks on the
> installed libraries and environment. I've tried to make it
> reasonable but don't do a lot of ruby work so may be missing some
> gems that would be nice to have.

Some of the tools needed by biongs are shipped with it, others are
downloaded and compiled at install time and we had the same approach
with bio-samtools and bio-bwa, everything during the gem installation.
BioNGS looks for software installed system widely or in its own (gem)
directory, with different kind of criteria. In case some software can
be shipped with biongs and is not installed on the hosting machine,
BioNGS disable the related tasks transparently.
Why I did the download or distribute the binaries with the gem ? So I
can support a precise version of a software and avoid the end user to
install that software.

Then: I'd like to create a biolinux image for RDF development/testing
installing some triple store and libraries, could you give me some
hints in Vienna ?


Ciao.
--
Ra

[Brad Chapman]

Raoul;

> Some of the tools needed by biongs are shipped with it, others are
> downloaded and compiled at install time and we had the same approach
> with bio-samtools and bio-bwa, everything during the gem installation.
> BioNGS looks for software installed system widely or in its own (gem)
> directory, with different kind of criteria. In case some software can
> be shipped with biongs and is not installed on the hosting machine,
> BioNGS disable the related tasks transparently.
> Why I did the download or distribute the binaries with the gem ? So I
> can support a precise version of a software and avoid the end user to
> install that software.

Okay, happy to discuss. The goal of CloudBioLinux is to avoid having
to implement your own package manager for distributed code.
Hopefully we can install these gems without needing to invoke any of
that.

> Then: I'd like to create a biolinux image for RDF development/testing
> installing some triple store and libraries, could you give me some
> hints in Vienna ?

Definitely, that would be great. I don't know much about RDF
libraries/triple stores but can help with including them if you have
pointers.

Thanks again,
Brad

[Scott Cain]

Here's a stupid question I should have asked sooner: what is the best way to get directly from the airport to MetaLab?

Thanks,
Scott

Sent from my iPad

[Peter Cock]

On Wednesday, July 13, 2011, Scott Cain <sc...@scottcain.net> wrote:
> Here's a stupid question I should have asked sooner: what is the best way to get directly from the airport to MetaLab?
>
> Thanks,
> Scott
>
>

Take the normal train (a few euro) or the fast CAT train (10 euros) to
the city centre, station Wien Mitte.

Then there is a choice of metro routes, shortest looks like U3 line
west then north one stop on the U2 line, stop is Rathuas (City Hall -
where the conference dinner is).

http://metalab.at/wiki/Lage

Peter

[Peter Rice]

Hi Scott (and any latecomers looking for help),

Take the SchnellBahn (train symbol with little red "S" logo) to Praderstern, ticket 3,60
euros. Then take the U-bahn (underground/metro) U2 to Rathaus (city hall) Your ticket is
still valid on the U-bahn.

MetaLab is at the South end of Rathaus strasse (town hall street), number 6 - big blue
number above a small door!

Peter

[Peter Rice]

Peter Cock wrote:

> Take the normal train (a few euro) or the fast CAT train (10 euros) to
> the city centre, station Wien Mitte.

From the airport, definitely better to use the normal train (S-bahn) ... the CAT only
stops at Wien Mitte, but Praderstern saves you a walk to the U-bahn and a change on the
U-bahn (though it does take a few minutes longer as it has more stops in the centre)

> Then there is a choice of metro routes, shortest looks like U3 line
> west then north one stop on the U2 line, stop is Rathuas (City Hall -
> where the conference dinner is).

> http://metalab.at/wiki/Lage

See you soon

Peter Rice