Clouds and NG sequencing

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Clouds and NG sequencing

Sri Girish Srinivasa Murthy
Hello,

I am graduate student in Luebeck, where Steffen is also located, and mostly working in the (almost) neighbouring Max Planck Institute to study Microbioata in Skin and Gut of Mouse. As an Ubuntian I joined Debian Med two weeks or so ago and with Steffen I have done some packaging with the help of Steffen (denoiser,python-cogent, python-pynast, qiime, mothur), an upload only pending the confirmation of upstream that this is ok to redistribute from the respective Authors but they somehow seem to be all on vacation.

I have strong interest to learn more about cloud computing and use it for NG sequencing and the data analysis. Steffen set up a server for this that I am going to share. Whoever on this list feels like discussing along, please drop me a quick Hello.

Best Regards,
Girish


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Re: Clouds and NG sequencing

Andreas Tille-5
On Tue, Jul 20, 2010 at 06:05:11AM +0000, Sri Girish Srinivasa Murthy wrote:
> Hello,
> I am graduate student in Luebeck, where Steffen is also located, and mostly working in the (almost) neighbouring Max Planck Institute to study Microbioata in Skin and Gut of Mouse. As an Ubuntian I joined Debian Med two weeks or so ago and with Steffen I have done some packaging with the help of Steffen (denoiser,python-cogent, python-pynast, qiime, mothur),

I have added all you ITPed packages to the Debian Med task and you can
view the entries on the tasks page[1] for biology.  I'm really keen on
hearing your opinion as a newcomer about this page as a whole because it
has grown quite large.  We somehow are considering a split but we have
no good idea what criterion for a split would make sense.  Just try to
bring in some idea in case you are looking from a different perspective
as we die before.

> an upload only pending the confirmation of upstream that this is ok to redistribute from the respective Authors but they somehow seem to be all on vacation.

Well, if this is the *only* reason to wait I would not mind very much.
It is considered as "good style" to ask authors but you do not really
need a permission in case the license is free.  So provided that the
license does not contain any nasty pitfalls I would go for the upload
(or Steffen for the sponsoring) and I would write a second e-mail to the
authors somehow like:

  "As I have informed you in my last mail I have builded Debian packages
   from your software.  They are now available on the Debian mirror and
   will be released in the next stable Debian release.  I hope you like
   this effort."

Especially the last bit to meet the Squeeze freeze sounds a good
argument to upload now and not later.  So the package might get some
testing (autobuilders might detect problems etc).

> I have strong interest to learn more about cloud computing and use it for NG sequencing and the data analysis. Steffen set up a server for this that I am going to share. Whoever on this list feels like discussing along, please drop me a quick  Hello.

I would like to say "Hello" in the name of this list.  It is not that
high volume that you should hesitate to send a mail about a specific
topic.

Kind regards and thanks for your effort

    Andreas.

[1] http://debian-med.alioth.debian.org/tasks/bio#pkgvcs-debs

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Re: Clouds and NG sequencing

Charles Plessy-12
In reply to this post by Sri Girish Srinivasa Murthy
Le Tue, Jul 20, 2010 at 06:05:11AM +0000, Sri Girish Srinivasa Murthy a écrit :

>
> I am graduate student in Luebeck, where Steffen is also located, and mostly
> working in the (almost) neighbouring Max Planck Institute to study
> Microbioata in Skin and Gut of Mouse. As an Ubuntian I joined Debian Med two
> weeks or so ago and with Steffen I have done some packaging with the help of
> Steffen (denoiser,python-cogent, python-pynast, qiime, mothur), an upload
> only pending the confirmation of upstream that this is ok to redistribute
> from the respective Authors but they somehow seem to be all on vacation.
>
> I have strong interest to learn more about cloud computing and use it for NG
> sequencing and the data analysis. Steffen set up a server for this that I am
> going to share. Whoever on this list feels like discussing along, please drop
> me a quick  Hello.

Hello Girish,

welcome in Debian Med, and many thanks for your help to increase our support
for high-throughput sequencing applications. Our packages are listed on our
‘web sentinel’ pages, but this does not indicate much how they fit together.
Do not hesitate to document on the Debian wiki how the packages you added can
be used as part of the same workflow. Also, we have an area on the main
website, that may be used as well—perhaps after a drafting phase on the wiki.
These pages are translated in many languages, so they are more suited for
non-specialists.

 - The web sentinels: http://debian-med.alioth.debian.org/tasks/
 - The Debian wiki: http://wiki.debian.org/DebianMed
 - The Debian website: http://www.debian.org/devel/debian-med/

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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Re: Clouds and NG sequencing

Steffen Möller
On 07/22/2010 03:10 AM, Charles Plessy wrote:

> Le Tue, Jul 20, 2010 at 06:05:11AM +0000, Sri Girish Srinivasa Murthy a écrit :
>  
>> I am graduate student in Luebeck, where Steffen is also located, and mostly
>> working in the (almost) neighbouring Max Planck Institute to study
>> Microbioata in Skin and Gut of Mouse. As an Ubuntian I joined Debian Med two
>> weeks or so ago and with Steffen I have done some packaging with the help of
>> Steffen (denoiser,python-cogent, python-pynast, qiime, mothur), an upload
>> only pending the confirmation of upstream that this is ok to redistribute
>> from the respective Authors but they somehow seem to be all on vacation.
>>
>> I have strong interest to learn more about cloud computing and use it for NG
>> sequencing and the data analysis. Steffen set up a server for this that I am
>> going to share. Whoever on this list feels like discussing along, please drop
>> me a quick  Hello.
>>    
> welcome in Debian Med, and many thanks for your help to increase our support
> for high-throughput sequencing applications. Our packages are listed on our
> ‘web sentinel’ pages, but this does not indicate much how they fit together.
> Do not hesitate to document on the Debian wiki how the packages you added can
> be used as part of the same workflow. Also, we have an area on the main
> website, that may be used as well—perhaps after a drafting phase on the wiki.
> These pages are translated in many languages, so they are more suited for
> non-specialists.
>
>  - The web sentinels: http://debian-med.alioth.debian.org/tasks/
>  - The Debian wiki: http://wiki.debian.org/DebianMed
>  - The Debian website: http://www.debian.org/devel/debian-med/
>
> Have a nice day,
>  
When the project(s) are going we should start thinking about some fancy
google-cookies on wiki.debian.org that summarize how to assemble working
environment for various aspects of NG sequencing. Besides an overview
section I am thinking about a smallish howto-like description of
workflows with Debian packages, eventually with a link to
myExperiment.org. Such things only we as a community could possibly come
up with - and I think we should.

Many greetings

Steffen



 


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