From jdj at 3dbiochem.com  Mon Aug  1 20:07:27 2011
From: jdj at 3dbiochem.com (Jim Johnson)
Date: Tue, 02 Aug 2011 00:07:27 +0000
Subject: [Bio-Linux] Providing python.h header files while installing
 ngs_backbone within Bio-Linux
Message-ID: <W4313912543109491312243647@webmail21>

Err: Python.h header files missing; install python-dev package.


Loading the development package for python (required by ngs_backbone, HTSeq, e.g.). Bio-Linux v. 6 missing python.h header files. The following installation command appears to fix this problem, q.v.:


sudo apt-get install python-dev


The installation was successful and ngs_backbone proceeded to behave (at least at the fastq clean-up stage). Tim Booth over at Bio-Linux provided this simple solution.


Just in case anyone runs into this problem (error will read '..cannot find python.h header files.')


Best of luck~

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From tbooth at ceh.ac.uk  Wed Aug  3 07:37:59 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 03 Aug 2011 12:37:59 +0100
Subject: [Bio-Linux] Python training - looking for suggestions
Message-ID: <1312371479.31691.114.camel@barsukas>

Hello Bio-Linux users,

In a chat this morning with our local training co-ordinator at CEH, she
mentioned how hard she was finding it to arrange a Python course for
people in the organisation, despite having a high level of demand and
the budget available to pay for commercial courses.

Therefore I wondered if anyone on this list could offer any suggestions.
I know there is any amount of self study material out there (I have
three books within reach right here!) but for programming novices they
really want a taught course (2 or 3 days).  Has anyone been on or heard
of such a course recently, or maybe even taught Python themselves?  CEH
are open to suggestions on this so if you have any thoughts please do
let me know.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From farhat.habib at gmail.com  Wed Aug  3 08:00:07 2011
From: farhat.habib at gmail.com (Farhat Habib)
Date: Wed, 3 Aug 2011 17:30:07 +0530
Subject: [Bio-Linux] Python training - looking for suggestions
In-Reply-To: <1312371479.31691.114.camel@barsukas>
References: <1312371479.31691.114.camel@barsukas>
Message-ID: <CABRTWHZKqHryAUXL+D4rjbHn8zAU7PeA1HfCt1q17yY2R-7K4Q@mail.gmail.com>

The MIT Introduction to Computer Science and Programming
http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00-introduction-to-computer-science-and-programming-fall-2008/
course is excellent for Python though it is not short. If you only
want programming and not so much computing side of it then you can
skip lectures related to complexity and algorithms.

-Farhat

--
Farhat Habib, PhD
Scientist-C, Center of Excellence in Epigenetics
Indian Institute of Science Education & Research, Pune
http://www.iiserpune.ac.in/~farhat
Twitter: @far_hat
Office: +91 20 2590 8080



On Wed, Aug 3, 2011 at 5:07 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> Hello Bio-Linux users,
>
> In a chat this morning with our local training co-ordinator at CEH, she
> mentioned how hard she was finding it to arrange a Python course for
> people in the organisation, despite having a high level of demand and
> the budget available to pay for commercial courses.
>
> Therefore I wondered if anyone on this list could offer any suggestions.
> I know there is any amount of self study material out there (I have
> three books within reach right here!) but for programming novices they
> really want a taught course (2 or 3 days). ?Has anyone been on or heard
> of such a course recently, or maybe even taught Python themselves? ?CEH
> are open to suggestions on this so if you have any thoughts please do
> let me know.
>
> Cheers,
>
> TIM
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
> --
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>


From raonyguimaraes at gmail.com  Mon Aug  8 15:46:40 2011
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Mon, 8 Aug 2011 16:46:40 -0300
Subject: [Bio-Linux] Fresh Install - Questions
Message-ID: <CALenah=q67tGOXbDXxjNr8UuTXr0Uv9-_etKH8JMa8-iZrQQLw@mail.gmail.com>

Hello All,

My name is Raony Guimar?es, I'm graduated in Biomedical Informatics and
starting a new PhD in Bioinformatics. I have a long time experience with
linux and decided to give a try on Biolinux 6.0.

My first question would be: Should upgrade or update the system after a
fresh install ?
Second question: Will I loose the packages for bioinformatics If I upgrade
the system?
Third Question: Is there a forum outside where I can ask all my questions or
only this mail-list ?

Thank You!


Atenciosamente,

  C------0      Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
G--------1
T--------1      msn/gtalk: raonyguimaraes at gmail.com
A-------0       skype: raonyguimaraes
C----0
   1              Member  @ LGMB - Molecular Genetics and Bioinformatics
Laboratory
 0--G
1-----T         Bachelor in Biomedical Informatics - USP Ribeir?o Preto
1--------A
0---------C     Creator of the Brazilian Portal of Biomedical Informatics
and Medicina do Futuro
1--------G      www.informaticabiomedica.org / www.medicinadofuturo.com.br
  1-----G
      T          Research Interests: Personalized Medicine and
Pharmacogenomics
    G--0        http://lattes.cnpq.br/0263349039132540
  A------0
T--------1
C--------0     "Biomedical Informatics: We Can Change The World..."
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From a.travis at abdn.ac.uk  Tue Aug  9 04:55:03 2011
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 09 Aug 2011 09:55:03 +0100
Subject: [Bio-Linux] Fresh Install - Questions
In-Reply-To: <CALenah=q67tGOXbDXxjNr8UuTXr0Uv9-_etKH8JMa8-iZrQQLw@mail.gmail.com>
References: <CALenah=q67tGOXbDXxjNr8UuTXr0Uv9-_etKH8JMa8-iZrQQLw@mail.gmail.com>
Message-ID: <4E40F5E7.20104@abdn.ac.uk>

On 08/08/11 20:46, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
> Hello All,
>
> My name is Raony Guimar?es, I'm graduated in Biomedical Informatics and
> starting a new PhD in Bioinformatics. I have a long time experience with
> linux and decided to give a try on Biolinux 6.0.

Hi, Raony.

Welcome to the wonderful world of Bio-Linux :-)

> My first question would be: Should upgrade or update the system after a
> fresh install ?

You should update

> Second question: Will I loose the packages for bioinformatics If I
> upgrade the system?

Bio-Linux is based on Ubuntu 10.04 LTS and if you upgrade you might 
encounter problems installing packages developed for ubuntu 10.04 LTS 
not installing in later versions because of incompatibilities. However, 
CBL (Cloud Bio-Linux) builds are available current versions of Ubuntu.

> Third Question: Is there a forum outside where I can ask all my
> questions or only this mail-list ?

Yes, there is the Debian Med forum, because Bio-Linux is becoming 
increasingly involved in using their packages.

HTH,

   Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk


From tbooth at ceh.ac.uk  Tue Aug  9 05:06:41 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 09 Aug 2011 10:06:41 +0100
Subject: [Bio-Linux] Fresh Install - Questions
In-Reply-To: <CALenah=q67tGOXbDXxjNr8UuTXr0Uv9-_etKH8JMa8-iZrQQLw@mail.gmail.com>
References: <CALenah=q67tGOXbDXxjNr8UuTXr0Uv9-_etKH8JMa8-iZrQQLw@mail.gmail.com>
Message-ID: <1312880801.3359.653.camel@barsukas>

Hi Raony Guimar?es,

Thanks for trying Bio-Linux. In answer to your questions:

1+2) You should install the regular package updates that become
available via the update manager, but if you upgrade the Ubuntu system
to the 11.04 release then a few of the bioinformatics packages will be
removed due to conflicts.  Most will be OK, but some will still be
installed but stop working.  Unfortunately I don't have a comprehensive
list of these just now.

3) Right now we have no forum dedicated to Bio-Linux, just this mailing
list.  We are planning to add new community areas to the website as part
of the next Bio-Linux development push so feedback like this is much
appreciated.

Cheers,

TIM

On Mon, 2011-08-08 at 20:46 +0100, Raony Guimaraes Corr?a Do Carmo
Lisboa Cardenas wrote:
> Hello All, 
> 
> My name is Raony Guimar?es, I'm graduated in Biomedical Informatics
> and starting a new PhD in Bioinformatics. I have a long time
> experience with linux and decided to give a try on Biolinux 6.0.
> 
> My first question would be: Should upgrade or update the system after
> a fresh install ?
> Second question: Will I loose the packages for bioinformatics If I
> upgrade the system?
> Third Question: Is there a forum outside where I can ask all my
> questions or only this mail-list ?
> 
> Thank You!
> 
> 
> Atenciosamente,
> 
> 
>   C------0      Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
> G--------1      
> T--------1      msn/gtalk: raonyguimaraes at gmail.com
> A-------0       skype: raonyguimaraes
> C----0           
>    1              Member  @ LGMB - Molecular Genetics and
> Bioinformatics Laboratory 
>  0--G          
> 1-----T         Bachelor in Biomedical Informatics - USP Ribeir?o
> Preto
> 1--------A      
> 0---------C     Creator of the Brazilian Portal of Biomedical
> Informatics and Medicina do Futuro
> 1--------G      www.informaticabiomedica.org /
> www.medicinadofuturo.com.br
>   1-----G       
>       T          Research Interests: Personalized Medicine and
> Pharmacogenomics
>     G--0        http://lattes.cnpq.br/0263349039132540
>   A------0     
> T--------1     
> C--------0     "Biomedical Informatics: We Can Change The World..."

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.