[Bioclusters] Re: Bioclusters Digest, Vol 10, Issue 6

Boney De Kumar bony at ccmb.res.in
Thu Aug 11 05:28:45 EDT 2005


hi guys
i am interested to join beta tester group. i am presently graduate student
=2E my work involve large scvale genome comparison and lot of wet lab work
of making trasgenic work.  for genome comarison i keep writing small
scripts.=20
feel free to contact me. thanking you.=20
with  regards


Bony De Kumar
National facility for transgenic and gene knock out mice
Lab#N301
CCMB, Uppal Road
Hyderabad
500 007
Phone91-040-27192899
     91-040-27160222-41(20 lines)

Bony at ccmb.res.in
Inbo at rediffmail.com
=20


On Thu, 11 Aug 2005 bioclusters-request at bioinformatics.org wrote:

> Send Bioclusters mailing list submissions to
> =09bioclusters at bioinformatics.org
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> =09https://bioinformatics.org/mailman/listinfo/bioclusters
> or, via email, send a message with subject or body 'help' to
> =09bioclusters-request at bioinformatics.org
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioclusters digest..."
>=20
>=20
> Today's Topics:
>=20
>    1. re: software skills course (Brian Cole)
>    2. re: software skills course (Tim Booth)
>    3. Re: re: software skills course (Vsevolod (Simon) Ilyushchenko)
>    4. RE: re: software skills course (Brodie, Kent)
>    5. Re: re: software skills course (Bob Gimlich)
>    6. Xserve Cluster setup (Nnabugwu, Ike (NIH/NIAMS))
>    7. Re: Xserve Cluster setup (Chris Dagdigian)
>    8. Re: re: software skills course (Richard Wonka)
>=20
>=20
> ----------------------------------------------------------------------
>=20
> Message: 1
> Date: Wed, 10 Aug 2005 12:37:21 -0400
> From: "Brian Cole" <COLEB2 at wyeth.com>
> Subject: [Bioclusters] re: software skills course
> To: <bioclusters at bioinformatics.org>
> Message-ID: <s2f9f53d.012 at ra01m42.gv.us.pri.wyeth.com>
> Content-Type: text/plain; charset=3DUS-ASCII
>=20
> I'm a contractor in pharmaceutical research for computational chemists. M=
uch of my job involves improving code written by scientists. As a result I =
also end up teaching them a lot along the way. I use mostly python to do my=
 work and others in the group have expressed interest in becoming more prof=
icient at python. I would be greatly interesting in reviewing anything you =
develop, please keep me informed.=20
>=20
> Thanks,
> Brian
>=20
> >>> gvwilson at cs.utoronto.ca 8/10/2005 7:58:27 AM >>>
> Hi,
>=20
> I'm working with support from the Python Software Foundation to develop
> an open source course on basic software development skills for people
> with backgrounds in science and engineering.  I have a beta version of
> the course notes ready for review, and would like to pull in people
> in sci&eng to look it over and give me feedback.  If you know anyone
> who fits this bill (particularly people who might be interested in
> following along with a trial run of the course this fall), I'd be
> grateful for pointers.
>=20
> Thanks,
> Greg Wilson
>=20
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org=20
> https://bioinformatics.org/mailman/listinfo/bioclusters
>=20
>=20
>=20
> ------------------------------
>=20
> Message: 2
> Date: Wed, 10 Aug 2005 17:41:17 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> Subject: [Bioclusters] re: software skills course
> To: bioclusters at bioinformatics.org
> Cc: gvwilson at cs.utoronto.ca, Bela Tiwari <btiwari at ceh.ac.uk>,=09Joe Wood
> =09<anjw at ceh.ac.uk>
> Message-ID: <1123692077.24081.25.camel at ivpcp044.nox.ac.uk>
> Content-Type: text/plain
>=20
> Hi Greg + list people,
>=20
> As part of a bioinformatics group in Oxford, UK, I was involved in
> putting on a similar (2 day) course in Perl.  The notes and exercises
> are on the web:
>=20
> http://envgen.nox.ac.uk/envgen/training/archives/000445.html
>=20
> The audience ranged from complete programming novices to some with
> moderate coding experience, so we got some good feedback on how the
> scientists approached the programming concepts, though we didn't cover
> anything particularly advanced or get into software design,
> re-usability, testing regimes etc.
>=20
> Also, though I have been programming for years I have never got around
> to learning Python so this looks like a great time to learn the basics
> while reviewing your notes.  I don't think I'll be able to make it over
> for the trial run of the course :-( but I'd really like to see the
> materials, and will send feedback.  I may even be able to find a real
> scientist to try them out on!
>=20
> Cheers,
>=20
> TIM
>=20
> > Message: 1
> > Date: Wed, 10 Aug 2005 07:58:27 -0400
> > From: Greg Wilson <gvwilson at cs.utoronto.ca>
> > Subject: [Bioclusters] re: software skills course
> > To: bioclusters at bioinformatics.org
> > Message-ID: <ddcpug$a08$6 at sea.gmane.org>
> > Content-Type: text/plain; charset=3DISO-8859-1; format=3Dflowed
> >=20
> > Hi,
> >=20
> > I'm working with support from the Python Software Foundation to develop
> > an open source course on basic software development skills for people
> > with backgrounds in science and engineering.  I have a beta version of
> > the course notes ready for review, and would like to pull in people
> > in sci&eng to look it over and give me feedback.  If you know anyone
> > who fits this bill (particularly people who might be interested in
> > following along with a trial run of the course this fall), I'd be
> > grateful for pointers.
> >=20
> > Thanks,
> > Greg Wilson
> >=20
>=20
>=20
>=20
>=20
> ------------------------------
>=20
> Message: 3
> Date: Wed, 10 Aug 2005 13:45:34 -0400
> From: "Vsevolod (Simon) Ilyushchenko" <simonf at cshl.edu>
> Subject: Re: [Bioclusters] re: software skills course
> To: "Clustering,=09compute farming & distributed computing in life
> =09science informatics"=09<bioclusters at bioinformatics.org>
> Message-ID: <42FA3D3E.2090901 at cshl.edu>
> Content-Type: text/plain; charset=3Dus-ascii; format=3Dflowed
>=20
> Greg,
>=20
> I can help review the materials - I work in IT in a biological lab, I'm=
=20
> involved in Perl development myself and help a number of scientists with=
=20
> their projects.
>=20
> Simon
>=20
> Greg Wilson wrote on 08/10/2005 07:58 AM:
> > Hi,
> >=20
> > I'm working with support from the Python Software Foundation to develop
> > an open source course on basic software development skills for people
> > with backgrounds in science and engineering.  I have a beta version of
> > the course notes ready for review, and would like to pull in people
> > in sci&eng to look it over and give me feedback.  If you know anyone
> > who fits this bill (particularly people who might be interested in
> > following along with a trial run of the course this fall), I'd be
> > grateful for pointers.
> >=20
> > Thanks,
> > Greg Wilson
> >=20
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> >=20
>=20
> --=20
>=20
> Simon (Vsevolod ILyushchenko)   simonf at cshl.edu
> =09=09=09=09http://www.simonf.com
>=20
> Terrorism is a tactic and so to declare war on terrorism
> is equivalent to Roosevelt's declaring war on blitzkrieg.
>=20
> Zbigniew Brzezinski, U.S. national security advisor, 1977-81
>=20
>=20
> ------------------------------
>=20
> Message: 4
> Date: Wed, 10 Aug 2005 12:56:48 -0500
> From: "Brodie, Kent" <brodie at mcw.edu>
> Subject: RE: [Bioclusters] re: software skills course
> To: "Clustering,=09compute farming & distributed computing in life
> =09science informatics"=09<bioclusters at bioinformatics.org>
> Message-ID: <8F78639AC56F4143B267FE5F5A1B92C8C59B at guyton.phys.mcw.edu>
> Content-Type: text/plain;=09charset=3D"us-ascii"
>=20
> Hey!  Very cool for us perl-newbies.  :-)   Much appreciated. =20
>=20
> > -----Original Message-----
> > From: bioclusters-bounces+brodie=3Dmcw.edu at bioinformatics.org
> > [mailto:bioclusters-bounces+brodie=3Dmcw.edu at bioinformatics.org] On
> Behalf
> > Of Tim Booth
> > Sent: Wednesday, August 10, 2005 11:41 AM
> > To: bioclusters at bioinformatics.org
> > Cc: gvwilson at cs.utoronto.ca; Bela Tiwari; Joe Wood
> > Subject: [Bioclusters] re: software skills course
> >=20
> > Hi Greg + list people,
> >=20
> > As part of a bioinformatics group in Oxford, UK, I was involved in
> > putting on a similar (2 day) course in Perl.  The notes and exercises
> > are on the web:
> >=20
> > http://envgen.nox.ac.uk/envgen/training/archives/000445.html
> >=20
> > The audience ranged from complete programming novices to some with
> > moderate coding experience, so we got some good feedback on how the
> > scientists approached the programming concepts, though we didn't cover
> > anything particularly advanced or get into software design,
> > re-usability, testing regimes etc.
> >=20
> > Also, though I have been programming for years I have never got around
> > to learning Python so this looks like a great time to learn the basics
> > while reviewing your notes.  I don't think I'll be able to make it
> over
> > for the trial run of the course :-( but I'd really like to see the
> > materials, and will send feedback.  I may even be able to find a real
> > scientist to try them out on!
> >=20
> > Cheers,
> >=20
> > TIM
> >=20
> > > Message: 1
> > > Date: Wed, 10 Aug 2005 07:58:27 -0400
> > > From: Greg Wilson <gvwilson at cs.utoronto.ca>
> > > Subject: [Bioclusters] re: software skills course
> > > To: bioclusters at bioinformatics.org
> > > Message-ID: <ddcpug$a08$6 at sea.gmane.org>
> > > Content-Type: text/plain; charset=3DISO-8859-1; format=3Dflowed
> > >
> > > Hi,
> > >
> > > I'm working with support from the Python Software Foundation to
> develop
> > > an open source course on basic software development skills for
> people
> > > with backgrounds in science and engineering.  I have a beta version
> of
> > > the course notes ready for review, and would like to pull in people
> > > in sci&eng to look it over and give me feedback.  If you know anyone
> > > who fits this bill (particularly people who might be interested in
> > > following along with a trial run of the course this fall), I'd be
> > > grateful for pointers.
> > >
> > > Thanks,
> > > Greg Wilson
> > >
> >=20
> >=20
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
>=20
>=20
> ------------------------------
>=20
> Message: 5
> Date: Wed, 10 Aug 2005 14:48:13 -0400
> From: Bob Gimlich <gimlich at gmail.com>
> Subject: Re: [Bioclusters] re: software skills course
> To: "Clustering,=09compute farming & distributed computing in life
> =09science informatics"=09<bioclusters at bioinformatics.org>
> Message-ID: <88b98a9e05081011485227ce0e at mail.gmail.com>
> Content-Type: text/plain; charset=3DISO-8859-1
>=20
> Greg,
>=20
> I'd be interested in reviewing.  What do you mean by 'following along
> with a trial run of the course'?  An online trial run?
>=20
> Bob Gimlich (http://gimlich.com)
>=20
> On 8/10/05, Greg Wilson <gvwilson at cs.utoronto.ca> wrote:
> > Hi,
> >=20
> > I'm working with support from the Python Software Foundation to develop
> > an open source course on basic software development skills for people
> > with backgrounds in science and engineering.  I have a beta version of
> > the course notes ready for review, and would like to pull in people
> > in sci&eng to look it over and give me feedback.  If you know anyone
> > who fits this bill (particularly people who might be interested in
> > following along with a trial run of the course this fall), I'd be
> > grateful for pointers.
> >=20
> > Thanks,
> > Greg Wilson
> >=20
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> >
>=20
>=20
> ------------------------------
>=20
> Message: 6
> Date: Wed, 10 Aug 2005 14:57:25 -0400
> From: "Nnabugwu, Ike (NIH/NIAMS)" <nnabugwi at mail.nih.gov>
> Subject: [Bioclusters] Xserve Cluster setup
> To: bioclusters at bioinformatics.org
> Message-ID:
> =09<4B9024D294BBEF45A18A1A360E22B24202877AC8 at NIHCESMLBX.nih.gov>
> Content-Type: text/plain; charset=3D"us-ascii"
>=20
> I have a head node running 10.3.9 and six cluster nodes that I am working=
 on
> setting up. To have the head node and cluster communicate in the private
> network, I have created /etc/hosts with entries i.e. 10.0.0.1 node01 etc,
> and have enabled dhcp. But I do not know how to setup dns to use external
> dns.Any pointer is appreciated.
>=20
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://bioinformatics.org/pipermail/bioclusters/attachments/20050810=
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> ------------------------------
>=20
> Message: 7
> Date: Wed, 10 Aug 2005 15:00:48 -0400
> From: Chris Dagdigian <dag at sonsorol.org>
> Subject: Re: [Bioclusters] Xserve Cluster setup
> To: "Clustering,=09compute farming & distributed computing in life
> =09science informatics"=09<bioclusters at bioinformatics.org>
> Message-ID: <42FA4EE0.2090109 at sonsorol.org>
> Content-Type: text/plain; charset=3Dus-ascii; format=3Dflowed
>=20
>=20
> Many of the Apple programs and services will honor NetInfo over=20
> /etc/services. The same thing goes for DNS stuff like /etc/resolv.conf=20
> so you really need to read up on how OS X handles network services,=20
> otherwise you'll end up in a odd greyzone where you are letting NetInfo=
=20
> handle some things and the standard unix-ish /etc/ files handle other=20
> things. Not good...
>=20
> My best advice is this, go to this URL:
> http://www.apple.com/server/documentation/
>=20
> ... the docs there will be helpful but the best one is the one on "OS X=
=20
> Command Line Administration". That PDF will explicitly cover DNS=20
> start/stop but you may need one of the other guides to explain how to=20
> configure DNS in the first place.
>=20
> Much depends on if you are doing this via the GUI or the command-line.=20
> There are nice GUI tools for adding external DNS servers to your=20
> configuraiton. The command line methods exist but are a bit more cryptic.
>=20
> Regards,
> Chris
>=20
>=20
>=20
>=20
>=20
> Nnabugwu, Ike (NIH/NIAMS) wrote:
> > I have a head node running 10.3.9 and six cluster nodes that I am worki=
ng on
> > setting up. To have the head node and cluster communicate in the privat=
e
> > network, I have created /etc/hosts with entries i.e. 10.0.0.1 node01 et=
c,
> > and have enabled dhcp. But I do not know how to setup dns to use extern=
al
> > dns.Any pointer is appreciated.
> >=20
>=20
>=20
> --=20
> Chris Dagdigian, <dag at sonsorol.org>
> Independent life science IT & informatics consulting
> Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
> PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net
>=20
>=20
> ------------------------------
>=20
> Message: 8
> Date: Thu, 11 Aug 2005 09:51:37 +0200
> From: Richard Wonka <richard.wonka at web.de>
> Subject: Re: [Bioclusters] re: software skills course
> To: bioclusters at bioinformatics.org
> Message-ID: <888655856 at web.de>
> Content-Type: text/plain; charset=3Diso-8859-1
>=20
>=20
> Hey List :-)
>=20
> AOL!
> I'm administrator with a light biological background and have got my prim=
er in python.
> Me and my colleagues (some of them bioscientists) would like see what thi=
s is like.
>=20
> Great!
>=20
> Richard
>=20
> > [...]
> > I'm working with support from the Python Software Foundation to develop
> > an open source course on basic software development skills for people
> > with backgrounds in science and engineering.  I have a beta version of
> > the course notes ready for review, and would like to pull in people
> > in sci&eng to look it over and give me feedback.  If you know anyone
> > who fits this bill (particularly people who might be interested in
> > following along with a trial run of the course this fall), I'd be
> > grateful for pointers.
> > [...]
> _________________________________________________________________________
> Mit der Gruppen-SMS von WEB.DE FreeMail k=F6nnen Sie eine SMS an alle=20
> Freunde gleichzeitig schicken: http://freemail.web.de/features/?mc=3D0211=
79
>=20
>=20
>=20
>=20
>=20
> ------------------------------
>=20
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>=20
>=20
> End of Bioclusters Digest, Vol 10, Issue 6
> ******************************************
>=20



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