[3dem] 3dem Digest, Vol 77, Issue 19
ndoriah@yahoo.co.uk
ndoriah at yahoo.co.uk
Thu Jan 30 23:18:38 PST 2014
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Subject: 3dem Digest, Vol 77, Issue 19
Date: Fri, Jan 31, 2014 03:01
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Today's Topics:
1. Workstation (rkhayat at ccny.cuny.edu)
2. Re: Workstation (Gabor Herman)
3. Tomography Congress (Jensen, Grant J.)
4. Re: Workstation (Lu Gan)
5. Re: Workstation (Steven Ludtke)
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Message: 1
Date: Thu, 30 Jan 2014 17:00:14 -0500 (EST)
From: <rkhayat at ccny.cuny.edu>
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Workstation
Message-ID: <201401302200.020010 at pelican.admin.ccny.cuny.edu>
Content-Type: text/plain; charset=us-ascii
Hi,
This may be a bit off topic. I need to purchase a workstation for single particle analysis and tomography. Can anyone suggest a vendor and a Linux flavor that would simplify the entire process? I'm also willing and able to assemble a system from components. I'm more concerned with the Linux flavor since there are so many compatibility issues involved.
Best wishes,
Reza
------------------------------
Message: 2
Date: Thu, 30 Jan 2014 14:14:30 -0800 (PST)
From: Gabor Herman <gabortherman at yahoo.com>
To: "rkhayat at ccny.cuny.edu" <rkhayat at ccny.cuny.edu>,
"3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Workstation
Message-ID:
<1391120070.73908.YahooMailNeo at web121503.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
I and one of my coworkers both purchased Linux systems from
ZaReaslon. We are both very happy with our purchases.
?
Gabor T. Herman, Ph.D.
Distinguished Professor of Computer Science
The Graduate Center of the City University of New York
http://www.dig.cs.gc.cuny.edu/~gabor/index.html
==============================================?
..
ANNOUNCEMENTS?
..
Gabor T. Herman: Fundamentals of Computerized Tomography:?
Image Reconstruction from Projections, 2nd ed.,?
Springer, 2009.
www.springer.com/978-1-85233-617-2?
..
SNARK09 (a programming system for the reconstruction
of 2D images from 1D projections, a much?
revised and updated version of SNARK05)
is now available at no charge.
http://www.dig.cs.gc.cuny.edu/software/snark09/?
..
Marilyn Kirsch: Selected Paintings 2000-2009,
Alchemilla Books, 2009.
www.alchemillabooks.com?
On Thursday, January 30, 2014 5:09 PM, "rkhayat at ccny.cuny.edu" <rkhayat at ccny.cuny.edu> wrote:
Hi,
>
>This may be a bit off topic. I need to purchase a workstation for single particle analysis and tomography. Can anyone suggest a vendor and a Linux flavor that would simplify the entire process? I'm also willing and able to assemble a system from components. I'm more concerned with the Linux flavor since there are so many compatibility issues involved.
>
>Best wishes,
>Reza
>_______________________________________________
>3dem mailing list
>3dem at ncmir.ucsd.edu
>https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
>
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Message: 3
Date: Fri, 31 Jan 2014 00:05:51 +0000
From: "Jensen, Grant J." <jensen at caltech.edu>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: [3dem] Tomography Congress
Message-ID: <CF1028DF.1815E%jensen at caltech.edu>
Content-Type: text/plain; charset="windows-1252"
Please mark your calendars that the 7th International Congress on Electron Tomography will be held Nov. 17-20 at the beautiful Occidental Grand Xcaret resort hotel near Cancun, Mexico. Following the tradition set by the highly successful previous meetings in Germany (1999), Amsterdam (2001), New York (2002), San Diego (2005), Brisbane (2008), and Heidelberg (2011), the conference will bring together researchers working on hardware development, software development, and applications of electron tomography, particularly in biology. It will showcase breakthroughs in both electron tomography technology and cell biology applications.
Topics covered will include:
? Recent developments in cryosectioning and FIB-milling
? Correlative light and electron microscopy
? Automatic tilt-series acquisition and reconstruction software
? Direct detectors
? High-throughput, large-scale reconstructions of plastic embedded samples
? Latest developments in sub-tomogram classification and averaging
? Map interpretation, model fitting
? Example recent high impact biological results
The hotel and surrounding area is truly gorgeous, so I hope everyone will enjoy taking a short break from winter with us in Cancun.
For registration, site information, and abstract submission, please see the conference web page at
http://www.zingconferences.com/conferences/electrontomography/
Register by Sept 30 or by May 25 for an "early bird" discounted rate. In an effort to spotlight all the most exciting projects, in addition to the invited speakers there will be many talks chosen from the submitted abstracts (due Sept. 1).
Hope to see you there!
Grant
--------------------------------------------------------------------------
Grant Jensen
Professor of Biology and Investigator, HHMI
California Institute of Technology, Mail code 114-96
1200 E. California Blvd.
Pasadena, CA 91125
626-395-8827 (phone)
626-395-5730 (fax)
JensenATcaltech.edu
http://www.jensenlab.caltech.edu
office location: 359 Broad (northwest corner of campus)
Administrative Assistant Karin Mallard
626-395-8893 (phone)
kmallardATcaltech.edu
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Message: 4
Date: Fri, 31 Jan 2014 08:40:14 +0800
From: Lu Gan <lu at anaphase.org>
To: Reza Khayat <rkhayat at ccny.cuny.edu>
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Workstation
Message-ID:
<CAPbw-UmX4cn3_+DHDa1887hNPrqUfjE=U3WSC1O3PJr=sB0dWw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Reza,
This question was recently addressed on the IMOD mailing list, so I'll
summarize what I think is a representative answer.
Linux: Ubuntu, Mint, CentOS
Hardware: Dell (can be expensive), local builders (like ZaReaslon? with
better customization)
If you're going to use IMOD and want to take advantage of GPU acceleration,
then you'll need an NVIDIA card (David Mastronarde recommended 700 series;
skip the 600s) and CUDA drivers.
-Lu
On Fri, Jan 31, 2014 at 6:14 AM, Gabor Herman <gabortherman at yahoo.com>wrote:
> I and one of my coworkers both purchased Linux systems from
> ZaReaslon. We are both very happy with our purchases.
>
> Gabor T. Herman, Ph.D.
> Distinguished Professor of Computer Science
> The Graduate Center of the City University of New York
> http://www.dig.cs.gc.cuny.edu/~gabor/index.html
> ==============================================
> .
> ANNOUNCEMENTS
> .
>
> Gabor T. Herman: Fundamentals of Computerized Tomography:
> Image Reconstruction from Projections, 2nd ed.,
> Springer, 2009.
> www.springer.com/978-1-85233-617-2
> .
>
> SNARK09 (a programming system for the reconstruction
> of 2D images from 1D projections, a much
> revised and updated version of SNARK05)
> is now available at no charge.
> http://www.dig.cs.gc.cuny.edu/software/snark09/
> .
>
> Marilyn Kirsch: Selected Paintings 2000-2009,
> Alchemilla Books, 2009.
> www.alchemillabooks.com
>
>
> On Thursday, January 30, 2014 5:09 PM, "rkhayat at ccny.cuny.edu" <
> rkhayat at ccny.cuny.edu> wrote:
>
> Hi,
>
> This may be a bit off topic. I need to purchase a workstation for single
> particle analysis and tomography. Can anyone suggest a vendor and a Linux
> flavor that would simplify the entire process? I'm also willing and able to
> assemble a system from components. I'm more concerned with the Linux flavor
> since there are so many compatibility issues involved.
>
> Best wishes,
> Reza
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
--
Lu Gan
Assistant Professor
Department of Biological Sciences
National University of Singapore
14 Science Drive 4
S1A, Lvl 2
Singapore 117543
www.anaphase.org
Tel: (65) 6516 8868
Fax: (65) 6776 7882
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Message: 5
Date: Thu, 30 Jan 2014 19:01:28 -0600
From: Steven Ludtke <sludtke at bcm.edu>
To: "rkhayat at ccny.cuny.edu" <rkhayat at ccny.cuny.edu>
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Workstation
Message-ID: <8971ECAA-EA06-4B78-8A0E-8ECC7922F2EF at bcm.edu>
Content-Type: text/plain; charset=us-ascii
I keep a FAQ page pretty up to date for this question, which has some additional refinements on the advice you've already heard. My one disagreement would be on DELL, who has poor hardware design (difficult to modify and repair) and extremely poor customer support when something breaks.
http://blake.bcm.edu/emanwiki/EMAN2/FAQ/Computer
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem)
Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu)
Co-Director CIBR Center (www.bcm.edu/research/cibr)
Baylor College of Medicine
sludtke at bcm.edu
On Jan 30, 2014, at 4:00 PM, rkhayat at ccny.cuny.edu wrote:
> Hi,
>
> This may be a bit off topic. I need to purchase a workstation for single particle analysis and tomography. Can anyone suggest a vendor and a Linux flavor that would simplify the entire process? I'm also willing and able to assemble a system from components. I'm more concerned with the Linux flavor since there are so many compatibility issues involved.
>
> Best wishes,
> Reza
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
------------------------------
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