[3dem] 3dem Digest, Vol 107, Issue 2

Lu Gan lu at anaphase.org
Tue Jul 5 07:37:50 PDT 2016


Dear Ben,

Thank you for the advice. I've tried Aspera, the beta Aspera server, and
Globus. Transfers topped out at 400 KB/sec in all cases and were frequently
disconnected. Despite the kind efforts of the EMPIAR team to help me
troubleshoot, the 100+GB upload took some 2 months (partly because I spent
time overseas during a disconnect).

An additional, albeit incomplete piece of evidence that my University was
doing the throttling: Aspera downloads (not uploads) from home nearly maxed
out my GigE fiber link. The same downloads at the office maxed out at ~ 200
KB/sec. I did not experiment with uploads from home for fear of getting
banned/flagged by my ISP.

For those who are considering uploading, but don't want to spend the time
to figure out your University's network policies: you're probably better
off mailing a hard drive to EMPIAR.


Cheers.
Lu

--
Lu Gan
Assistant Professor
Department of Biological Sciences
Centre for BioImaging 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

On Tue, Jul 5, 2016 at 10:26 PM, Benjamin Himes <himes.benjamin at gmail.com>
wrote:

> Dear Lu,
>
> If you observe better upload via drive/dropbox, maybe the following would
> be relevant?
>
> "Aspera makes use of UDP transfer technology. Some institutes block the
>> UDP port (port 33001) by default and it is not possible to get them
>> enabled. If this is the case for you then we recommend that you use Globus
>> which relies on GridFTP."
>>
>
> Have you given the alternative to Aspera a shot?
>
> Is this apparent "throttling" of uploads specific to EMPIAR a common
> experience with other list users? (please chime in!)
>
> -Ben H.
>
> *************************************
> Benjamin Himes
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> 2050 Biomedical Science Tower 3 (BST3).
> 3501 5th Ave, Pittsburgh, PA 15260
>
> *(412) 648-7262 <%28412%29%20648-7262> *(Office)
> *(412)648-8998 <%28412%29648-8998>* (Lab fax)
> *************************************
>
> No trees were killed to send this message, but
> a large number of electrons were terribly inconvenienced.
>
> It is an abiding passion of human beings to attempt to read and re-view
> history as an orderly progression of events running according to a
> well-coordinated and rational script. Don't be fooled.
>
>
> On Tue, Jul 5, 2016 at 10:15 AM, Lu Gan <lu at anaphase.org> wrote:
>
>> Dear Ben,
>>
>> I can't speak for Rado, but I suspect many academics will have a similar
>> problem: Universities may severely throttle your upload bandwidth. In our
>> recent EMPIAR upload experience, we got 400 KB/sec max, independent of the
>> upload client. This limitation was not due to our geographical location
>> because I can get several MB/sec when using Google drive and sometimes
>> Dropbox (when the latter is not being throttled).
>>
>>
>> Cheers.
>> Lu
>>
>> --
>> Lu Gan
>> Assistant Professor
>> Department of Biological Sciences
>> Centre for BioImaging 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
>>
>> On Tue, Jul 5, 2016 at 8:48 PM, Benjamin Himes <himes.benjamin at gmail.com>
>> wrote:
>>
>>> Dear Rado,
>>>
>>> Is there any reason in particular you elected to not share your data
>>> through the EMPIAR <https://www.ebi.ac.uk/pdbe/emdb/empiar/>?
>>>
>>> "EMPIAR, the Electron Microscopy Pilot Image Archive, is a public
>>> resource for raw, 2D electron microscopy images. Here, you can browse,
>>> upload, and download and reprocess the thousands of raw, 2D images used to
>>> build a 3D structure."
>>>
>>> -Ben H.
>>>
>>> *************************************
>>> Benjamin Himes
>>> Department of Structural Biology
>>> University of Pittsburgh School of Medicine
>>> 2050 Biomedical Science Tower 3 (BST3).
>>> 3501 5th Ave, Pittsburgh, PA 15260
>>>
>>> *(412) 648-7262 <%28412%29%20648-7262> *(Office)
>>> *(412)648-8998 <%28412%29648-8998>* (Lab fax)
>>> *************************************
>>>
>>> No trees were killed to send this message, but
>>> a large number of electrons were terribly inconvenienced.
>>>
>>> It is an abiding passion of human beings to attempt to read and re-view
>>> history as an orderly progression of events running according to a
>>> well-coordinated and rational script. Don't be fooled.
>>>
>>>
>>> On Tue, Jul 5, 2016 at 8:32 AM, <3dem-request at ncmir.ucsd.edu> wrote:
>>>
>>>> Send 3dem mailing list submissions to
>>>>         3dem at ncmir.ucsd.edu
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>         https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>> or, via email, send a message with subject or body 'help' to
>>>>         3dem-request at ncmir.ucsd.edu
>>>>
>>>> You can reach the person managing the list at
>>>>         3dem-owner at ncmir.ucsd.edu
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of 3dem digest..."
>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>>    1. Phase plate test dataset (Radostin Danev)
>>>>    2. Postdoctoral position - Advanced Microscopy and Modelling
>>>>       (Eric Gilles Hanssen)
>>>>    3. Re: Phase plate test dataset (Radostin Danev)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Tue, 5 Jul 2016 10:38:33 +0200
>>>> From: Radostin Danev <danev at biochem.mpg.de>
>>>> To: <3dem at ncmir.ucsd.edu>
>>>> Subject: [3dem] Phase plate test dataset
>>>> Message-ID: <08a401d1d698$9d39d0c0$d7ad7240$@biochem.mpg.de>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>>
>>>> Dear Colleagues,
>>>>
>>>>
>>>>
>>>> As I mentioned at the 3DEM GRC I am happy to share a small subset of
>>>> phase
>>>> plate images acquired with defocus.
>>>>
>>>> I put the first 20 images of a 20S proteasome dataset on my Dropbox,
>>>> here:
>>>>
>>>> https://www.dropbox.com/sh/omjjhwhhqsjvsm6/AAAAg32yTzc4_CvrjtdQI_Raa?dl=0
>>>>
>>>> There are also picked particle coordinates in *_automatch.star and CTF
>>>> parameters in *_ctffind3.log files.
>>>>
>>>> Other data:
>>>>
>>>> - accel. voltage 300 kV
>>>>
>>>> - pixel size 1.054 A
>>>>
>>>> - Cs 2.62 mm
>>>>
>>>> - particle diameter 190 A
>>>>
>>>>
>>>>
>>>> With D7 symmetry this subset of ~ 7,300 particles refines to ~ 2.9 A
>>>> resolution.
>>>>
>>>>
>>>>
>>>> All the best,
>>>>
>>>>
>>>>
>>>> Rado
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ===================================
>>>>
>>>> Radostin Danev, Ph.D.
>>>>
>>>> Max Planck Institute of Biochemistry
>>>> Department of Molecular Structural Biology
>>>> Am Klopferspitz 18
>>>> 82152 Martinsried
>>>> Germany
>>>>
>>>> e-mail: danev at biochem.mpg.de
>>>>
>>>> phone: +49 (89) 8578-2651
>>>> fax: +49 (89) 8578-2641
>>>>
>>>> ===================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
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>>>> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160705/26bb81b7/attachment-0001.html
>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Tue, 5 Jul 2016 10:39:48 +0000
>>>> From: Eric Gilles Hanssen <ehanssen at unimelb.edu.au>
>>>> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>>>> Subject: [3dem] Postdoctoral position - Advanced Microscopy and
>>>>         Modelling
>>>> Message-ID: <4E057941-24F1-43B7-B41B-2D14A3263E9A at unimelb.edu.au>
>>>> Content-Type: text/plain; charset="windows-1252"
>>>>
>>>> Dear all,
>>>> The University of Melbourne is advertising in new post doctoral
>>>> position for advanced imaging see below.
>>>> Please contact Prof Leann Tilley for more info ltilley at unimelb.edu.au
>>>> <mailto:ltilley at unimelb.edu.au>
>>>> Regards
>>>> Eric
>>>>
>>>> Postdoctoral Research Fellow ? Advanced Microscopy
>>>> Department of Biochemistry and Molecular Biology, University of
>>>> Melbourne
>>>>
>>>> This position is funded by an Australian Research Council Laureate
>>>> Fellowship Program. The vision of the program is to develop sophisticated
>>>> and integrated bio-metrology (measurement) methods to study a complex
>>>> cellular processes in the malaria parasite. You will work with a team of
>>>> experts to develop and implement novel imaging methods, biophysical
>>>> techniques and computational studies that will enable, for the first time,
>>>> whole organism mapping and modelling of malaria parasites. The Program will
>>>> work as an interdisciplinary collaboration for high-resolution bio-imaging
>>>> and computational modelling. The host laboratory is situated in the Bio21
>>>> Molecular Science and Biotechnology Institute, on the University campus.
>>>> You will work with colleagues from the University?s Departments of
>>>> Biochemistry and Molecular Biology, Maths and Stats and from the School of
>>>> Engineering.
>>>> Salary: $66,809* - $90,657 p.a. (*PhD Entry Level $84,458 p.a.) plus
>>>> 9.5% superannuation
>>>> Job No: 0041023
>>>> For position information and to apply online go to http://about.unimelb
>>>> <http://about.unimelb.edu.au/careers>.edu.au/careers<
>>>> http://about.unimelb.edu.au/careers>, and under the relevant option
>>>> (?Current Staff? or ?Prospective Staff?) search by the job title or number.
>>>>
>>>> http://jobs.unimelb.edu.au/caw/en/job/888403/postdoctoral-research-fellow-advanced-microscopy
>>>>
>>>>
>>>>
>>>> Assoc/Prof Eric Hanssen
>>>>
>>>> Head - Bio21 Advanced Microscopy Facility
>>>> Principle Fellow - Department of Biochemistry and Molecular Biology
>>>>
>>>> The University of Melbourne
>>>> Bio21 Institute - 30 flemington rd - VIC 3010
>>>> +61 3 8344 2449
>>>> www.microscopy.unimelb.edu.au<http://www.microscopy.unimelb.edu.au>
>>>>
>>>>
>>>>
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>> URL: <
>>>> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160705/f331499c/attachment-0001.html
>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Tue, 5 Jul 2016 14:31:35 +0200
>>>> From: Radostin Danev <danev at biochem.mpg.de>
>>>> To: <3dem at ncmir.ucsd.edu>
>>>> Subject: Re: [3dem] Phase plate test dataset
>>>> Message-ID: <092301d1d6b9$2b29ab60$817d0220$@biochem.mpg.de>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>>
>>>> My Dropbox public links were suspended due to "excessive traffic". I
>>>> uploaded the dataset to our FTP server (could be a bit slow):
>>>>
>>>>
>>>>
>>>> bmftp.biochem.mpg.de
>>>>
>>>> user: MPIB
>>>>
>>>> pass: biochemie
>>>>
>>>>
>>>>
>>>> All the best,
>>>>
>>>>
>>>>
>>>> Rado
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Radostin
>>>> Danev
>>>> Sent: 05 July 2016 10:39
>>>> To: 3dem at ncmir.ucsd.edu
>>>> Subject: [3dem] Phase plate test dataset
>>>>
>>>>
>>>>
>>>> Dear Colleagues,
>>>>
>>>>
>>>>
>>>> As I mentioned at the 3DEM GRC I am happy to share a small subset of
>>>> phase
>>>> plate images acquired with defocus.
>>>>
>>>> I put the first 20 images of a 20S proteasome dataset on my Dropbox,
>>>> here:
>>>>
>>>> https://www.dropbox.com/sh/omjjhwhhqsjvsm6/AAAAg32yTzc4_CvrjtdQI_Raa?dl=0
>>>>
>>>> There are also picked particle coordinates in *_automatch.star and CTF
>>>> parameters in *_ctffind3.log files.
>>>>
>>>> Other data:
>>>>
>>>> - accel. voltage 300 kV
>>>>
>>>> - pixel size 1.054 A
>>>>
>>>> - Cs 2.62 mm
>>>>
>>>> - particle diameter 190 A
>>>>
>>>>
>>>>
>>>> With D7 symmetry this subset of ~ 7,300 particles refines to ~ 2.9 A
>>>> resolution.
>>>>
>>>>
>>>>
>>>> All the best,
>>>>
>>>>
>>>>
>>>> Rado
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ===================================
>>>>
>>>> Radostin Danev, Ph.D.
>>>>
>>>> Max Planck Institute of Biochemistry
>>>> Department of Molecular Structural Biology
>>>> Am Klopferspitz 18
>>>> 82152 Martinsried
>>>> Germany
>>>>
>>>> e-mail: danev at biochem.mpg.de
>>>>
>>>> phone: +49 (89) 8578-2651
>>>> fax: +49 (89) 8578-2641
>>>>
>>>> ===================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>> URL: <
>>>> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160705/96ff3bba/attachment.html
>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> Subject: Digest Footer
>>>>
>>>> _______________________________________________
>>>> 3dem mailing list
>>>> 3dem at ncmir.ucsd.edu
>>>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> End of 3dem Digest, Vol 107, Issue 2
>>>> ************************************
>>>>
>>>
>>>
>>> _______________________________________________
>>> 3dem mailing list
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>>
>
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