[3dem] Ampere specific bug in AreTomo

Mon Nov 28 17:16:39 PST 2022

Hi Shawn,

Could you describe the nature of the bug? Was it in an Nvidia library, or
an AreTomo kernel? We all have similar image processing approaches, and it
is likely the cryoEM community would benefit from you sharing a gist or
something.

Cheers
Ben

On Mon, Nov 28, 2022 at 1:53 PM <3dem-request at ncmir.ucsd.edu> wrote:

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> Today's Topics:
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>    1. AreTomo 1.3.3 fixed a bug specific to Ampere GPU (Shawn Zheng)
>    2. Frozen samples shipment (Pedro Rodriguez)
>    3. Scientist position on cryo correlative bio-imaging at Alba
>       Light Source, Spain (Joaqu?n Ot?n)
>    4. Reminder - Tenure Track Faculty Position in Cryo-EM
>       (Martin Lawrence)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 27 Nov 2022 17:51:15 -0800
> From: Shawn Zheng <szheng at msg.ucsf.edu>
> To: 3dem at ncmir.ucsd.edu, "CCPEM at JISCMAIL.AC.UK" <CCPEM at jiscmail.ac.uk>
> Subject: [3dem] AreTomo 1.3.3 fixed a bug specific to Ampere GPU
> Message-ID:
>         <CAPLubHaMAieDT0_BLGbotjcOsh46UvO-EvfREH+pDgjv=+
> 8vjg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Colleagues,
>
> Thanks for the helps from Herman Fung, Edoardo D Imprima, and Huabin Zhou,
> an elusive bug in AreTomo 1.3.0, causing blurry reconstruction only when
> Ampere GPUs are used, has been fixed in the new release. As always, your
> feedback is greatly appreciated.
>
> Best
> Shawn
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> ------------------------------
>
> Message: 2
> Date: Mon, 28 Nov 2022 11:55:34 +0800
> From: Pedro Rodriguez <kidaguacate at gmail.com>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Frozen samples shipment
> Message-ID:
>         <
> CALc9H9+rqWe3OMpELAQF129ey0g+7C10ZWw8W-sO3cHYkvtnTg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> We want to ship frozen grids to Israel from our lab in GTIIT, Shantou. For
> that, we use the Dry Shipper Dewar CX100 from ICBiomedical. Until now it
> has not been possible because the courier companies in China refuse to send
> it, even though it does not contain liquid and does not need refrigeration.
>
> I would like to know if someone on this list has experience in this type of
> shipment from/to China and if they could offer me a contact of a company
> that is in charge of the courier service for this type of shipment.
>
> Thanks in advance for the support,
>
> Pedro RODRIGUEZ
> CryoEM lab
> GTIIT-Shantou
> China
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> ------------------------------
>
> Message: 3
> Date: Mon, 28 Nov 2022 15:54:26 +0100
> From: Joaqu?n Ot?n <joton at cells.es>
> To: 3dem <3dem at ncmir.ucsd.edu>, CCPEM at JISCMAIL.AC.UK
> Cc: Eva Pereiro <epereiro at cells.es>
> Subject: [3dem] Scientist position on cryo correlative bio-imaging at
>         Alba Light Source, Spain
> Message-ID: <a4bfa8f7-2fe5-41a2-96da-e8ed265e2bbe at cells.es>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear colleagues,
>
> ?In the frame of the EU project iNEXT-Discovery, a scientist position is
> open to work within the multidisciplinary MISTRAL team and Methodology
> group in order to develop the software tools to automatize the
> correlation process between the 3D visible light fluorescence data from
> the cryo structured illumination microscope and the tomograms from the
> cryo soft X-ray microscope at MISTRAL, also in close collaboration with
> B24 beamline at Diamond Light Source (UK).
>
> Deadline is 12th December. More info and application:
>
> https://urldefense.com/v3/__https://public.cells.es/jobs/*!/jobs/scientist-position-for-cryo-correlative-bio-imaging-at-the-mistral-beamline__;Iw!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHdC8pSen$
>
>
> With best wishes,
>
> Joaqu?n
>
>
> --
>
> <
> https://urldefense.com/v3/__https://www.albasynchrotron.es/en/__;!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHR4A65D-$
> >
>
>         Joaqu?n Ot?n
> Methodology Group - Experiments Division
> ALBA SYNCHROTRON LIGHT SOURCE
> Carrer de la Llum 2-26 | 08290 | Cerdanyola
> <https://urldefense.com/v3/__https://www.google.com/maps/search/Carrer*de*la*Llum*2-26**A7C*08290**A7C*Cerdanyola?entry=gmail&source=g__;KysrKyslKyslKw!!Mih3wA!BCibFCrAMnIktbR0RcrZ6AFgVs-6GrxWLBzCn9OqeoENSJWYuyg577oF7PCBbbNVBi3KSOA0vvdq7MyBPYJb9SEdNyQ$ >
> del Vall?s| Barcelona |
> Spain <
> https://urldefense.com/v3/__https://www.albasynchrotron.es/en/about/coming-to-alba__;!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHYA96oxx$
> >
> (+34) 93 592 4441
>
> https://urldefense.com/v3/__http://www.albasynchrotron.es__;!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHWCrQ-K5$
> <
> https://urldefense.com/v3/__http://www.albasynchrotron.es__;!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHWCrQ-K5$
> >| joton at cells.es
> <mailto:joton at cells.es> | legal notice
> <
> https://urldefense.com/v3/__https://www.albasynchrotron.es/en/about/legal-notice__;!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHc6CPWho$
> > / av?s legal
> <
> https://urldefense.com/v3/__https://www.sincrotroalba.cat/ca/que-es-alba/avis-legal__;!!Mih3wA!GJuLDTFKYhgyHqOpS0uHgTG_NkmnroFPRqsDqQRJGHfF1dpNuCLNv01xzlrfpXbvuIjl4o1pHTHZRVYk$
> > / aviso legal
> <
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> ------------------------------
>
> Message: 4
> Date: Mon, 28 Nov 2022 11:52:51 -0700
> From: Martin Lawrence <lawrence at montana.edu>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Reminder - Tenure Track Faculty Position in Cryo-EM
> Message-ID:
>         <CAKvkAjVJ88eYeY_7EeBo_ikCGWgxWoZEvv-ekbdEoF=
> 5GXxxwQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear 3D-EM Community,
>
> Montana State University (MSU) invites applications for a tenure-track
> faculty position in cryogenic electron microscopy.  The position is
> formally a joint appointment between the Department of Chemistry and
> Biochemistry, and the Department of Microbiology and Cell Biology.  The
> candidate will join an active structural biology group with existing
> expertise in X-ray crystallography, NMR and mass spectrometry, and
> developing
> expertise in cryo-EM.
>
> The TEM Core <
> https://urldefense.com/v3/__https://www.montana.edu/cryo-electron-microscopy/__;!!Mih3wA!AeucTQbWQHNnV7e188cVWtxWtj2E29SQAqJ13V3K6cc_W2qt8Fd_f8CJvttpbp3HZHcONzNsmGOPu3aVWTiENtM$
> > facility
> at MSU houses a 200 kV Talos Arctica microscope equipped with a Gatan K3
> camera, and a 120 kV Spirit for screening purposes.  Potential applicants
> with expertise in single particle analysis and/or cryo-electron tomography
> are encouraged to apply.  Review of applications will begin November 28th
> and
> continue until the position is filled.  Thus, if you are interested in this
> position, please submit your application as soon as possible.
>
> Montana State University maintains a highly collaborative,
> interdisciplinary environment with research programs broadly focused in
> multiple areas, including  metalloproteins and metals in biology, innate
> and acquired immunity, virology, pathogen microbiology, host/pathogen
> interactions, microbial biofilms, cell and developmental biology and
> neurobiology/neuroscience.  There are numerous opportunities for
> collaborations in these areas.
>
> Montana State University is located in the Northern Rocky Mountain
> community of Bozeman Montana, immediately north of Yellowstone National
> Park.  Bozeman is regularly recognized for its high quality of life,
> including its outdoor, cultural and educational amenities:
>
> https://urldefense.com/v3/__http://www.montana.edu/about-msu/bozeman/__;!!Mih3wA!AeucTQbWQHNnV7e188cVWtxWtj2E29SQAqJ13V3K6cc_W2qt8Fd_f8CJvttpbp3HZHcONzNsmGOPu3aVkDpabh0$
> <
> https://urldefense.com/v3/__http://www.montana.edu/marketing/about-msu/bozeman/__;!!Mih3wA!AeucTQbWQHNnV7e188cVWtxWtj2E29SQAqJ13V3K6cc_W2qt8Fd_f8CJvttpbp3HZHcONzNsmGOPu3aVC62n1sQ$
> >.
>
> For further details and to apply, please visit:
>
> https://urldefense.com/v3/__https://jobs.montana.edu/postings/33131__;!!Mih3wA!AeucTQbWQHNnV7e188cVWtxWtj2E29SQAqJ13V3K6cc_W2qt8Fd_f8CJvttpbp3HZHcONzNsmGOPu3aV3UwrGpU$
>
> For inquiries and additional questions, please contact:
>
> Martin Lawrence
> lawrence at montana.edu
>
> Martin Lawrence
> Professor of Chemistry and Biochemistry
> Montana State University
> Bozeman, MT
> 406-994-5382
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