What we really need is a tweet from Nature, declaring their
embarrassment at having been suckered into becoming DeepMind's
advertising arm.
On 14/05/2024 01:56, Paul Adams wrote:
The letter may have had (or helped have) an impact already:
On X today from Pushmeet Kohli @ DeepMind
"We love the excitement & results from the community on AlphaFold 3
and are doubling the AF Server daily job limit to 20. Happy to also
share that we're working on releasing the AF3 model (incl weights) for
academic use, which doesn’t depend on our research infra, within 6
months".
On May 13, 2024, at 11:11 AM, Wankowicz, Stephanie
<[email protected]> wrote:
If it does what it claims – incredibly impressive. The issue we have
is there is no way to verify or validate the claims it is making.
The letter is a call and start of a conversation about how the
ever-changing landscape of communication and publication of science
should be.
-Stephanie Wankowicz
------------------------------------------------------------------------
*From:*CCP4 bulletin board <[email protected]> on behalf of
Krieger, James M <[email protected]>
*Sent:*Monday, May 13, 2024 10:22 AM
*To:*[email protected]<[email protected]>
*Subject:*Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
This Message Is From an External Sender
This message came from outside your organization.
It definitely is impressive but it also has clear limitations
On 13 May 2024, at 15:22, Sylvia Fanucchi
<[email protected]> wrote:
You don't often get email from
[email protected] why this is
important
<https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmVluUFn$>
Is it just me who is really impressed by it? Am I missing something?
GetOutlook for Android
<https://urldefense.com/v3/__https://aka.ms/AAb9ysg__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7ArXNQatL$>
------------------------------------------------------------------------
*From:*CCP4 bulletin board <[email protected]> on behalf of
Rafael Marques <[email protected]>
*Sent:*Monday, May 13, 2024 3:13:16 PM
*To:*[email protected] <[email protected]>
*Subject:*Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility
I tried it yesterday and I was really shocked by how fast it is.
When I was preparing to submit my second job, the first one was
already finished, which made me think that I was definitely doing
something wrong. Probably I was...
Best wishes
Rafael Marques
On 13 May 2024 09:53, Harry Powell
<[email protected]> wrote:
Hi folks
This arrived in my inbox this morning, and I believe that it may
provoke some discussion…
Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν
Best wishes!
Harry
> From: Stephanie Wankowicz <[email protected]>
> Sent: Saturday, May 11, 2024 3:31 PM
> To: James Fraser <[email protected]>; Pedro Beltrao
<[email protected]>; Benjamin Cravatt
<[email protected]>; Roland Dunbrack
<[email protected]>; Anthony Gitter
<[email protected]>; Kresten Lindorff-Larsen
<[email protected]>; Sergey Ovchinnikov <[email protected]>; Polizzi,
Nicholas F. <[email protected]>; Brian Shoichet
<[email protected]>
> Subject: AlphaFold3 Transparency and Reproducibility
>
>
> This email from [email protected] originates from
outside Imperial. Do not click on links and attachments unless
you recognise the sender. If you trust the sender, add them to
your safe senders list
<https://spam.ic.ac.uk/SpamConsole/Senders.aspx>
<https://urldefense.com/v3/__https://spam.ic.ac.uk/SpamConsole/Senders.aspx*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AkQKssvO$>to
disable email stamping for this address.
>
> Hello,
>
>
> As many of you, we were incredibly disappointed with the
lack of code or even executables accompanying the publication of
AlphaFold3 in Nature. AlphaFold3 was released without the means
to test and use the software in a high-throughput manner. This
does not align with the principles of scientific research, which
rely on the ability of the community to evaluate, use, and build
upon existing work.
>
>
>
> We have written a letter, which will be posted on Zenodo
and submitted as a Letter to the Editor in the coming days.
>
>
>
> Please see the entire letter here.
<https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link>
<https://urldefense.com/v3/__https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AqTp0-CX$>If
you want to endorse this letter, please fill out your name,
affiliation, and email in the form.
>
>
>
> Additionally, a PDF version of the letter can be found here
<https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing>
<https://urldefense.com/v3/__https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmjNPgIH$>.
>
>
>
> Thank you,
>
>
>
> Stephanie Wankowicz, UCSF
>
> Pedro Beltrao, ETH
> Benjamin Cravatt, Scripps
> Roland Dunbrack, FCCC
> Anthony Gitter, UW Madison
> Kresten Lindorff-Larsen, Copenhagen
> Sergey Ovchinnikov, MIT
> Nicholas Polizzi, DFCI/HMS
> Brian Shoichet, UCSF
> James Fraser, UCSF
>
>
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--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences,
LBL (https://biosciences.lbl.gov)
Principal Investigator, Computational Crystallography Initiative,
LBL (http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy
Institute (http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source
(http://als-enable.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus
Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, UC
Berkeley (http://bioeng.berkeley.edu)
Member of the Graduate Group in Comparative Biochemistry,
UC Berkeley (http://compbiochem.berkeley.edu)
Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul
ORCID: 0000-0001-9333-8219
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.
Executive Assistant: Michael Espinosa [ [email protected] ][
1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ [email protected] ][ 1-510-486-5455 ]
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