Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-17 Thread Edward K. Ream 
On Thu, Sep 16, 2021 at 5:36 PM David Szent-Györgyi 
wrote:

The National Library of Medicine of the National Institutes of Health has a
> section of its Web site devoted to him
> .
>
...

> he wrote an essay... "Lost in the Twentieth Century"
> 
>

"We are living in the transition from prescientific to the scientific
thinking, hence the 'tumult'.

I couldn't agree more. The "demon haunted world" does not go quietly.

"I also became interested in vegetable respiration, being convinced that
there is no basic difference between man and the grass he mows".

He has a way with words :-) The rest of the paper is poignant. It's hard to
believe that the 20th century existed as it did. The history of those times
is more scary than any horror movie.


> he wrote another essay, "Looking Back"
> 
>

A lovely essay.  The description of what it takes to write well may inspire
anyone to work more and worry less about so-called "talent".

Many thanks for sharing these links.

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-16 Thread David Szent-Györgyi 
On Wednesday, September 15, 2021 at 7:44:42 AM UTC-4 Edward K. Ream wrote:

> Namely the Nobelist Albert Szent-Györgyi. 
> 
>

The National Library of Medicine of the National Institutes of Health has a 
section of its Web site devoted to him 
. 

While I did not know Albert adult-to-adult, I grew up well aware of his 
work and the regard in which other scientists held him. My mother and 
father started their careers in basic research in his lab, and we all lived 
in the same town on Cape Cod, so his family and mine spent a lot of time 
together. 

His English was first-rate, an accomplishment since English and Hungarian 
are not related, and learning either is difficult for the person whose 
language is the other. I was fortunate to hear him give a lecture aimed at 
the generalist. 

Albert is worthy of note because receiving the 1937 Nobel in Physiology or 
Medicine did not lead him to cease conducting pioneering research. The 
above-linked article on the investigation of the molecular motor of muscle 
mentions groundbreaking work that his lab did in isolation during World War 
II. That work continued after the war, and moved with him to the United 
States. The loss of a wife and daughter to cancer led him to shift his 
focus to that disease when he was in his late seventies; he continued that 
work until shortly before his death at 93. 

His birth and upbringing in Habsburg Hungary, a country that had yet to 
leave behind prescientific structures and roots, along with his interest in 
basic research spurred in him an interest the lag in society's progression 
from a prescientific to a scientific basis. That, combined with his 
experience as a public figure during a turbulent period in Hungary, meant 
that he was privately and publicly involved in political matters. The 
enmity of the German Nazis and their Hungarian allies drove him into 
hiding. Later on, risk to his life earned through his opposition to the 
coming Communist order in Hungary led him to move to the United States. 
There, he continued to involve himself in politics - he was one of the 
eminent scientists who contacted the Kennedy Administration to educate it 
on the nature of nuclear weapons and the threat that they posed. 

When he reached seventy, when most retire, he wrote an essay that drew on 
all that, "Lost in the Twentieth Century" 
,
 
which opens the 1963 *Annals of Biochemistry*. In 1971, in his late 
seventies, he wrote another essay, "Looking Back" 
,
 
which is primarily about science but places it in context of life and 
conditions in the US. Anyone who share's Edward's broad perspective on 
science, technology, and society should look them up. 

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-15 Thread Edward K. Ream 


On Wednesday, September 15, 2021 at 6:41:02 AM UTC-5 Edward K. Ream wrote:

> On Tue, Sep 14, 2021 at 10:12 PM David Szent-Györgyi  
> wrote:
>
>> AlphaFold is an extraordinary advance in the speed of the development of 
>> knowledge. Compare the rapidity of the understanding of the structure of 
>> COV-2 with the decades of labor required in the 1950s and 1960s for 
>> determination of the structure of myosin, the protein that is the largest 
>> constituent of skeletal muscle, as described in this article on the 
>> investigation of the molecular motor of muscle 
>> . 
>>
>
> Great to know your scientific pedigree!
>

Namely the Nobelist Albert Szent-Györgyi. 


Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-15 Thread Edward K. Ream 
On Tue, Sep 14, 2021 at 9:26 PM David Szent-Györgyi 
wrote:

> My day job is technical support for basic research in life science, and
> abuts drug discovery, which is targeted work. Below is a note that I sent
> to my colleagues at the end of 2020, when last winter's COVID outbreaks
> were at a terrible high.
>

Thanks for the personal note!

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-15 Thread Edward K. Ream 
On Tue, Sep 14, 2021 at 10:12 PM David Szent-Györgyi 
wrote:

> AlphaFold is an extraordinary advance in the speed of the development of
> knowledge. Compare the rapidity of the understanding of the structure of
> COV-2 with the decades of labor required in the 1950s and 1960s for
> determination of the structure of myosin, the protein that is the largest
> constituent of skeletal muscle, as described in this article on the
> investigation of the molecular motor of muscle
> .
>

Great to know your scientific pedigree!

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread David Szent-Györgyi 
AlphaFold is an extraordinary advance in the speed of the development of 
knowledge. Compare the rapidity of the understanding of the structure of 
COV-2 with the decades of labor required in the 1950s and 1960s for 
determination of the structure of myosin, the protein that is the largest 
constituent of skeletal muscle, as described in this article on the 
investigation of the molecular motor of muscle 
. 

(No, I'm not a biochemist; my parents were - they spent their working lives 
on the regulation of muscle contraction). 

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread David Szent-Györgyi 
My day job is technical support for basic research in life science, and 
abuts drug discovery, which is targeted work. Below is a note that I sent 
to my colleagues at the end of 2020, when last winter's COVID outbreaks 
were at a terrible high. 

--- note begins ---
This is really interesting work in life science and work in drug discovery, 
driven by computation:

>From <
https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology
>:


*. . . In the meantime, we’re also looking into how protein structure 
predictions could contribute to our understanding of specific diseases with 
a small number of specialist groups, for example by helping to identify 
proteins that have malfunctioned and to reason about how they interact. 
These insights could enable more precise work on drug development, 
complementing existing experimental methods to find promising treatments 
faster.We’ve also seen signs that protein structure prediction could be 
useful in future pandemic response efforts, as one of many tools developed 
by the scientific community. Earlier this year, we predicted several 
protein structures of the SARS-CoV-2 virus, including ORF3a, whose 
structures were previously unknown. At CASP14, we predicted the structure 
of another coronavirus protein, ORF8. Impressively quick work by 
experimentalists has now confirmed the structures of both ORF3a and ORF8. 
Despite their challenging nature and having very few related sequences, we 
achieved a high degree of accuracy on both of our predictions when compared 
to their experimentally determined structures.*

An associated video:


--- note ends ---

>

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread Edward K. Ream 
On Tue, Sep 14, 2021 at 1:05 PM jkn  wrote:

The link to the PDF worked for me, thanks
>

You're welcome :-) Good luck chasing the white rabbit...

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread jkn 
The link to the PDF worked for me, thanks

J^n


On Tuesday, September 14, 2021 at 4:20:51 PM UTC+1 Edward K. Ream wrote:

> On Tuesday, September 14, 2021 at 8:07:34 AM UTC-5 Edward K. Ream wrote:
>
> > I've converted the Alpha sources (almost all python) to a study outline. 
> I'll make it available once I finish editing it.
>
> Still true, but the "raw" python code is pretty much impenetrable. Heh, I 
> had to reread the Nature article to verify that yes, neural networks  *are 
> *involved. The article says so right at the beginning, but I have not yet 
> discovered where the neural networks make their appearance in the code!
>
> In effect, the supplementary data for the article contains the code's 
> theory of operation:
>
> https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf
>
> Not sure if this .pdf file is freely available. I can send it to anyone 
> who is interested.
>
> The supplementary .pdf is *not* easy reading. Probably one needs multiple 
> PhD's to understand it.
>
> Edward
>

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread Edward K. Ream 
On Tuesday, September 14, 2021 at 10:20:51 AM UTC-5 Edward K. Ream wrote:

The supplementary .pdf is *not* easy reading. Probably one needs multiple 
> PhD's to understand it.
>

Here are the supplementary videos that we mortals can enjoy.

Supplementary Video 1 


Video of the intermediate structure trajectory of the CASP14 target T1024 
(LmrP) A two-domain target (408 residues). Both domains are folded early, 
while their packing is adjusted for a longer time.
Supplementary Video 2 


Video of the intermediate structure trajectory of the CASP14 target T1044 
(RNA polymerase of crAss-like phage). A large protein (2180 residues), with 
multiple domains. Some domains are folded quickly, while others take a 
considerable amount of time to fold.
Supplementary Video 3 


Video of the intermediate structure trajectory of the CASP14 target T1064 
(Orf8). A very difficult single-domain target (106 residues) that takes the 
entire depth of the network to fold.
Supplementary Video 4 


Video of the intermediate structure trajectory of the CASP14 target 
T1091. A multi-domain target (863 residues). Individual domains’ structure 
is determined early, while the domain packing evolves throughout the 
network. The network is exploring unphysical configurations throughout the 
process, resulting in long ‘strings’ in the visualization.

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread Edward K. Ream 
On Tuesday, September 14, 2021 at 8:07:34 AM UTC-5 Edward K. Ream wrote:

> I've converted the Alpha sources (almost all python) to a study outline. 
I'll make it available once I finish editing it.

Still true, but the "raw" python code is pretty much impenetrable. Heh, I 
had to reread the Nature article to verify that yes, neural networks  *are 
*involved. 
The article says so right at the beginning, but I have not yet discovered 
where the neural networks make their appearance in the code!

In effect, the supplementary data for the article contains the code's 
theory of operation:
https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf

Not sure if this .pdf file is freely available. I can send it to anyone who 
is interested.

The supplementary .pdf is *not* easy reading. Probably one needs multiple 
PhD's to understand it.

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread Edward K. Ream 
On Tue, Sep 14, 2021 at 6:03 AM Alexey Tikhonov 
wrote:

> Wow! Thanks for sharing!
>

You're welcome. I've converted the Alpha sources (almost all python) to a
study outline. I'll make it available once I finish editing it.

Edward

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Re: Wow: AlphaFold .ipynb and Google Colab

2021-09-14 Thread Alexey Tikhonov 
Wow! Thanks for sharing!

понедельник, 13 сентября 2021 г. в 21:16:22 UTC+7, Edward K. Ream: 

> AlphaFold (See this Nature article 
> ) solves one of the 
> grand challenges in computational science.  Full sources for AlphaFold are 
> available here .
>
> The AlphaFold sources contain  AlphaFold.ipynb 
> , 
> a Jupyter notebook.The FAQ in the notebook contains a reference to Google 
> Colab. OMG!  Take a look at the Colab FAQ 
> !
>
> "Colab allows anybody to write and execute arbitrary python code through 
> the browser, and is especially well suited to machine learning, data 
> analysis and education. More technically, Colab is a hosted Jupyter 
> notebook service that requires no setup to use, while providing free access 
> to computing resources including GPUs."
>
> !
>
> Edward
>

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Wow: AlphaFold .ipynb and Google Colab

2021-09-13 Thread Edward K. Ream 
AlphaFold (See this Nature article 
) solves one of the 
grand challenges in computational science.  Full sources for AlphaFold are 
available here .

The AlphaFold sources contain  AlphaFold.ipynb 
, 
a Jupyter notebook.The FAQ in the notebook contains a reference to Google 
Colab. OMG!  Take a look at the Colab FAQ 
!

"Colab allows anybody to write and execute arbitrary python code through 
the browser, and is especially well suited to machine learning, data 
analysis and education. More technically, Colab is a hosted Jupyter 
notebook service that requires no setup to use, while providing free access 
to computing resources including GPUs."

!

Edward

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