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ErikaT
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Microbiome Immunity Project - Project Update, January 2020

Hi everyone,

Here's the latest update from the Microbiome Immunity Project researchers. In addition to analyzing all the data they get back from WCG, they've created an innovative technique to help predict protein function. You can learn all about it here.

Thanks to everyone for your support of this project!
ErikaT
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Jim1348
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Re: Microbiome Immunity Project - Project Update, January 2020

That is very, very impressive, whether I understand it or not. It is a pleasure to work on such a project.
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sptrog1
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Re: Microbiome Immunity Project - Project Update, January 2020

It is actually comforting to me to note that only 275 thousand unique protiens were found in the 456 million results. I was worried that they might strain their eyeballs after having said that if they could see the structure, they could tell the function. Thank God for duplicates.
I also have hope for the future processing.
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Re: Microbiome Immunity Project - Project Update, January 2020

@ErikaT: Thanks for the information! Interesting read!

@sptrog1:
From where do you know that they do not run working units on their own machines? Are there any public information available?

Well, 275k unique proteins is much compared to the knowledge we had in this space before the project. You can read the protein you calculate in the work unit. A work unit description is like MIP1_00269443_1000_0. The first number represents the protein and the second number the experiment for the protein. Usually around 2000 experiments/calculations are needed to predict a protein. This conforms with the given data: 436 millions results / 275 thousand proteins = 1658
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[Edit 1 times, last edit by Former Member at Jan 21, 2020 4:28:50 PM]
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Jim1348
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Re: Microbiome Immunity Project - Project Update, January 2020

Well, 275k unique proteins is much compared to the knowledge we had in this space before the project.

Also, I suspect that there are classes of proteins. If you know some from each class, you probably don't have to do all of them. But that is a guess. I am willing to do as many as necessary.
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[VENETO] boboviz
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Re: Microbiome Immunity Project - Project Update, January 2020

In addition to analyzing all the data they get back from WCG, they've created an innovative technique to help predict protein function.

It seems strange to me, cause they are using Rosetta code
Or not?
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Re: Microbiome Immunity Project - Project Update, January 2020

Or Not? is a superfluous question. The executable is clearly named after it's origins
wcgrid_mip1_rosetta_7.16_windows_intelx86

How many versions and branches of 'Rosetta Code' are there, and still only 32bit in 2020. It's being developed for as long as I can remember, probably going at least as far back as WCG is old since their first project was HPF1, Dr Baker based.
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supdood
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Re: Microbiome Immunity Project - Project Update, January 2020

Let's remember that our computing is determining protein structure, not predicting protein function, which is what the new technique does.

What I am unclear on is how this statement can be true given the extent of work done at the Rosetta@Home project:
"State-of-the-art methods to date relied only on protein sequence information...because researchers never had access to enough protein structure data to make such predictions widely applicable....We tackled...the data availability problem by enrolling your help through the Microbiome Immunity Project and generating a collection of 3D protein structural models of an unprecedented scale."
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