Posts by krypton

1) Message boards : Cafe Rosetta : Who has access to the results ? (Message 87563)
Posted 25 Oct 2017 by krypton
Post:
The raw results can only be accessed by folks in the bakerlab, though the key results are made available with the publication of a paper.

The University of Washington patents everything that could potentially benefit pharmaceutical companies, before publication. If the companies do decide to use any of the data, they would give money to UW, which would then go back towards research!
2) Message boards : Rosetta@home Science : what would be considered low energy? (Message 87544)
Posted 19 Oct 2017 by krypton
Post:
Hi Dirk,

The problem is we don't really know what the lowest energy is for a given sequence. We need to do lots of sampling to answer this question, that is why we need Rosetta@home compute resources!

It would be analogous to finding the lowest point on earth, without knowing what it is. We can make one person walk the earth or we can send 1000s of people to explore earth. The more people we send to explore, the higher chance one of them will find it. Also if multiple people independently report a similar lowest point they discovered and they happen to be standing in the same location, that is a good indication that we did enough sampling (found the global minimum instead of a local minimum).
3) Message boards : Rosetta@home Science : Cancer, healthy and normal cells are it really? (Message 81506)
Posted 21 Apr 2017 by krypton
Post:
You might be interested in the following database:
http://cancer.sanger.ac.uk/cosmic

COSMIC is a database of mutations found in cancer cells. If you compare the DNA sequences between these cells and "normal" cells. You should, in theory, be able to figure out what DNA changes you need to make to reverse cancer for that particular cell line.

DNA editing of cells is the future, we will one day be able to reverse these mutations! In the meantime, scientists are focusing on how to detect these cells and kill them!

Cancer, healthy and normal cells are it really?
When an organism undergoes an attack, two phenomena can occur, some of the cells go into "immortal" mode and duplicate in an anarchic way and this gives a tumor or "cancer", but the other cells called "healthy" are " Normal ", apparently they are, but in reality they go into" cell death "mode and this is mainly that kills the person with cancer, more than the" anarchic "cells.
Is it not possible to study these "healthy" cells, and reverse the two processes by forcing "immortal" cells to go into "cell death" mode, and forcing the so-called "healthy" cells to pass from "Cell death" mode to truly healthy mode?
Yours; @ + *_*

Cancer, les cellules saines et normales le sont elles vraiment ?
Lorsque un organisme subit une agression, deux phénomènes peuvent se produire, une partie des cellules passent en mode "immortelle" et se dupliquent de façon anarchique et cela donne une tumeur ou "cancer", mais les autres cellules dites "saines" sont elles "normales ?", apparement elles le sont, mais en réalité elles se mettent en mode "mort cellulaire" et c'est cela principalement qui tue la personne atteinte d'un cancer, plus que les cellules "anarchiques".
N'est il pas possible d'étudier ces cellules soit disant "saines", et inverser les deux processus en forçant les cellules "immortelles" à passer en mode "mort cellulaire", et forcer les cellules soient disant "saines" à passer du mode "mort cellulaire" au mode réellement sain ?
Bien à vous; @+ *_*

4) Message boards : Number crunching : DNS Problems and Late Work Units (Message 81286)
Posted 10 Mar 2017 by krypton
Post:
It looks like we are back!!

We can help the "return of Dns" writing to Icaan President on Twitter
@Icaan, @Icaan_presindent, @IcannOmbudsman
Please, #RescueRosettaathome, #RescueBakerlabdotorg

5) Message boards : Rosetta@home Science : Rosetta@home no longer mentioned in papers? (Message 81258)
Posted 2 Mar 2017 by krypton
Post:
Do you have a particular paper in mind? I just tried clicking through a couple random papers that used Rosetta@home and Rosetta@home is mentioned.

OK. Good to hear that, at least in 2017, this practice of properly acknowledging scientific contributions has been resumed.

To the best of my knowledge, according to international science journal standards, any publication which does not acknowledge the Rosetta@home DC community although results from that community's efforts were used for that particular scientific work, would require the writing of an appropriate corrigendum.

David Bakers Rosetta@home undoubtedly is one of the top-notch DC projects in the world. Therefore, it serves a key example for what is possible with scientific computing on a volunteer community basis. If that community is not mentioned, however, nobody will ever know about its wonderful possibilities and interest might soon fade away.

Michael.

6) Message boards : Rosetta@home Science : Rosetta@home no longer mentioned in papers? (Message 81239)
Posted 27 Feb 2017 by krypton
Post:
It's mentioned in both papers published this year so far:
"We also thank Rosetta@home and Charity engine participants for donating their computer time."

Rosetta@home should be in all the acknowledgements where used, unless we made an error :(
7) Message boards : Number crunching : RALPH@Home ? (Message 81232)
Posted 25 Feb 2017 by krypton
Post:
thanks for alert!
Ralph is down again.

And no link to beta project in rosetta's home page.

8) Message boards : Rosetta@home Science : CASP12 (Message 81096)
Posted 27 Jan 2017 by krypton
Post:
It would be nice to hear a little more about the CASP 12 results. Were there any interesting insights into the state of the art in protein folding from the meeting last month?


Hi svincent,

If you are interested I uploaded slides from our CASP12 presentation here:
https://docs.google.com/presentation/d/1ZQ3Uvh-PPGz9VBJlohKlMHuW7FceAGQEgvpSsvBBy1A

But in short:
1) we have a method (GREMLIN:co-evolution) for predicting contact from given a multiple sequence alignment.
2) we used boinc before casp to precompute protein families with unknown structure. At least one of the targets (T0866) matched a precomputed model and was used by the server! This was a highlight this casp.
3) we developed a new method "map_align" that can take predicted co-evolution contacts and search the entire PDB. Sometimes two proteins may have VERY different sequences (beyond anything you would call homologs) but have very similar structures. If we find a hit in the PDB that matches the contacts, we can use it as a starting point in modeling. We had some great sucess using this method on target T0886.


Tell me if you have any quesionns

-krypton (aka sergey)
9) Message boards : Rosetta@home Science : Solving structures using Metagenomic sequences! (Message 81082)
Posted 24 Jan 2017 by krypton
Post:
Hi All,

Just wanted to say thanks for all the donated computer time. Without you we would not have been able to this work!



The data (including link to PDF) can be found here:
https://gremlin2.bakerlab.org/meta.php

Some links for those that want to learn more:
http://jgi.doe.gov/seeking-structure-metagenome-sequences/
http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles/
https://www.theatlantic.com/science/archive/2017/01/unravelling-lifes-origami/513638/

-krypton
10) Message boards : Rosetta@home Science : CASP12 (Message 80829)
Posted 8 Nov 2016 by krypton
Post:
Some batches of _casp12_ on Ralph....


Hi bobviz,
There are some test related to casp12.

-krypton
11) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80613)
Posted 9 Sep 2016 by krypton
Post:
Thank boboviz,

I have some urgent stuff we need for a paper. I'll be submitting those to ralph!

There's plenty of work now but we just reached a breaking point with our database server.


I repeat myself: if you have some "urgent" work to do, use Ralph

We are working on a temporary solution since our full upgrade will take some time, on the order of months I am told.

Keith, Darwin, and Patrick, our sys admins, are working on getting it set up now


So, you have not jet the disks and they will arrive in the future (near??).
After that you have to install new os and configure it.
See you on Christmas.... :-P
12) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80597)
Posted 7 Sep 2016 by krypton
Post:
We are in process of buying new hardware, which should help! In the meantime we are enabling the old hardware one piece at a time, allowing the system to catchup. Hopefully all will be ready in a day!

I have to ask what's going on atm.

Servers all seemed to be reset the other day, lots of tasks showing on the homepage and server status page now but little or nothing coming down, though at the same time lots of tasks seem to be in progress.

Meanwhile validation is anything up to a day and a half behind with some of my team.


I share your concern.
The server status page bears little resemblance to what we experience, even reporting tasks has become a lottery, validation is way behind and external statistics reporting is sporadic.

Has Rosetta@home become a victim of it's own success?

13) Message boards : Number crunching : Crowdfounding for new servers? (Message 80588)
Posted 2 Sep 2016 by krypton
Post:
We estimated that we'd need about 40K for an upgrade. We've been able to combine funding from a couple different sources and raise 10K! It's not enough for a complete upgrade, but we decided to use the money to upgrade our hard-drives/storage. We've been experiencing some slow down due to high I/O loads and lack of space. We'll be getting solid state drives!

I've asked the sys-admins to provide us with a break down of upgrades we'd need. I'll post that soon!

We'll get back to you on that. I think Sergey is looking into it.


While waiting, some ideas:
A list of scientific crowdfounding
A guide to scientific crowdfounding

And Dell refurbished servers if you want to save money

14) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80571)
Posted 28 Aug 2016 by krypton
Post:
Hi boboviz,

Any luck now? What error message did you get? I'm debugging the issue.
Problems remain: cannot upload wus after rosetta server stop this morning...

15) Message boards : Number crunching : Crowdfounding for new servers? (Message 80462)
Posted 2 Aug 2016 by krypton
Post:
Since 2011 the donate button has raised $1,231 for Rosetta@home related things. This isn't quite enough to do any major upgrades...

We have 5 webserver, 1 database and 1 filesystem server. We'd want to at minimum upgrade the database and filesystem server. I'm still talking to the system admin people to get a estimate of how much money we'd need. But, once you start adding large data storage and lots of memory for SQL databases, these things could get really expensive!
16) Message boards : Number crunching : Crowdfounding for new servers? (Message 80437)
Posted 26 Jul 2016 by krypton
Post:
Sorry for the delay in replies, CASP has been taking most of my time. =[

I've requested a full history of donations for rosetta@home. I've also contacted our system admin people to figure out how money we'll need for upgrades.

We'll have a report soon!

And no admins write here :-(

Maybe they could fill us in on their situation, and for what purposes they would use the money. I am sure a lot of people would be willing to contribute.

(The federal government spends a large amount of money on medical research, but maybe not at their level.)

17) Message boards : Rosetta@home Science : The Protein folding revolution! (Message 80412)
Posted 22 Jul 2016 by krypton
Post:
The protein folding effort we've been working on has been featured in Science:

http://science.sciencemag.org/content/353/6297/338.full

They also made a youtube video:
https://www.youtube.com/watch?v=cAJQbSLlonI

BOINC and Rosetta@home was heavy used for this work, thanks for all the contributions!

“We didn't [cheat],” Sergey Ovchinnikov, a grad student in Baker's lab, says with a chuckle.

-krypton (aka Sergey)
18) Message boards : Number crunching : Credit granted pending stack (Message 80395)
Posted 19 Jul 2016 by krypton
Post:
UW/IPD gets lots of money for various projects. Some of these are commercial (translational research, KumaMax etc.) and they do NOT use BOINC. Bill & Melinda Gates money funds 5-10 different labs that aren't even part of UW.

I wish we had access to some of that money for basic research and boinc!

Rosetta@home is primarily used to do research into topics that are non-commercial and purely scientific. Hence we don't see that money, and rely on compute donations from BOINC. The money we do get for basic research, most ends up going to paying for actual lab experiments (which are VERY expensive).

I personally pay, out of my own pocket, to host some of research I do... due to limited funds/resources.

I'll have to check how the money donated on the boinc website gets allocated to boinc related issues! Update: I've emailed the folks that manage the funds to check how much money we get from the donate button here, and if it goes directly to boinc improvement. I know about ~2 years ago we had a major upgrade to robetta (the public server, which uses rosetta@home).

Is it possible to see a reporting about donations/grants/whatsoever and how they use money? Or these numbers are not public?
It's not polemic, only curiosity


Ok, i do a little research by myself and i find:
In June 2014 the IPD established its Translational Research Center, which is operated with a $1.4 million Opportunity Grant from the Life Sciences Discovery Fund (LSDF). The LSDF funding to the IPD was matched 4-fold by generous contributions from private donors ($3.2 M), UW ($1.4 M), and the Washington Research Foundation ($1 M).
Dr. Pultz was recently awarded a competitive $250K proof of concept matching grant from the LSDF to conduct animal efficacy studies and safety testing of the lead KumaMax variant, an effort which is being matched by an additional $176K in philanthropic donor funding.
In the last update, we mentioned that Governor Jay Inslee’s 2014 Supplemental Budget (4-13-13) included $1 million to support the IPD mission, enabling the UW to recruit a talented computational biologist, Dr. Frank DiMaio
This January, the IPD was awarded $12M in funding by the Bill & Melinda Gates Foundation to support vaccine research.
May 15, 2014. With a very generous $8 M gift from the Washington Research Foundation (WRF), the IPD has launched the WRF-IPD Innovation Fellows Program supporting research partnerships between the IPD and other Seattle-area research institutes or UW departments


Yeap, my 20 dollars are very important.


While those numbers might seem impressive, there's no indication of how many of those donations are earmarked directly to the Rosetta@Home program fund. At the same time, $28.426M is still very much a shoestring budget in the bioinformatics world and the things people are stomping their feet for on these forums may not make the cut in terms of priorities when slicing up this particular pie; All said, the fact remains that your $20 donation may be the loudest voice you have in advocating for something like a server upgrade, etc.
19) Message boards : Number crunching : Credit granted pending stack (Message 80368)
Posted 14 Jul 2016 by krypton
Post:
Thanks for the reports! We've restarted the project this morning.
20) Message boards : Number crunching : RALPH@Home ? (Message 80335)
Posted 10 Jul 2016 by krypton
Post:
Thanks for the report! I had the powers-above restart it, but forgot to reply here.
Still down...



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