Posts by Zarck

1) Message boards : Number crunching : REQUEST ACCESS TO NVIDIA PARABRICKS (Message 92204)
Posted 24 Mar 2020 by Zarck
Post:
NVIDIA Provides Researchers Free Access to Parabricks to Speed ​​Up Search for Covid-19 Vaccine

geek culture By Gregori Pujol March 24, 2020 at 9:05 am
 0 comments
The availability of Parabricks, the GPU-optimized bioinformatics software suite dedicated to genomic analysis, will help accelerate research on the understanding of the new coronavirus and the fight against Covid-19.

A real race against the clock is underway and mobilizes players from around the world. In particular, those of health and research. In response to the pandemic, NVIDIA has decided to share with researchers working on it, software tools capable of speeding up the discovery process in order to better understand the coronavirus and provide faster responses.

For the past few days, NVIDIA has been providing a free 90-day Parabricks license for any researcher involved in the fight against the coronavirus. Covering the entire GATK (Genome Analysis Toolkit) pipeline, which is the industry standard for identifying SNP (Single-nucleotide Polymorphysm) and DNA comparisons, Parabricks is taking advantage of GPU acceleration to reduce lead times. genomic analysis up to 50 times.

All researchers with access to NVIDIA GPUs can complete this form to request a free Parabricks license. For researchers working on Oxford Nanopore long read sequence data, a set of GPU-optimized software tools is available on GitHub. In addition, the following applications immediately integrate NVIDIA GPU accelerations: Medaka, Racon, Raven, Reticulatus, Unicycler.

Researchers are sequencing the coronavirus and genomes of people with Covid-19 to better understand, among other things, the spread of the disease, and to identify the populations most at risk; but genomic analysis takes time and requires computing power.

Parabricks software, whose team joined NVIDIA in December 2019, is able to reduce the time required to call variants on human whole genome sequences (WGS), reducing it from a few days to less than one time, using only one server. Given the unprecedented spread of the pandemic, achieving results in hours rather than days can have a very significant impact on the understanding of the virus, its evolution and, therefore, on vaccine development.

NVIDIA is also mobilizing its ecosystem of partners in this urgent effort to help the research community. Discussions are currently underway with cloud service providers and centers with supercomputers in order to provide additional computing resources and offer free access to Parabricks solutions on their platforms.
2) Message boards : Number crunching : REQUEST ACCESS TO NVIDIA PARABRICKS (Message 92203)
Posted 24 Mar 2020 by Zarck
Post:
https://www.nvidia.com/en-us/docs/nvidia-parabricks-researchers/?cjevent=411ecc336db111ea8001002b0a18050d

@+
*_*
3) Message boards : Number crunching : Waiting for memory (Message 89275)
Posted 14 Jul 2018 by Zarck
Post:
I have 11 GB of free ram, and the Roasetta project shows me "Waiting for memory" a solution? Thank you.

@ +
*_*
4) Message boards : Number crunching : Fan speed with Rosetta (Message 88098)
Posted 18 Jan 2018 by Zarck
Post:
Now when I run Rosetta my fans start to run faster, I do not have this problem with WCG for example, a solution? Thank you in advance for your answer.
5) Message boards : Rosetta@home Science : Cancer, healthy and normal cells are it really? (Message 81388)
Posted 29 Mar 2017 by Zarck
Post:
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; @+ *_*
6) Message boards : Cafe Rosetta : Funding (Message 80651)
Posted 14 Sep 2016 by Zarck
Post:
You have a funding problem to change your servers? you try Bitcoin utopia?

http://www.bitcoinutopia.com/list-of-campaigns/#.V9nGP3jFRq4

http://www.bitcoinutopia.com/create/#.V9nHKHjFRq4

@+
*_*
7) Message boards : Number crunching : impossible to return the Rosetta units. (Message 80282)
Posted 24 Jun 2016 by Zarck
Post:
I get Rosetta units, they are calculated, but could not return the results, I have no problems with other projects as WCG GPUGrid etc. a solution ? thank you in advance for your reply @ + *_*

Je reçois des unités de Rosetta, elles sont calculées, mais impossible de renvoyer les résultats, je n'ai pas problèmes avec d'autres projets comme Wcg, Gpugrid etc. une solution ? merci. @+ *_*
8) Message boards : Number crunching : By the time the display of calculations being proteins are very dark (Message 80171)
Posted 12 Jun 2016 by Zarck
Post:
By the time the display of calculations being proteins are very dark Why?

https://www.dropbox.com/s/wq4tia9xzrblvb9/Capture%20d%27%C3%A9cran%202016-06-12%2015.48.46.png?dl=0

@+
*_*
9) Message boards : Number crunching : Impossible for me to return results... (Message 78662)
Posted 1 Sep 2015 by Zarck
Post:
Boinc not send Rosetta units calculated...

I stopped my participation in your project...

Boinc 7.6.9.

http://boinc.berkeley.edu/dl/?C=M;O=D

@+
*_*
10) Message boards : Number crunching : 150 000 $ (Message 77526)
Posted 30 Sep 2014 by Zarck
Post:
http://www.nvidia.com/object/global-impact-award.html

11) Message boards : Number crunching : Personalized the graphic display (Message 77017)
Posted 16 Jul 2014 by Zarck
Post:
I wish personalized the graphic display(posting) of Rosetta's proteins, when we click " to show graphs " the window has no good position, nor the good size, is it possible to modify these parameters? Thank you for the answer.

Je souhaite personnalisé l'affichage graphique des protéines de Rosetta, lorsque l'on clique sur "montrer les graphiques" la fenêtre n'a pas la bonne position, ni la bonne taille, est il possible de modifier ces paramètres ? merci pour la réponse.
12) Message boards : Number crunching : Cuda 6 -> Easy GPU support for Rosetta ? (Message 76631)
Posted 17 Apr 2014 by Zarck
Post:
Cuda 6 -> Easy GPU support for Rosetta ?

http://on-demand.gputechconf.com/supercomputi...6%20-GPU-Acceleration.pdf

https://developer.nvidia.com/cuda-toolkit

@+
*_*
13) Message boards : Number crunching : Unified Memory in CUDA 6 (Message 76514)
Posted 9 Mar 2014 by Zarck
Post:
http://devblogs.nvidia.com/parallelforall/unified-memory-in-cuda-6/

Soon available in Boinc ?

Bientôt disponible dans Boinc ?

@+
*_*
14) Message boards : Number crunching : Unified memory by AMD. CPU + GPU. (Message 76513)
Posted 9 Mar 2014 by Zarck
Post:
http://developer.amd.com/wordpress/media/2012/10/hsa10.pdf

The subject seems timely for everyone,

Le sujet semble d'actualité pour tout le monde,

@+
*_*
15) Message boards : Number crunching : AMD Mantle VS Microsoft Direct X12 (Message 76512)
Posted 9 Mar 2014 by Zarck
Post:
"Microsoft hints that DirectX 12 will imitate Mantle, but AMD insists its API has a bright future"

http://www.extremetech.com/gaming/177407-microsoft-hints-that-directx-12-will-imitate-and-destroy-amds-mantle

@+
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16) Message boards : Number crunching : Harlan is a high level language for general purpose GPU computing (Message 75827)
Posted 8 Jul 2013 by Zarck
Post:
https://github.com/eholk/harlan

Used for Rosetta ?

@+
*_*
17) Message boards : Number crunching : OpenMM (Message 75623)
Posted 18 May 2013 by Zarck
Post:
I could be wrong, but Rosetta "could" be part of the variety of software available there. Rosetta doesn't really cure anything per se, it's more a powerful tool to help researchers find cure in a more efficient way. We in part make this tool better.

This is why I crunch for rosetta... I help rosetta and rosetta helps out whoever uses it to find a cure (The human proteome folding @ WCG uses rosetta I believe to fold).


I have a GeForce TITAN, there is there any GPU units for my card?

Tank you for you reply.

@+
*_*

http://ambermd.org


No Rosetta software does not use GPU at all, THE END.



Tank you for you reply;

@+
*_*

https://developer.nvidia.com/category/zone/cuda-zone

http://developer.amd.com/tools-and-sdks/heterogeneous-computing/
18) Message boards : Number crunching : OpenMM (Message 75607)
Posted 12 May 2013 by Zarck
Post:
I could be wrong, but Rosetta "could" be part of the variety of software available there. Rosetta doesn't really cure anything per se, it's more a powerful tool to help researchers find cure in a more efficient way. We in part make this tool better.

This is why I crunch for rosetta... I help rosetta and rosetta helps out whoever uses it to find a cure (The human proteome folding @ WCG uses rosetta I believe to fold).


I have a GeForce TITAN, there is there any GPU units for my card?

Tank you for you reply.

@+
*_*

http://ambermd.org
19) Message boards : Number crunching : OpenMM (Message 75585)
Posted 8 May 2013 by Zarck
Post:
Rosetta support OpenMM ?

http://

https://simtk.org/xml/index.xml

@+

*_*
20) Message boards : Number crunching : AMD CodeXL, tools for Rosetta ? (Message 74055)
Posted 19 Oct 2012 by Zarck
Post:
http://developer.amd.com/tools/hc/CodeXL/pages/default.aspx#download

http://developer.amd.com/tools/hc/CodeXL/pages/default.aspx

@+
*_*


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