ARGOMENTO:

Gabry ha scritto:

ciao a tutti ci sono delle wu credo quelle che cominciano con homopt che mi vanno spesso in errore... capita anche a voi?

Confermo, almeno ci vanno subito e non sprecano praticamente niente di CPU time...

Dal forum, uno degli sviluppatori

Hi,
I'll be resubmitting the *gbnnotyr* protein design trajectories to boinc over the next few hours. The tests I ran on ralph showed that the checkpointing issue is resolved. To make sure that there are no other issues, I will submit these trajectories 'slowly' starting with a modest sized batch, and according to the responses I get on the thread I will increase the number of work units over the next few days. Please keep me posted about these problems. Your reports have been invaluable in tracking this problem down!

Mi aspetto lavoro su ralph....

Grandissime news dal forum di Rosetta!

David Baker:

We got some good news today. A manuscript that many of you contributed to through Rosetta@home was just accepted for publication in Science magazine, perhaps the most widely read scientific journal. The paper shows that accurate structures can be calculated using Rosetta for proteins up to 200 amino acids long if even a small amount of experimental data (from NMR experiments) is available to guide the search. This is an exciting advance because it could make it very much faster and easier to experimentally determine protein structures. Thanks everybody for your contributions to this work, and to our ongoing research efforts!

Bravi, bravi, bravi e basta!!

Vorrei vedere workunits che vadano sotto gpu!

Bravissimi quelli di Rosetta, è una fortuna avere gente così!

Hobbista ha scritto:

Vorrei vedere workunits che vadano sotto gpu!

Ehhh, non sei il solo!!!
Ma mi sa che devi armarti di molta pazienza....

non c'è che dire... sempre grandi!!!!!!!

Prendo spunto da questo post di V.D. su Rosetta:
www.boincitaly.org/i...emid=2&func=view&catid=10&id=42003#41975

Allo stato attuale le mie wu girano a poco più di 2 ore su un i7 @ 3,4Ghz (le prime che mi inviavano erano leggermente più lunghe), in che modo posso modificare questo tempo?

Ciao, se non riesci a capire come fare leggendo qui dimmelo che sistemo quella pagina (e ti spiego come fare ovviamente).

Ragazzi anche io ho una curiosità, ma quanti pc ci vogliono per fare un rac di 10000??

Dipende con cosa... Per arrivare solo a quel rac ne basta anche uno solo, con una buona schedozza video acceso un paio d'ore al giorno sui progetti giusti. Oppure un paio di i7 24/24 su rosetta... Non è univoca la risposta...

7D9 ha scritto:

Ciao, se non riesci a capire come fare leggendo qui dimmelo che sistemo quella pagina (e ti spiego come fare ovviamente).

No mi sono perfettamente chiare le procedure ed anche il senso del CPU run time: l'unica cosa è non so come si potrebbe comportare l'account manager che uso per gestire i miei progetti, visto che in tal caso dovrei aggiornare manualmente il client e quando l'ho fatto con SETI mi ha mandato in palla tutto.

DarkSky82 ha scritto:

No mi sono perfettamente chiare le procedure ed anche il senso del CPU run time: l'unica cosa è non so come si potrebbe comportare l'account manager che uso per gestire i miei progetti, visto che in tal caso dovrei aggiornare manualmente il client e quando l'ho fatto con SETI mi ha mandato in palla tutto.

puoi anche evitare di aggiornare manualmente
il manager si aggiornerà automaticamente alla prima comunicazione com il server

Era un po' che non scaccolavo Rosetta... è normale che una WU prenda 500MB???

Non so quanto prendesse ogni wu, ma ieri con 4 rosetta, 1 gpugrid e win7 in idle erano occupati 2,8-3 gb di ram... Ora, win ne occupa 0,7-0,8, il resto era tutto di boinc...

A me si aggirano intorno ai 200-250 MB a WU.

Sarà stata una WU particolare, anche perchè arrivata al 20% il consumo di RAM è sceso a 150MB...

7D9 ha scritto:

A me si aggirano intorno ai 200-250 MB a WU.

Idem.
Alcune singole wu, però, mi sembrano più "esose"....

Due interventi interessanti dal team di rosetta...

Hi all,
my name is Tim Whitehead and I've been a postdoc in the Baker lab for about a year. My projects deal with the prediction and design of protein-protein interfaces. In this thread, Sarel has explained the design problem for protein-protein interfaces. Progress in this area can drive the next generation of treatments against pathogens like Mycobacterium tuberculosis or Influenza.

I have been working with Sarel on the design and experimental characterization of designs that target disparate proteins on both pathogens. We have a couple of successes thus far, which we are extremely excited about, but need to have better and better designs to show the validity of our design approach.

In this thread, Sarel has explained why and how we are targeting Influenza by designing a protein inhibitor of a protein that is displayed on the surface of the virus.

For Tuberculosis, our task is slightly more difficult. TB is caused by a bacterium called Mycobacterium tuberculosis. The bacteria is encased in a waxy coating of mycolic acid, which hurts our body's ability to expell the bacterium (for more information, see en.wikipedia.org/wiki/Mycobacterium_tuberculosis).
Instead of designing an enzyme that could degrade the coating, we are targeting a protein that is involved in the `synthesis` of mycolic acid. You may have already seen BOINC descriptions that say "docking of designs against 2CGQ" - 2CGQ is the protein that we are trying to inhibit. I am hoping that your contribution from ROSETTA@HOME will give us the increased quality of our designs that we need. Thanks for the help!

My name is Eva-Maria Strauch and I am one of the post-docs in the Baker lab working on the design of protein-protein interactions. I am very excited about having the possibility to run on R@H, thanks to your generous contributions! Protein design requires a lot of sampling since there are so many many different possibilities to be considered carefully. This will work out now faster with your help!

I am currently designing proteins to bind to a model system which we use to calibrate our computational protocols. This particular target is the back end of a human immune-system antibody (Fc fragment, which is what you will see under the work unit descriptions en.wikipedia.org/wiki/Fc_region). The cool thing about Fc is that nature provides us with several proteins that bind to it, hence it taught us very important lessons on how to design possible binding proteins to it. We now want to see whether we've figured this one out and can mimic nature's ability to come up with binders towards this target. Success will further contribute to the optimization of our protocols to generate several protein-based inhibitors to attack cancer and infectious diseases. Questions we want to answere with this design project are: How well do we perform in comparison with nature? and if we understood all the information we got out of those native interactions, are we able to produce several de novo binding proteins that mimic the atomic interactions seen with native interaction Fc has with different proteins? This project will contribute to our understanding of how proteins recognize one another. Promising designs will be experimentally verified and also further characterized to see how well we performed, and what was possibly missing that we should include into our computational design protocol.
Thanks again for your contribution!