ARGOMENTO:

Commanders ha scritto:

Ragazzi, capita solo a me oppure succede anche a voi che durante lo scarico delle WU il download delle stesse si ferma? Non è una cosa che noto su un solo pc, sia con l'adsl lenta che su una veloce, ma anche su pc diversi. Durante il download delle WU, non ad una % fissa, le stesse si fermano per poi ripartire dopo un bel po. Per darle il colpetto, devo sospendere la rete e poi metterla disponibile e solo così ricomincia il download, ma a volte si ferma poco dopo. Questa cosa capita solo con Rosetta con gli altri progetti direi di no anche se non hanno lo stesso peso delle WU di Rosetta.

Ho già notato pure io questo comportamento strano durante lo scarico delle nuove WU...non ho idea a cosa sia dovuto...

Commanders ha scritto:

Ragazzi, capita solo a me oppure succede anche a voi che durante lo scarico delle WU il download delle stesse si ferma? Non è una cosa che noto su un solo pc, sia con l'adsl lenta che su una veloce, ma anche su pc diversi. Durante il download delle WU, non ad una % fissa, le stesse si fermano per poi ripartire dopo un bel po. Per darle il colpetto, devo sospendere la rete e poi metterla disponibile e solo così ricomincia il download, ma a volte si ferma poco dopo. Questa cosa capita solo con Rosetta con gli altri progetti direi di no anche se non hanno lo stesso peso delle WU di Rosetta.

Si, si. E' un po' di tempo....
Quasi quasi faccio un post sul loro forum

Ma che significa il link "Reports and plots of results from active work units" che vedo nella pagina utente di Rosetta?
Ogni volta che ho provato a cliccarlo dopo un bel po' di attesa ricevo sempre un "Sorry, the data requested does not exist."

Speriamo che la nuova versione del client risolva il problema delle wu cryo_
A me vanno in errore tutte (e anche a molti sul forum)

Rick! ha scritto:

Ma che significa il link "Reports and plots of results from active work units" che vedo nella pagina utente di Rosetta?

Praticamente faceva vedere i "risultati" delle simulazioni che avevi condotto per ogni singola wu...
Se non ricordo male era possibile visualizzare la struttura della wu calcolata

ciao a tutti!
ho avuto un problema con l' invio di una wu anche se poi dopo l' ha inviata, il messaggio di errore era:

error reported by file uploaded server: EOF on socket read: asked for 16382, got 12604

cosa vuol dire?
grazie

Gabry ha scritto:

ciao a tutti!
ho avuto un problema con l' invio di una wu anche se poi dopo l' ha inviata, il messaggio di errore era:

error reported by file uploaded server: EOF on socket read: asked for 16382, got 12604

cosa vuol dire?
grazie

si aspettavano 16382 byte invece gliene hai inviati 12000 e rotti.

ah ecco che strano però... anche perchè dopo un pò lo ha inviato

Alcune novità sui progetti di Rosetta:

To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4. We synthesized these proteins, tested them, and identified one that sticks to Mdm4 about 75 times better than it sticks to Mdm2. We sent this protein, called Mdm4 Binder 17 (MB17) to St. Jude's Childrens Research Hospital so the cancer experts could test it in cancer cells. So far, they have confirmed that MB17 strongly prefers to stick to Mdm4 over Mdm2 (about 170 times better, in their experiments). They also found that MB17 works correctly inside living cells, a major milestone for a designed protein. In the mean time, we've created new versions of MB17 that preference Mdm4 even more (about 370 times more than Mdm2), some that pinch-hit and prefer Mdm2 instead of Mdm4 (about 120 times more than Mdm4), and some that like both Mdm4 and Mdm2 equally well. The folks at St. Judes are starting to work with these improved variants as well. This is the first time that the cancer research community has ever had a tool to knock out just Mdm4 while leaving Mdm2 alone, so naturally, the folks at St. Jude's are pretty excited. They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise. I'm sorry for the long delays between posts. Things are pretty busy around here. For those of you seeing this thread for the first time, I've re-posted below what I posted previously about this topic:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work.

Ma quanto caspita mi piace questo progetto?????
Avessi un processore 3000 core.....

Qui invece un post in cui viene spiegato cos'è "l'energy function" in rosetta:

This is my first time posting here. My name is Patrick Conway and I'm a 3rd year graduate student in the Baker Lab. I'm working on improving the Rosetta energy function.

You might be asking "What is the energy function?" It's a very central aspect of Rosetta (and I'm not just saying that to justify my thesis). It is a set of mathematical equations that computes an "energy" for a given protein conformation. As a protein conformation changes, the energy can either go up or down. The reason that proteins nearly always take only one conformation is because that conformation is drastically lower in energy than any other possible conformation.

Our gold standard for benchmarking energy function performance is to compare native structures obtained from experimental xray crystallography and compare it to alternate conformations (decoys). The native should win out, but that doesn't always happen, which means I still have a job. As it is, our current default has been around for many years. In the past few years, there has been a lot of promising work on various aspects of the energy function. Now the developer community is undertaking an effort to consolidate these improvements into a new default energy function.

In order to make a meaningful comparison between natives and decoys for an energy function, we have to do a full scale search for the best decoys that Rosetta can find. This is a very expensive operation and the Rosetta@home horsepower is an extremely valuable resource for this project. At this point, we have 420,000 competitive decoys from 84 different proteins collected from an R@H run last year. For every change in the energy function, we do local optimization on these decoys in order to "update them," then we use a decoy discrimination measure that quantifies how well the native structure stands out from the decoys. We've had tremendous success in several areas: using flexible covalent bonds instead of rigid covalent bonds, implementing a new solvation model (FACTS), optimizing hydrogen bonding and electrostatics, developing more detailed assessments of aromatic ring orbital interactions, and using an improved sidechain conformation library.

However, we've been training our energy function on the entire data set and we need to do independent verification of our results using a new data set. We're hoping that it's not "too good to be true!" Some of you may have noticed "idealdead_test" (DEAD=Decoy set to End All Decoy sets) jobs running lately. These jobs are generating decoys for a set of 130 proteins. These proteins are relatively small monomers without ligands and with high-resolution experimental data (for our gold standard). I am generating abinitio predictions of these protein sequences with and without native fragment information. This allows me to cover a wide range of structures, from near native to far native. Once again, the key idea is to challenge the energy function to pick out the true native by generating competitive decoys.

If there is interest, I am willing to delve more into the process of improving the energy function and the changes that we are making.

In questo post, uno degli admin, spiega la creazione di proteine fluorescenti:

Hi, this is Lucas, I'm a postdoc in the Baker Lab working on enzyme design, design of ligand binders, and some design algorithms, especially applying very simple learning approaches to protein design.
For the last few months I have been working with Yakov Kipnis in the Baker lab on the design of completely de novo fluorescent proteins. If you are familiar with Green Fluorescent Protein and its relatives (Yellow, red, etc.) you know that these proteins are workhorses of modern biology. They make very small sub-microscopic things visible inside a cell or tissue, and work on these was awarded a Nobel prize a couple of years ago to Roger Tsien and co-workers.
Now with the power of recent advances in Rosetta in the design of de novo proteins we are trying to create entirely new, and better, fluorescent proteins. These will be brighter and last longer. They will be more controllable by the researcher, for example having the ability to turn "on" upon command, something that would make lots of biologists happy.
If we are successful, we hope that these will be useful for lots of cell biologists and biotechnologists. We envision their use for very sensitive medical testing and diagnostics, both ex vivo (for example blood tests) or in vivo. We are especially excited about those medical applications -- our proteins could make a tumor glow under UV illumination, so a surgeon can carefully remove it without damaging nearby tissue, but also without leaving any tumor behind. And we hope that once these proteins become available, lots of other medical applications -- that are currently imposible with existing fluorescent proteins -- will become feasible. We also think it would be incredibly beautiful and powerful to create a new class of glowing proteins.

Qui invece uno degli admin dice che saranno più attivi su twitter e di seguirli.

In an effort to adopt the technology of the early-twenty-teens, and to help facilitate communication, we're going to be sending more short updates about Rosetta at home science on our twitter feed @rosettaathome.
Many of you are already likely subscribed, but if you are interested please follow us on twitter. We'll of course continue to post longer-form updates here, but we're hoping to increase our frequency of updates to the user community through twitter.

rosetta è stato il "mio" primno progetto di scaccolo.Ho scoperto Boinc grazie ad un articolo che lessi non ricordo dove (nel web ...) si parlava di rosetta e del calcolo distribuito

bene o male ho sempre un pc con WU in corso per rosy

se svilupassero app GPU ne gioverebbero molto (quelli del progetto) ... pinageremo un pò noi per le tasche meno pesanti ... ma a lungo andare si spera sempre di aver contribuito a qualcosa di giusto

boboviz ha scritto:

Alcune novità sui progetti di Rosetta:

Ma quanto caspita mi piace questo progetto?????
Avessi un processore 3000 core.....

Sono d'accordissimo! Infatti è uno dei progetti su cui macino di più!

Importanti novità sulla home page di rosetta: adesso c'è il tweet!!

Signori, fermi tutti!
Questo è un post di un admin imboscato in un thread sui computer quantistici:

GPU computing is much closer to reality for Rosetta, as it is completely routine for many other compute tasks. There is actually some preliminary work on this for Rosetta from a couple of developers as many tasks are amenable to GPU algorithms. It is just preliminary, proof-of-concept, and the fact is that as an academic group there is not a ton of man-power around to devote to the coding task of fully implementing this work. Could happen soon though

Anche solo proof of concept ma è un passo avanti.
Fino a ieri dicevano che era impossibile, almeno adesso stanno studiando se è possibile!!

Rosetta che approda sulla GPU?
Finché non vedo non credo, speriamo non sia una

Sono allibito... E' la volta buona che piazzo una gpu seria!

Ma aspettiamo e vediamo...

Ho bisogno di un consiglio, qual'è la durata ideale da impostare per le WU di rosetta? Io ho impostato 4 ore, mi consigliate di aumentare o va bene così?

Mister_K ha scritto:

Ho bisogno di un consiglio, qual'è la durata ideale da impostare per le WU di rosetta? Io ho impostato 4 ore, mi consigliate di aumentare o va bene così?

Non c'è una durata migliore o peggiore. Dipende, per esempio, quante ore tieni acceso il pc al giorno.
Per quelli di rosetta sarebbe meglio avere tempi lunghi (da 6 ore in su), ma non è obbligatorio...