ARGOMENTO:

7D9 ha scritto:

akd ha scritto:

Mi sono sempre chiesto che vantaggi dà questa opzione... Non mette a rischio i dati già calcolati in caso di crash del sistema?

In passato abbiamo notato che la non selezione di questa opzione era causa della maggior parte degli errori al riavvio di BOINC. Il motivo alla base non lo so.

Ma dal sito di rosetta :

boinc.bakerlab.org/rosetta/forum_thread.php?id=669

Why should I set BOINC to keep application in Memory?

This is less of a problem now that "Checkpointing" is more frequent for the Rosetta application.

However, If the application is removed from memory during an application swap, it will loose the work performed since the last checkpoint. In the case of Rosetta the checkpoints occur each time the percentage advances. If you do not keep the application in memory, and you set the swap interval to less than the time it takes your machine to reach a checkpoint, the work units can appear to be 'hung".

This is why the recommended configuration is to set "Keep applications in memory" to "YES". As an added protection, it is also recommended to set a value of nominally 120 min between application swaps. Either of these settings alone has been shown to reduce the problem, but they can be used togeather for better results

It should be noted that ALL BOINC projects suffer from loss of CPU cycles if the applications are not kept in memory. Any work that is not saved at a checkpoint before a swap, is lost when a swap occurs. On applications like Rosetta and Climate prediction this loss is significant (15 to 30 min). On projects like Predictor, SETI and Einstein, the loss is less but it is still there (usually 60 seconds using the default setting for writing to disk). People who wish to squeeze every cycle out of their machine, usually keep applications in memory for this reason.

It is important to note that the memory we are talking about is not actual RAM but in fact is virtual memory (on disk), so the actual impact of this is not that significant. In addition you can adjust how much memory is used by the application in this regard.

e ancora :

boinc.bakerlab.org/rosetta/rah_requirements.php

If you are running multiple BOINC projects using the BOINC Manager, we recommend setting your general preferences to "Leave applications in memory while preempted." To do this, after creating an account, do the following:

1. Click the "Your account" link on the main home page under "Returning participants" or click the "Participants" link above.
2. Login if you haven't already.
3. Click the "View or edit general preferences" link on your account page.
4. Click "Edit preferences".
5. Select "yes" for the "Leave applications in memory while preempted?" option.

Please refer to the Questions and answers forum for more information.


Quindi ?

sarebbe meglio attivarla ( di default non lo e' )?
Da pero' problemi ?

Beh.. I post che hai riportato confermano quello che già stavamo dicendo.
Si, è meglio impostarla su yes, tanto non dà nessun problema.

Gran bel post, grazie!

Altri articoli in fase di stesura:

The third manuscript I am working on is called "Blind docking of pharmaceutically relevant compounds using RosettaLigand". This describes the current state of our efforts towards improving methods for designing new small molecule drugs to combat diseases. The challenge addressed by this paper is to predict how drug molecules bind to proteins--determining how they bind is necessary to improve their efficacy and to identify good candidate molecules in the first place. In two earlier papers we had described the incorporation of small molecule modeling into Rosetta to create the new RosettaLigand drug docking methods, and tested the method on publicly available data sets. However, many of you will not be surprised that much of current drug discovery is being carried out in pharmeceutical companies, and the compounds they are testing are generally not made public (they are akin to trade secrets). We wanted to learn whether RosettaLigand was successful in docking drug compounds in actual drug discovery efforts, and were very fortunate when a large drug company agreed to let Ian Davis, who is working on the project, visit one of their company sites and analyze the results they had gotten with RosettaLigand on their private set of compounds. The results are described in this paper and are very encouraging, not only does RosettaLigand appear to be one of the best current methods for this crucial step in drug design, but also there are some clear avenues for improvement (which weren't evident with the public datasets) which we are now starting to work on.


The fourth manuscript describes rosetta@home predictions in CASP8. as you know with your great help we were again the top ranked group in CASP this year. The manuscript begins:

The CASP8 experiment provided an invaluable opportunity to extensively benchmark the Rosetta protein structure prediction method on a wide range of comparative modeling and free modeling targets. For the targets for which a sequence-detectable structural template existed, target-template sequence alignments were generated, and the Rosetta rebuild and refine protocol was used to generate low energy models. For the small number of targets for which a reliable template could not be identified modeling was carried out using the Rosetta de novo modeling protocol. All targets were subjected to extensive high resolution refinement with the physically realistic Rosetta all-atom forcefield using Rosetta@home.

this one has a due date--March 15--so we have to hurry up a bit!

7D9 ha scritto:

Altri articoli in fase di stesura:

Ottimo. Gli articoli sono importanti (all'estero) anche per ottenere finanziamenti!

Ed ecco il quinto articolo che spero uscirà a breve, quello che mi ha colpito più di tutti:

The fifth manuscript describes a very exciting recent discovery made in collaboration with another research group. As many of you know, a large number of diseases, including Alzheimer's, are associated with the folding of a protein not into its normal active state but instead into long repeating fibrils. These are called "amyloid fibrils" and the associated diseases are referred to as "amyloid" diseases. We used Rosetta to design molecules predicted to block the formation of the fibrils, and, strikingly, when these molecules are added to the disease state protein under conditions where it normally forms fibrils, none are formed. We are very excited about this amyloid blocker, but as always I must stress that there are a lot of steps before a finding like this leads to an actually distributed drug.

Aspetteremo di vedere quando e su che riviste saranno pubblicati.

Anche il sesto articolo sembra interessante, anche se, come dice David stesso, è un progetto long-term....

The sixth manuscript describes our recent results on designing new DNA cutting enzymes that can cut the DNA double helix at very specific target sites. The enzymes we design only cut at one particular 20 base sequence. Remember that DNA is made of four different bases, A T G and C so a particular 20 base site might for example be AGAATAGGATCCAGATCGTC. This long a sequence is extremely unlikely to occur more than once in the human genome, so if we design an enzyme to cut at a particular place in the genome it is likely to cut only at that site (of course we can check this because the sequence of the human genome is known).

why would we want to do this? suppose you have a mutation in a gene and it is making you sick. if we can make an enzyme which cuts near the site of mutation and introduce this enzyme and a "correct" copy of the gene into your cells, the enzyme will cut the DNA and the cut will be repaired likely by copying the correct version we have added as well (cells repair breaks in DNA by copying the most closely related piece of DNA around). thus, with such enzymes we can potentially cure diseases by "gene therapy".

the manuscript describes progress towards this long range goal. we show we can design new enzymes that cut at new sites, and by examining how they work in detail we reveal some pretty big surprises in how the naturally occurring enzyme works which are fascinating in their own right and provide considerable insight into how to achieve the longer term goals of using redesigned enzymes for gene therapy.

Ed ecco il settimo articolo:

The seventh paper is also related to your CASP8 predictions. The assessors asked us and a couple of other groups who made models that were geometrically and energetically nearly indistinguishable from native structures to write a paper describing how we were able to consistently able to generate physically plausible structure models. This was much less work for me than the preceding six manuscripts--I had only to describe the key concepts behind rosetta@home and the search for very low energy structures that are familiar to those of you who follow the screen saver from time to time.

Nei prossimi mesi vedremo un po' bel po' di pubblicazioni.
Sono ansioso di vedere su che riviste usciranno.
Il secondo articolo è già stato accettato dalla "Proceedings of the National Academy of Sciences", che non è di certo il giornalino scolastico.

Prof Baker:

Not all the writing I do is research papers, I have to write grants to get research funding as well (unfortunately). Today I'm putting together a proposal to use Rosetta to computationally design compounds which block the formation of the amyloid fibrils which accumulate in a number of different diseases (this is a followup on the fifth manuscript described below). My collaborator and I will send this proposal to the recently announced NIH "Challenge Grant" program, part of the recently passed federal stimulus package.

Nessuno che li traduca?

Venturini Dario ha scritto:

Nessuno che li traduca?

Intendi tradurre queste brevi descrizioni o gli articoli interi (che li vedo abbastanza tecnici)?

Direi le brevi descrizioni

boboviz ha scritto:

Venturini Dario ha scritto:

Nessuno che li traduca?

Intendi tradurre queste brevi descrizioni o gli articoli interi (che li vedo abbastanza tecnici)?

come dice Dario, le descrizioni!!

gli articoli, se escono su riviste specializzate, sono "a pagamento" almeno a breve termine!! Non puoi rilasciarli gratuitamente senza autorizzazioni della rivista e dell'autore!

Da martedì dovrei avere un pelo di tempo libero in più.
Li traduco io se non lo fa nessun altro prima.

7D9 ha scritto:

Da martedì dovrei avere un pelo di tempo libero in più.
Li traduco io se non lo fa nessun altro prima.

Mi sa che puoi già segnare sull'agenda: traduzioni descrizioni

Prof Baker:

Rosetta@home has received a substantial monetary contribution from an anonymous donor! Following the suggestion of the donor, the University of Washington has used the money to start a special “Rosetta@home fund” that will be used to pay part of David Kim’s salary (David is the architect of Rosetta@home and the person who keeps the project running), upgrade the servers as needed, and allow us to make more rapid progress on the disease-releated research Rosetta@home is carrying out. If you would like to make a (tax-deductible) contribution to the project, the link is Rosetta@home fund . David will be adding a link to this from the Rosetta@home home page in the next day or two. Thank you for your contributions to the project!

Questa è una notizia che mi ha fatto veramente piacere. Sono contento di sapere che c'è ancora gente con i soldi che fa delle donazioni. E soprattutto anonime.

Chissà se le donazioni sono deducibili anche da noi (specie verso l'estero)...

7D9 ha scritto:

Prof Baker:

Rosetta@home has received a substantial monetary contribution from an anonymous donor!

Questa è una notizia che mi ha fatto veramente piacere. Sono contento di sapere che c'è ancora gente con i soldi che fa delle donazioni. E soprattutto anonime.

Già.
Sarei curioso di sapere a quanto corrisponde il "substantial"...

akd ha scritto:

Chissà se le donazioni sono deducibili anche da noi (specie verso l'estero)...

alcuni dicono di no

Proprio quel post avevo in mente... Era x vedere se anche altri ne sapevano qualcosa...