Rosetta-News

[Der Diplomat]

Was ist an einem Podcast schwierig?
Außer, dass jemand eine Datei besprechen muss.
(Hihi, eine Datei besprechen )
Haben unsere Vereinssserver (bzw. des Hosters) die Puste die Podcasts zu hosten? Oder kann man dafür die kostenlosen Dienste von YouTube etc... verwenden?

[Dennis Kautz]

Ich denke, Youtube wäre besser... einfach, weil wir dort ein breiteres Publikum haben, als die üblichen Verdächtigen, die unsre Seite sowieso schon kennen.

[Maion]

Es gibt wieder Neuigkeiten:

For those who didn't see it, I'm reprinting below Rhiju's post describing the science behind the new RNA work units. Also--I hope you are enjoying the new graphics! It is now much easier to see the sidechain packing problem that your calculations are trying to solve. Watch carefully and you will be ready to win at the interactive game version in which you will be able to guide the protein into a better packed lower energy structure. A super computer scientist, Adrien Treuille, is now working on this and we hope to have a prototype out for you to play with in several months.

Here is Rhiju's post:

Rosetta@home has been used to predict protein structure and design new
proteins. Improving protein enzymes that process carbon dioxide,
designing a protein vaccine for HIV, and understanding the basic
physical principles underlying protein folding are all being carried
out in the workunits that you are currently running or will be running
in the near future. Why study this other biopolymer, RNA?

Indeed, for a long time, RNA was mainly thought of as a passive
messenger in the cell, sort of a temporary copy of DNA (the storehouse
of information in our cells) from which proteins were translated. That
view changed dramatically in the 1980s with the discovery that RNA can
do more than carry information -- it can fold up into intricate
stuctures and carry out chemical reactions, just like proteins can. In
fact, its ability carry out the function of both DNA and proteins
provide a convenient answer to the chicken-and-egg problem of how
proteins and DNA evolved ... RNA came first! For more on the RNA
world, see
Wikipedia,
for example.

In addition to being important in early life, the known roles of RNA
in our present cells are currently exploding. From small RNAs
("Breakthrough of the Year" in Science in 2002, and the subject of last year's
Nobel prize winning work) to the catalytic heart of the ribosome, RNAs
play fundamental roles in biology that go beyond merely passing
messages. From a medical standpoint, most antibiotics target RNA in
the ribosome; the genomes of HIV, SARS, and other retroviruses are
composed of RNA; and RNA "aptamers" are beginning to be used as easily
evolvable drugs.

With Rosetta, we are making a serious stab at solving one of the most
fundamental puzzles for this interesting molecule... how RNA
folds. We're starting small, though some of the molecules you'll see
on our screen are important pieces of HIV. The hope is that we'll be
able to soon predict the folds of bigger RNAs -- a challenge that is
all the more important because RNA structures are difficult to solve
experimentaly. In the further future, using these structure prediction
tools to design or enhance ribozymes (that is, RNA enzymes) for
medical therapy is not that far-fetched ... stay tuned!

Quelle

[Michael H.W. Weber]

Sieht aus, als bekäme unser geplantes DC-Projekt Konkurrenz.

Michael.

[dago.net]

Vielleicht hätte ich einen neuen thread machen sollen, aber ich dachte ich hänge es mal hier an:

http://boinc.bakerlab.org/rosetta/forum ... hp?id=3036

Hat jemand die gleichen Probleme? Scheint nur den download neuer WUs zu betreffen, der upload klappt wohl noch.

[VadderSchlumpf]

hi

bei mir versucht er auch schon ewig was runterzuladen und es klappt nich... noch seh ichs nich so eng, hab noch einiges zum abarbeiten.

aber gut, dass ich das problem nicht als einziger hab

lg,
tim

[RT1984]

Kann euch beruhigen, mir gehts ganz genauso. Da zahlt es sich aus, wenn man ein zweites Projekt laufen hat.

[Der Diplomat]

Ich hatte auf einem Rechner im Verein Rosetta abgestellt, weil ich ständig Fehler erhalten hatte. Ich kann mir vorstellen, dass die die Zugänge abgestellt haben, weil die Wutzen alle fehlerhaft waren...
Wir werden es sicherlich bald erfahren.

[arminius]

There's an issue with the external interface for the download servers. I sent a message out to our sys admin. This, indeed, has happened before and we'll look into what's causing the instability. In the mean time, boinc.bakerlab.org will handle the downloads.

(Posted 29 Mar 2007 18:45:59 UTC)

[dago.net]

Scheint wieder alles zu laufen (der rote Stau in BoincView ist jedenfalls weg). Es gibt doch immer wieder Idioten, die sich aufspielen, aber wenn sich nicht so viele Leute beschwert hätten, wäre man vielleicht erst später auf das Problem aufmerksam geworden. Es lebe die Community.

http://boinc.bakerlab.org/rosetta/forum ... true#38685
http://boinc.bakerlab.org/rosetta/forum ... true#38704

Greetz
dago

[Der Diplomat]

Neues von David Baker

[Der Diplomat]

Die Version 5.59 ist draußen.

Rosetta@home is at version 5.59. There are several new features:

1. There were issues for Rosetta@home on a small fraction of Macs for the last couple updates. This appears to be fixed. Thanks to all the Mac users who posted here, attached their computers to Ralph, and helped us resolve this issue!

2. The "percentage complete" steadily increases every five seconds during the workunit. It should be reasonably accurate except in the occasional workunit that goes a little over your preferred CPU run time; this happens when your workunit has an exceptionally promising score, and Rosetta decides to continue crunching. In those cases, the percentage complete is slowly updated so that the estimated time to completion stays around 10 minutes.

3. The "estimated time to completion" is occasionally a little off at the beginning of the workunit; no need to worry about it!

4. We have implemented a more accurate energy function for RNA, thanks to your efforts with the previous apps.

5. We have implemented a new mode of Rosetta that simultaneously simulates folding and docking of two symmetric chains. This was inspired by a protein whose crystallographic data we are trying to "phase" as well as the many proteins in Nature that form symmetric dimers.