Posts by Christoph Jansen

21) Message boards : Number crunching : infection trojan in .exe rosetta ! (Message 43232)
Posted 5 Jul 2007 by Profile Christoph Jansen
Post:
Hi all,

I just went to the rosetta download site and downloaded the app in question. I checked it with an up-to-date version of G-Data Internet Security and got no positive. I of course looked up the Trojan you got and it is recognized by that antivirus program for some time now (couple of months or so).

So I'd venture to say it is a false positive. This happened to me on another BOINC app some time ago. I sent in the file to the manufacturer and two days later I got the confirmation it was clean and the false positive was mended in the next update which it then was.

But maybe you should also download the version that is currently lying on the server under http://boinc.bakerlab.org/rosetta/download/rosetta_beta_5.70_windows_intelx86.exe just to make sure it is identical with what you downloaded before and if F-Secure will issue a warning. Can't be careful enough, although it is impropable that someone temporarily exchanged it for an infected version and now changed it back.

Regards,

Christoph
22) Message boards : Number crunching : turn off hyperthreading? (Message 42982)
Posted 1 Jul 2007 by Profile Christoph Jansen
Post:
Hi everybody,

here is an article on the effect of hyperthreading under a number of different conditions, although it describes its effect in the special MATLAB environment. I thought after there has been so much discussion on the topic it might be interesting for some here to see a light shed on it from various perspectives.

Somewhen in the next week or so there will be a German version toohere, for now it is also in English until the final edits have been made.

Regards,

Christoph
23) Message boards : Rosetta@home Science : Bioengineered protein cuts HIV genome and frees cells from infection (Message 42852)
Posted 29 Jun 2007 by Profile Christoph Jansen
Post:
Hi,

scientists from Dresden and Hamburg (both Germany) have created a protein that can cut the HIV genome into pieces which are thus inactivated. Infected tissue culture cells were freed from the HIV virus in that way. This is an absolute first: an HIV infection has never, not even under laboratory conditions, been successfully reversed.

Here is a short article on the topic.

To achieve this the researchers started with a recombinase from a bacteriophage and turned it into a related enzyme by forced evolution over 120 generations of intermediate stages. Recombinases are very specific enzymes that can recognise genomic sequences and cut/paste them at a defined point.

It took the scientists five years to achieve that goal - and this is where Rosetta comes into play: using Rosetta such site-specific enzymes might be designed directly in the future, and it might only take months, weeks or even days, depending on the projects growth in efficiency, accuracy and computing power. Once the correct sequence is known, a DNA strand coding the protein can be readily made using methods available.

Rosetta already now tries computing RNA structures, so it might even be possible to also compute the exact RNA or DNA target that an enzyme has to interact with once the viral genome has been sequenced. This way target and drug molecules may both be accurately modeled using the same technique. That would save a lot of additional time compared to current methods.

So, keep crunching as you see: protein design can already do a lot with traditional lab methods, but with Rosetta it might become a totally different playground in the future.

Regards,

Christoph
24) Message boards : Number crunching : Let's stand up to the -1 moron (Message 42444)
Posted 22 Jun 2007 by Profile Christoph Jansen
Post:
its gotta be automated - i can't believe anyone could be sad enough to do that manually!


I'd also say it does not have to be automated. I myself have been "sad" enough to manually give a plus to a lot of those posts in threads that had been systematically minused. I thought maybe it would spoil the fun if the effect was virtually nil - and it also made keeping track of applied minuses harder. I just thought it might be better to do it quietly to not give that thing any open attention, which I guess is the main intention of it all.


Regards,

Christoph
25) Message boards : Rosetta@home Science : Rosetta@home video COMPLETED (Message 41236)
Posted 21 May 2007 by Profile Christoph Jansen
Post:
Hi Laurelin,

it's been some time since my last post here. I just recovered from some time of illness and was mostly busy keeping my everyday life going. Are you still interested in the voiceover translation? I could still do it.

Maybe this could revive the video a little after the time that has passed. And you could insert a written link in the opening credits to the english version for those who find it in German and would like to see the original, so you get kind of a crosslink between versions.

Regards,

Christoph
26) Message boards : Number crunching : How's this for a crazy accepted energy graph? (Message 41216)
Posted 20 May 2007 by Profile Christoph Jansen
Post:
Looks like:

It is just a jump to the left
And then a step to the right [...]

Let´s do the time-warp again
Let´s do the time-warp again
27) Message boards : Number crunching : problem mit rosetta (Message 41118)
Posted 18 May 2007 by Profile Christoph Jansen
Post:
hi habe probs mit rossetta,

meine resulte werdeen immer weniger statt mehr, obwohl ich boinc immer an habe und er immer neue macht,
und der rang bleibt auch seit über eine woche gleich.

kann mir pls jemand helfen??


Hallo sykO,

die einsehbaren letzten Resultate werden nach einer bestimmten Zeit gelöscht, damit die Datenbank nicht ausufert. Die gesammelten Credits werden dadurch aber nicht weniger. Durch das regelmäßige Löschen pendelt sich irgendwann die Zahl der "Results" bei einem relativ stabilen Wert ein, weil immer so viele gelöscht werden, wie Du in der gleichen Zeit nachlieferst.

Dein Rang in Rosetta@home ist in der letzten Woche von 63000 auf 57000 gestiegen (niederiger ist besser, Nummer 1 ist der Anwender mit der höchsten Zahl von Credits). Ich denke, Du verwechselst das mit dem "RAC", dem sog. recent average credit. Das ist die Zahl der im Schnitt pro Tag von Dir produzierten Punkte. Auch die pendelt sich irgendwann ein, wenn Dein(e) Rechner immer in etwa die gleiche Zeit eingeschaltet ist.

Genaue Statistiken über Dich findst Du hier bei BOINCstats. Unten auf der Seite sind auch Tabellen und Diagramme zur Entwicklung Deiner Position im Gesamtvergleich.

Grüße,

Christoph

28) Message boards : Number crunching : teraFLOPS estimate? (Message 35515)
Posted 25 Jan 2007 by Profile Christoph Jansen
Post:
Hi David,

first of all: the active users are pretty constant during the last 2 months. In other words: Rosetta gains about as many users as it loses in the same time.

Another effect that I guess is this: many Mac users have turned away from Rosetta because of too little credits per WU. But these machines contributed to the credits dealt out by the new credit system a lot. In numbers: a certain Mac may have claimed something around 10 to 15 credits per hour but was only granted 3 to 5. In words: these machines claim many credits per decoy, but do not really give the performance. Credits were inflated by some degree by these machines. With them gone, this inflation is gone too.

On the other hand a lot of the new machines are pretty fast and their architecture brings it with it that they show in the benchmarks much poorer than they really are. This means, that e.g. a Core 2 Duo may claim 30 credits per hour but is granted 50 or 60 or 70, meaning it contributes much less to the accumulated credits dealt out than it takes out. This way the credits the project shows are lower than the really would be regarding the processing power.

In short: Macs leaving and new machines coming in which have more crunching power than they show in the benchmarks both lower the credits.

To further show what I mean:Here is the link to the thread where I did an example calculation showing how the new credit system works in this respect. Three posts higher there is another example of what happens when a Mac reports first and when a Core 2 reports first.

If you read the example carefully you will note: if all machines were Core 2s, then all machines would get the same low credits als claimed and granted would be equal. To say it another way: the more high-power machines we have the less will the credits really reflect the crunching power behind the project unless someone really comes up with a new benchmarking system that tells what a machine does on Rosetta and not on the uniform and pretty useless BOINC benchmark.

[Edit] What I am saying about "inflation" is in no way intended as a pun against pre-Intel Macs, on the contrary. The Rosetta project, the way it presently does its calculations, is not optimized for pre-Intel Macs in any way and thus underrates the true power of these machines. Leaving Rosetta was thus just natural for many Mac users who either feel disregarded or think they can contribute more in other places. I really value this project, but I am not sure if it was still my choice if I was a pre-Intel Mac user myself [/Edit]
29) Questions and Answers : Windows : Can't attach to rosetta@home (Message 35182)
Posted 21 Jan 2007 by Profile Christoph Jansen
Post:
Hi,

on the second computer: did you try to "attach to an existing account" (you need to type the password twice if you do that) or "create a new account" (you have to type the password only once)?

In the dialog box that comes up after entering the project URL the standard setting is to "create a new account". You need to alter that by clicking on the circle besides the option to "attach to an existing account", else you get an error message.

If that is not your problem, please ask again and tell us what you exactly did and which URL you entered.

Regards,

Christoph
30) Questions and Answers : Getting started : How to replace my profile picture? (Message 34871)
Posted 16 Jan 2007 by Profile Christoph Jansen
Post:
Hi rinselberg,

looks like the image you kept on seeing was saved in your temporary files. A lot of info is not updated when you revisit a web site to save resources/bandwidth and it looks like your system did not notice the changed image. That often happens and results in seemingly unchanged info while in fact the altered page/site/image is visible to first-time viewers immediately.

Regards,

Christoph
31) Message boards : Rosetta@home Science : Does the N-terminus fold first? (Message 34810)
Posted 15 Jan 2007 by Profile Christoph Jansen
Post:
I cannot comment on how the folding commences, but I'll try an answer to the question about the N-terminus.

The genetic code is read from the DNA by enzymes that generate a messenger RNA, or m-RNA, which carries the information about the coded amino acids out of the cell core. This m-RNA carries special sequences which indicate from which end it must be read.

At another place other RNA, the t-RNA or transfer RNA, is loaded with amino acids. Each t-RNA carries a triplet of bases which fits to a certain triplet in the m-RNA. These triplets are called "codon" and "anticodon". Each amino acid is bound to the t-RNA with its COOH group and the amino group is kind of "dangling" free. The amino group (NH2) of the first amino acid of a protein will later be unbound, so it forms the N-terminus. On the other end the last COOH group will be unbound, forming the C-terminus. This is how it happens:

Now the ribosomes (kind of the protein factories of a cell) come into play: They find the starting sequence on the m-RNA and thread it into the protein synthesis mechanism in the right direction. When reaching the first codon that represents an amino acid, a t-RNA with the proper anticodon is attached to the m-RNA.

The m-RNA is now advanced a little and the second t-RNA is attached. Now the bond between the COOH group of the first amino acid and its t-RNA is broken and the COOH group forms a bond to the amino group of the second one. As you see, the amino group of the first amino acid does not form a bond to another amino acid, it is free and forms the N-terminus.

The first t-RNA is released by this process as it is no longer connected to an amino acid. The whole process commences with the third amino acid (and all those after that): go sideways by one codon, attach third t-RNA, break bond of second COOH end to t-RNA and attach it to third amino end, release second t-RNA, go sideways by one codon, attach fourth...

By breaking the bond between an amino acid and its t-RNA this acid is also no longer connected to the ribosome in any way. This means that the amino acid chain, that will later form a protein, slowly threads out of the robosome. [You can also see this whole process in one sequence of the Rosetta at Home video. Have a look at it, it is quite intuitive if you know what happens.]

Finally the last codon is reached and the last COOH bond to its t-RNA is released without forming a bond to another amino acid. This last COOH group now forms the free C-terminus.

This is how the protein is formed from the amino end (N-terminus) to the COOH end (C-terminus). That is why all proteins are synthesized from the N- to the C-terminus.


32) Message boards : Rosetta@home Science : Rosetta@home video COMPLETED (Message 34429)
Posted 9 Jan 2007 by Profile Christoph Jansen
Post:
Hi again,

I have now translated the text and have tried to record it with a microphone. It works quite well, but I rather think I could use some help by people who speak parts of the text. If I speak all characters it sure gets dull quickly. So if anybody thinks he is able to speak a part, especially the voice of D. Bath (really sounds ridiculous if I try to speak like a girl, believe me...), please step forward.

The text can be found here. Improvements are of course welcome, although I have tried to not translate it into plain German but to keep a little of the original "impromptu" character of the wording.
33) Message boards : Rosetta@home Science : Rosetta@home video COMPLETED (Message 34394)
Posted 8 Jan 2007 by Profile Christoph Jansen
Post:
Hi,

really great. Is it possible to make a synchronized version by underlying a new sound track? I could write out the texts and translate them into German. [I would also read them, I am used to speaking in front of people. But maybe there is somebody here who can do that better and has a really "audiocompatible" voice?]
34) Message boards : Number crunching : Help --- Need to write a propsoal about Rosetta (Message 34331)
Posted 7 Jan 2007 by Profile Christoph Jansen
Post:
X-Ray crystallography can be pretty quick when applied to small molecules or simple crystals with few atoms per unit cell. Still, calculating the structure of large proteins from X-Ray data is a challenge.

The major problem before being able to take an X-Ray is refining the proteins. It means finding a source in which the desired protein is relatively abundant (e.g. a special tissue in a certain animal/plant) and finding a way of separating it from the whole rest of the cells without damaging the protein and altering its structure.

After that you have to crystallize it in a way that gives you usable single crystals, which can be a nightmare as your parameters are pretty limited, if you do not want to spoil it by still altering the structure after taking the protein all that way. As you deal with very light atoms, you pretty surely need to take an X-Ray at low temperatures. Crystals containing water, which is almost inevitably the case with proteins, often break and there goes you single crystal. The obstacles can be really discouraging.

[EDIT] I forgot: for larger proteins you will of course need their sequence, else you are just groping in the dark when trying to calculate an X-Ray structure from scratch. After the Human Genome Project that should not be the biggest problem, but otherwise, e.g. when dealing with animals or plant whose genome is unknown, you of course will have to do that too. Just regard it as painful as the rest, as you'll need a lot of pure protein for it.[/EDIT]

Then you have your X-Ray data and start a nice puzzle with some hundred atoms for the protein and of course for water and possibly salts too. Takes time, patience and, so you still have one at this stage, a really loving partner.

All in all it is a kind of work where often a group of several people may share their doctorate (or subsequent doctorates) just to get a single structure in a time frame of two, three or even more years. This of course means spending a lot of money. And just think of all those "John Doe" Proteins that are just somewhere in a cell, seeming to do nothing special, which you will be really hard put to separate as they are just there, but not in especially high number. (And as these are not kind of prominent you will hardly get a special grant to turn to research on them while there seem to be more valuable targets.)

So, Rosetta may take the fun out of the game for some hardcore researchers, but according to my experience these people may also turn to apnoe diving or heliskiing on the Mount Everest, it is about as satisfying for those who take fun in a maximum of pain. Most others will just fall to their knees and thank the Lord for it.

Just compare it: years with open end research and the nagging doubt whether it really is the native structure until it has been affirmed by the same or some other method or taking a big computational effort and being pretty sure that what you get is good enough to tell you anything there is to know about a protein. Not to speak of future advances, after all we just have begun to turn to the computational way and there is no doubt the methods and computers will improve drastically over time. And the more people contribute the sooner will Rosetta be able to try out new ways in depth. CASP7 clearly showed that the Rosetta community has contributed something of great value.

Almost a proposal in itself ;-)
35) Message boards : Cafe Rosetta : Last one to post here wins! (Message 34073)
Posted 4 Jan 2007 by Profile Christoph Jansen
Post:
Maybe this is small enough to be overlooked and nobody comes after me...
36) Questions and Answers : Unix/Linux : processing workunit 46891678 on hostid=378386 (Message 32921)
Posted 19 Dec 2006 by Profile Christoph Jansen
Post:
Hi Nicholas,

as I wrote, the progress counter stops while a decoy is running. It is for example 5.000 % after the first decoy and then jumps to, say, 7.322 % after the next. Some decoys take very long. There are work units on which I get 200 decoys in 8 hours, sometimes it is only 20 or even less.

As you have a Celeron with 1,7 GHz long decoys can take up to an hour or so. What I do not understand is that it shows you are only using so little of your processor. But I do not have a Linux machine, so I cannot compare.

A good idea would be to go to the Number Crunching Board and ask your question about the processor load to the broader public. Only very few people ever look into the Questions & Answers section. But questions directly put in the number crunching forum are mostly answered and there are some people there who know quite a lot about all that stuff.

Regards,

Christoph
37) Questions and Answers : Unix/Linux : processing workunit 46891678 on hostid=378386 (Message 32912)
Posted 19 Dec 2006 by Profile Christoph Jansen
Post:
Hi Nicholas,

and welcome to Rosetta! I cannot say anything on the percent of CPU usage, maybe there is somebody else who uses Linux himself and knows about it. But I can help you with the other part of your question.

The "estimated time" always increases because Rosetta works different than many other projects. Rosetta calculates the progress after each model it has finished. The moment it has finished a model, called a "decoy", your progress % are going up and the estimated time to completion goes down.

From that point on you will see the estimated time go up again, but only because Rosetta does not tell the BOINC manager that it is making progress. The result is that the estimated time always seems to go up and the progress % looks like it is stuck. But that is not the case, Rosetta is working fine. It is just some kind of misalignment of BOINC's and Rosetta's way of calculating progress.

Regards,

Christoph
38) Questions and Answers : Windows : Computer Summary page question (Message 32813)
Posted 17 Dec 2006 by Profile Christoph Jansen
Post:
Hi Paul,

although I am at best a novice and far from wise or great: Yes, it refers to one single core. So you have to multiply with the number of cores/cpus to get the overall performance of your machine.

Regards,

Christoph
39) Questions and Answers : Web site : how to detach from project after a reformat (Message 32726)
Posted 15 Dec 2006 by Profile Christoph Jansen
Post:
Hi Jameson,

you might try a merge. Go to your account, click "view" beside the item "computers on this account" and select one of the machines you want to merge into one. Scroll down to the bottom and try "merge this computer".

If BOINC sees a machine that can be merged with the one you selected, it will be listed. You can select it and then click "Merge hosts". The newer of both machines will be the one to "survive", the other one is deleted.

If BOINC does not list another machine, you just see "select all" and "unselect all" links and the button, but no clickable PC. Call again or go directly to the Moderators COntact Point Thread and ask for assistance. It usually is a good point to get help on how to do things or at least a reason why a certain action may not be possible.

Regards,

Christoph
40) Message boards : Rosetta@home Science : Rosetta@home Web Site Translations (Message 32581)
Posted 13 Dec 2006 by Profile Christoph Jansen
Post:
Hi,

if there is a new round of translations implementation I would like to rework the last de.po a little. I think I already removed most of the misspellings in the last file I sent (which is not one the currently online) but am not sure if the "link bug" has been removed in there too (on the "science" page a CASP link is extended over a number of paragraph as I forgot set a % instead of %s at the end).

And it would be nice to also include the newest features in the de.po like the "results" and the "how to view your structure predictions".

Regards,

Christoph


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