Posts by hugothehermit

1) Message boards : Number crunching : Is RALPH down? (Message 60157)
Posted 14 Mar 2009 by hugothehermit
Post:
Yay for Ralph.


What Mod.Sense said, well meant :)

A had a brain freeze yesterday.

I had to talk to my ISP, and I think I went to every department explained my problem to every employee, sometime during this experience my head just stopped working, probably to protect me from making a habit out of it :)












\"He was drunk\" seen whistling nervously near the door.
2) Message boards : Number crunching : Is RALPH down? (Message 60131)
Posted 13 Mar 2009 by hugothehermit
Post:
Saenger
Isn\'t it the same guys\'n\'gals that maintain Rosetta proper, i.e. this forum?


That is a good question, and truthfully I don\'t know.

But I suspect not.

3) Message boards : Number crunching : Is RALPH down? (Message 60130)
Posted 13 Mar 2009 by hugothehermit
Post:
I sent an email, I hope he isn\'t swamped with people that are \"helpful\" like me :)
4) Message boards : Number crunching : Is RALPH down? (Message 60129)
Posted 13 Mar 2009 by hugothehermit
Post:
David Kim used to fix Ralph, Keith E. Laidig fixed Rosie.

But I\'m not sure these days. I\'ve been away for a while.
5) Message boards : Number crunching : Is RALPH down? (Message 60127)
Posted 13 Mar 2009 by hugothehermit
Post:
Has anyone emailed the Ralph team?

6) Message boards : Cafe Rosetta : 有中国人吗?? (Message 60094)
Posted 12 Mar 2009 by hugothehermit
Post:
what is the poster\'s name/ID? (I don\'t have that program, either, and all I get are a bunch of squares displayed)


Just click on the name, or here

The name means tranquility; peacefullness[sic] cite

你好 hello :)

Edit: oops, I didn\'t read Sid\'s post.
7) Message boards : Cafe Rosetta : 有中国人吗?? (Message 60074)
Posted 11 Mar 2009 by hugothehermit
Post:
I think it translates to: \"does anybody here talk Chinese\".

Edit: for some spelling, formatting and some legibility.
Edit: got rid of the stuff that needed spelling, formatting and some legibility
8) Message boards : Number crunching : minirosetta v1.25 bug thread (Message 53347)
Posted 26 May 2008 by hugothehermit
Post:
Something is wrong

Mine
Wingman

both <1 second with this error:


<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: in::file::zip minirosetta_database_rev21566.zip does not exist!
ERROR:: Exit from: ..\\..\\src\\apps\\public\\boinc\\minirosetta.cc line: 91
called boinc_finish

</stderr_txt>
]]>

Edit:

I searched my computer and found

minirosetta_database_rev20421.zip
minirosetta_database_rev20940.zip
minirosetta_database_rev22619.zip
minirosetta_database_rev20940.zip

So you are not sending the \"minirosetta_database_rev21566.zip\" file properly, it would seem.

Though it seems strange to me that you want the 21566, when you have a 22619, but then again I have no idea what you are up to :)
9) Message boards : Cafe Rosetta : Translating the video on Youtube (Message 51388)
Posted 14 Feb 2008 by hugothehermit
Post:
I believe that the one I posted is reasonably accurate, I will post it again as I think, I might have copied an error in the attribution, some comments that shouldn\'t be translated and also for a little formating.

If anyone finds an error please post it in this thread.

Venturini Dario if you need any help with some of the word meanings, post here someone will help.

Start translating after this line.


David Baker:

\"The problem you\'re focusing on at Rosetta@Home, is the prediction of protein structures from their amino acid sequences.

Almost all human diseases are caused by mutations in proteins that affect their three dimensional structures and functions, and so if we can reliably predict protein structures we could understand how mutations cause disease and from there perhaps go on to develop therapies.\"


Bill Schief:

\"I\'m working on trying to design immunogens that will elicit antibodies against the HIV, so are [a] critical part of a vaccine.
Design proteins that will present that piece of HIV in just the right conformation so that protein, once it\'s taken off a computer and turned into a real physical protein that\'s put into a person\'s blood will cause that person to make antibodies against the epitope of HIV.\"


David Baker:

\"Up until recently, it has been pretty much thought impossible to reliably predict the structure of proteins from their sequences. Instead protein structures are currently determined using time consuming and expensive experiments, which can only be applied to a small subset of proteins. If instead we could accurately and reliably predict protein structures, it would revolutionize much of molecular biology.

To carry out this work, we\'ve developed a computer program called Rosetta. Success in our work would have broad ranging implications for human health, ranging from the development of a vaccine for HIV to the eradication of Malaria\"


Unknown : Laurelin ?

\"The sequence of amino acids that make up proteins is directly determined from the genetic code, otherwise known as the sequence of molecules in DNA.
DNA, like proteins, is also made of molecular sub-units with specific properties.
Within the nucleus a kind of imprint of DNA is transcribed into a similar molecule called RNA.
Carrier molecules transport amino acids to an enormous structure called a ribosome.
The ribosome translates the information in RNA into a chain of amino acids\"


Divya Bhat:

\"You know, think about putting a rope in a box with no gravity and think about how many different ways this rope could actually fall in that box. So you know the number of combination, the number of possibilities, are pretty much astronomical.\"


Unknown: Laurelin ?

\"A strand of amino acids, the order of which has been determined by the genetic code, can indeed be thought of as rope or chain-like. However, the properties of the links, in this case amino acids, cause portions of the chain to be attracted to or repelled from each other. As well as elements in the cellular environment.

What the Rosetta program does, is calculate the likelihood of these interactions between segments of the chain, based upon favourable energy levels.
The most likely 3D structure of the chain will take the least amount of free energy to fold.\"


David Kim:

\"So last summer I started modifying Rosetta to be used with the BOINC distributed computing platform. Before BOINC we had around 400 computers that we can run our calculations on locally, but now with BOINC we have thousands of computers that we can run our jobs on, located all around the globe, and it\'s really exciting to see how it developed.\"


David Baker:

\"What we\'re doing at Rosetta@Home, is analogous to searching the surface of a large rocky planet for the lowest elevation point. Imagine you have a team of human explorers working with you, and they\'re all exploring around the planet. The team is small, it is quite likely that no explorer will actually find the lowest elevation point, particularly if there are a lot of tall mountains that lead to explorers getting trapped at particular places on the planet. Now instead imagine that you have a very large team of explorers and they each parachute down randomly on the surface of the planet and then start searching for the lowest elevation point. The more explorers you have, the more likely it is that at least one of them will find the lowest elevation point of the planet. Now on Rosetta@Home, we\'re instead searching the energy landscape for a protein trying to find the lowest energy structure for the amino acid sequence. The more computers there are doing these searches, the more likely it is that somebody will actually find it.\"


Unknown: Laurelin ?

\"In each step of the Rosetta search process, a move is made in which part of the protein structure is randomly altered. The top left panel of the screen saver shows each move as it is being made. If Rosetta calculates that the energy has decreased with the move, it is accepted, and displayed in the middle panel.
The lowest energy structure found so far is displayed in the next panel over. Shown below this is the actual shape of the protein, if it is known. The panel to the right tracks how closely each accepted move compares to the known protein structure. The bottom panel tracks the energy of each move. The energy after the most recent move is located on the right. In the bottom right corner is a graph which plots the energy versus how close the shape is to the actual protein. From this graphic you can tell when your search has entered a new region of the energy landscape.\"


Rhiju Das:

\"So one of the dreams of many people on this project is that out of the - say million users - on Rosetta@Home, there is going to be some, maybe some kids, some 9 years old girls in Korea, who grow up looking at these fascinating proteins on their screens and develop a very strong intuition for what molecules do and they\'re going to grow up and become great biophysicists and because of this intuition that developed when they were young they will be able to solve the problem immediately.\"


David Baker:

\"This is a whole new step forward in the relationship between scientists and the public. To solve the problem of protein structure prediction it\'s quite clear that it\'s really not possible without the contributions of people from all over the world like yourselves, because it\'s such a big computing problem that it just cannot be done with any in-house resources so we can only do it collaboratively as a collaboration between us and you and through this collaboration we can solve a problem which I really think couldn\'t be solved otherwise\"
10) Message boards : Cafe Rosetta : Translating the video on Youtube (Message 51259)
Posted 9 Feb 2008 by hugothehermit
Post:
This is what I got.

..............

David Baker:

\"The problem you\'re focusing on at Rosetta@Home, is the prediction of protein structures from their amino acid sequences.

Almost all human diseases are caused by mutations in proteins that affect their three dimensional structures and functions, and so if we can reliably predict protein structures we could understand how mutations cause disease and from there perhaps go on to develop therapies.\"


Bill Schief:

\"I\'m working on trying to design immunogens that will elicit antibodies against the HIV, so are [a] critical part of a vaccine.
Design proteins that will present that piece of HIV in just the right conformation so that protein, once it\'s taken off a computer and turned into a real physical protein that\'s put into a person\'s blood will cause that person to make antibodies against the epitope of HIV.\"


David Baker:

\"Up until recently, it has been pretty much thought impossible to reliably predict the structure of proteins from their sequences. Instead protein structures are currently determined using time consuming and expensive experiments, which can only be applied to a small subset of proteins. If instead we could accurately and reliably predict protein structures, it would revolutionize much of molecular biology.

To carry out this work, we\'ve developed a computer program called Rosetta. Success in our work would have broad ranging implications for human health, ranging from the development of a vaccine for HIV to the eradication of Malaria\"


Unknown : Laurelin / D. Bath ?

\"The sequence of amino acids that make up proteins is directly determined from the genetic code, otherwise known as the sequence of molecules in DNA.
DNA, like proteins, is also made of molecular sub-units with specific properties.
Within the nucleus a kind of imprint of DNA is transcribed into a similar molecule called RNA.
Carrier molecules transport amino acids to an enormous structure called a ribosome.
The ribosome translates the information in RNA into a chain of amino acids\"


Divya Bhat:

\"You know, think about putting a rope in a box with no gravity and think about how many different ways this rope could actually fall in that box. So you know the number of combination, the number of possibilities, are pretty much astronomical.\"


Unknown: Laurelin / D. Bath ?
\"A strand of amino acids, the order of which has been determined by the genetic code, can indeed be thought of as rope or chain-like. However, the properties of the links, in this case amino acids, cause portions of the chain to be attracted to or repelled from each other. As well as elements in the cellular environment.

What the Rosetta program does, is calculate the likelihood of these interactions between segments of the chain, based upon favourable energy levels.
The most likely 3D structure of the chain will take the least amount of free energy to fold.\"


David Kim:
\"So last summer I started modifying Rosetta to be used with the BOINC distributed computing platform. Before BOINC we had around 400 computers that we can run our calculations on locally, but now with BOINC we have thousands of computers that we can run our jobs on, located all around the globe, and it\'s really exciting to see how it developed.\"


David Baker:

\"What we\'re doing at Rosetta@Home, is analogous to searching the surface of a large rocky planet for the lowest elevation point. Imagine you have a team of human explorers working with you, and they\'re all exploring around the planet. The team is small, it is quite likely that no explorer will actually find the lowest elevation point, particularly if there are a lot of tall mountains that lead to explorers getting trapped at particular places on the planet. Now instead imagine that you have a very large team of explorers and they each parachute down randomly on the surface of the planet and then start searching for the lowest elevation point. The more explorers you have, the more likely it is that at least one of them will find the lowest elevation point of the planet. Now on Rosetta@Home, we\'re instead searching the energy landscape for a protein trying to find the lowest energy structure for the amino acid sequence. The more computers there are doing these searches, the more likely it is that somebody will actually find it.\"


Unknown: Laurelin / D. Bath ?

\"In each step of the Rosetta search process, a move is made in which part of the protein structure is randomly altered. The top left panel of the screen saver shows each move as it is being made. If Rosetta calculates that the energy has decreased with the move, it is accepted, and displayed in the middle panel.
The lowest energy structure found so far is displayed in the next panel over. Shown below this is the actual shape of the protein, if it is known. The panel to the right tracks how closely each accepted move compares to the known protein structure. The bottom panel tracks the energy of each move. The energy after the most recent move is located on the right. In the bottom right corner is a graph which plots the energy versus how close the shape is to the actual protein. From this graphic you can tell when your search has entered a new region of the energy landscape.\"


Rhiju Das:
\"So one of the dreams of many people on this project is that out of the - say million users - on Rosetta@Home, there is going to be some, maybe some kids, some 9 years old girls in Korea, who grow up looking at these fascinating proteins on their screens and develop a very strong intuition for what molecules do and they\'re going to grow up and become great biophysicists and because of this intuition that developed when they were young they will be able to solve the problem immediately.\"


David Baker:

\"This is a whole new step forward in the relationship between scientists and the public. To solve the problem of protein structure prediction it\'s quite clear that it\'s really not possible without the contributions of people from all over the world like yourselves, because it\'s such a big computing problem that it just cannot be done with any in-house resources so we can only do it collaboratively as a collaboration between us and you and through this collaboration we can solve a problem which I really think couldn\'t be solved otherwise\"

..............................



The most likely 3D structure of the chain will take the least amount of free energy to fold.


This may be correct, but it does confuse the issue of folding proteins and what R@H does.

Edit for names that I could find and a bit of legibility .
11) Message boards : Rosetta@home Science : Tryptophan (Message 50388)
Posted 6 Jan 2008 by hugothehermit
Post:
Interesting observation. Here\'s a post in Vijay Pande\'s blog at F@H on this subject.

http://folding.typepad.com/news/2007/11/on-turkey-and-t.html


Thanks for the link svincent.

It turns out that Trp is one of the most bulky amino acids, with its ring structure. Being a bulky ring, Trp is one of the most hydrophobic amino acids, and is thus present in protein cores.

Moreover, Trp has a very important properties in the study of protein folding. Due to its ring structure, Trp fluoresces (i.e. gives off light at a particular frequency, when hit with light of another frequency), and so Trp is a very important probe of protein folding. When a protein is unfolded, usually its Trp residues are exposed to solvent, but when folded, Trp is buried. This difference leads to differences in how it fluoresces, which can be measured very precisely.



Maybe R@H needs a tweak, assuming I\'m reading that, and also viewing the structure, correctly.

The WU(s) that contained it should be in this list:

130356009
130163643
130163642
130163641
130163640
130163639
130163491
129312370
129096848
129096485
12) Message boards : Number crunching : Ok, you\'ve got my attention H&FS (Message 50343)
Posted 5 Jan 2008 by hugothehermit
Post:
What\'s H&FS?


Housing and Food Services

this thread

Ethan I believe started this whole mess (R@H) by offering computer time to the biochemistry department, at least it\'s who I blame, as I lie in bed trying to work out if I could cross a genetic algorithm and repulsive particle swarm algorithm to find the global minimum, while scratching my head over how the bond angles have anything to do with the energy function, worrying about quantum chemistry that should help if you just added hydrogens to the PDB structures, not to mention the amino acids that I have looked up to find out what will join with what. Yep I definitely blame Ethan :)

My head hurts :P
13) Message boards : Rosetta@home Science : Tryptophan (Message 50342)
Posted 5 Jan 2008 by hugothehermit
Post:
I noticed (in the graphics of R@H) that an AA tryptophan looked like it was on the outside of a protein during the full atom relax mode (I\'m unsure which WU).

Can someone point me to a PDB that contains a TRP that is not buried within the protein. There are probably lots, I\'ve just never seen one before. Ta

Edit: to make more sense.
14) Message boards : Number crunching : Problems with version 5.90/5.91 (Message 50171)
Posted 29 Dec 2007 by hugothehermit
Post:
117198862

Exit status -1073741819 (0xc0000005)
15) Message boards : Number crunching : CRT invalid display type (Message 49590)
Posted 11 Dec 2007 by hugothehermit
Post:
here

...will show the error CRT invalid display type, the source is ati2mtag. This occurs with Catalyst 7.7 and higher.

... the workaround is to install Catalyst 7.6.


here Why this error is not \"This error will not cause any issues to the system or performance.\" and more like \"Yea, other than freezing the game having to reboot, no performance problems\"

Hope that helps.
16) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 49364)
Posted 4 Dec 2007 by hugothehermit
Post:
Count me in, I\'ve sent an e-mail to modzilla.
17) Message boards : Rosetta@home Science : Minimum energy function. (Message 49260)
Posted 1 Dec 2007 by hugothehermit
Post:
I guess no one is going to answer this here or at POEM@home :(

I\'ve had a bit to drink, but here goes.

I believe Tinker has an energy function, I also believe that I read somewhere that it has been converted into C or C++.

I am a software engineer, if you forget that amino acids are chemicals and that sequences become proteins, and simply think of the parameters as numbers, a host of computer science techniques data mining/manipulation/etc. could be applied to this mound of data.


You should be able to do this with the protein structures in the PDB. I\'m not sure how.


I can never do a de-novo/ab-initio on an unknown because there is no way I can tell which configuration has the lower free energy. Even a decent approximation would be useful as I could then use my program as an input filter to provide \"promising\" start points for more sophisticated folders.


The way (I think) they do this is to take homologue (use PSI-BLAST at PDB) proteins and cut them into pieces (somewhere between 3 and 12 Amino Acids, though of course this would be dependent on lots of things)fit those pieces back together, then check if enough water hating Amino Acids are going to be on the inside of the protein structure. I don\'t think that minimum energy has anything to do with this step. You should also disregard the known structure so as not to contaminate your data.

Hopefully that made sense.
18) Message boards : Number crunching : Problems with web site (Message 49057)
Posted 26 Nov 2007 by hugothehermit
Post:
http://boinc.berkeley.edu/dev/forum_thread.php?id=2208

The developers are looking into different options.

1. is to teach Akismet what is SPAM and what isn\'t. At this moment it doesn\'t know, so posting URLs, even pointing to a thread elsewhere on the same forum, is considered spam.

2. is to use reCAPTCHA for signing up through the website.

3. this code is available, see change log 13835, do not allow a profile to be made unless you have at least credit.


http://akismet.com/faq/

Where does the spam go?

When the plugin catches something as spam it saves it in the database for 15 days in case you want to check it out manually and then automattically deletes it. In the unlikely event something gets incorrectly identified as spam you can correct it and it submits the \"false positive\" back to Akismet for analysis and improvement of our system. If a spam comment happens to get through and you mark it as spam within WordPress, it does the same thing. Akismet becomes more effective the more you use it.


If I\'m reading that right, then someone would need to have access to the DB so they could set it straight on what is spam and what is not. I\'ll put my hand up for about 1 hour a day for a month or two.

Though why on earth BOINC didn\'t start with a blank blacklist is beyond me.


19) Message boards : Number crunching : Problems with web site (Message 49033)
Posted 25 Nov 2007 by hugothehermit
Post:
I didn't last long, but I won't resort to spam so...

buy my doughnuts

These are really my doughnuts, the picture is taken by me and I declare that it is GPL , or any other copyright copy left or copy anything you want.

I made these from flour, yeast, sugar and can give you the recipe, they were baked in 180C peanut oil and rolled in cinnamon and sugar.


Please remember to buy my doughnuts
buy my doughnuts
buy my doughnuts

PS they are not available in stores or from me personally, and in fact they are already eaten.



20) Message boards : Cafe Rosetta : Electronic Sports Leagues (ESL) says "Good Bye" (Message 49032)
Posted 25 Nov 2007 by hugothehermit
Post:
ESL has done a huge amount of work for Rosett@Home, I wish you all the best for your future projects*

*This is of course an outright lie, I hope you hit so many errors, bad times and things that go BOINC, you will come back to Rosetta@Home :D

Note: sometimes jokes don't translate well into other cultures yet alone other languages, so let me say, this is supposed to be amusing and not cause offense.
I added this because I have offended Canadians among other people with my Australian sense of humour, Like how do you ... no I better not :)



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