Posts by Pece Kocovski

1) Message boards : Rosetta@home Science : Help a newbie out. Work Unit explained? (Message 60093) Posted 12 Mar 2009 by Pece Kocovski Post: Thank you both cenit and Mod.Sense for your excellent answers! With the info you both gave me, I am now more than happy to be donating my idle computer time to Rosetta@home (among a few other projects of similar interest) and will try and convince many others to do the same! All of you working on Rosetta@home: (researchers,scientists,programmers,coders etc. etc.) keep up the excellent work! Cheers!
2) Message boards : Rosetta@home Science : Help a newbie out. Work Unit explained? (Message 60071) Posted 11 Mar 2009 by Pece Kocovski Post: Hi, Well first of all, if there is somewhere where this question is allready answered, please direct me to it, because I had trouble finding it. So I started lending my computer out to all these science projects a few days ago (I decided to let Rosetta take the most amount of resources). So BOINC has been working away happily, letting Rosetta have access to my computer so it can process the Work Units. Now, I have gotten a few modest results (my computer is not very good/when I have the computer on, I tend to use it) and I understand what proteins are and what tertiary structure is, hydrogen bonds, di sulphide bonds etc. etc. and I understand that the processing is trying to find out the lowest energies for certain proteins but what I do not understand is the way the results are presented. So I am looking at this page: http://boinc.bakerlab.org/rosetta/results.php?userid=304847 (Not sure if others can access my stats) So lets say I click on one of the completed tasks at random: Like number 234126438 (Task ID)/213439838 (Work unit ID) http://boinc.bakerlab.org/rosetta/result.php?resultid=234126438 http://boinc.bakerlab.org/rosetta/workunit.php?wuid=213439838 So on the first link, my first confusion is the name. Wth? Is that just dished out at random, or does the name actually mean something (like does that name somehow equal the Ubiquitin-protein ligase as an example)? Then there is the "stderr out" bar that then goes on to list a whole bunch of text that at first glance seems like a whole bunch of blah. Second glance did not change my view: <core_client_version>6.4.7</core_client_version> <![CDATA[ <stderr_txt> BOINC:: Initializing ... ok. [2009- 3- 9 23:25:57:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. Registering options.. Registered extra options. Initializing core... Initializing options.... ok Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev26003.zip <unzip> <-oq> <../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev26003.zip> <-d./> Firstarg=true; pp=-d./ firstarg: <-d./> End of unzipping. Setting database description ... Setting up checkpointing ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _U8X7X_00001 BOINC:: Initializing ... ok. [2009- 3-10 0:25:14:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. Registering options.. Registered extra options. Initializing core... Initializing options.... ok Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev26003.zip <unzip> <-oq> <../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev26003.zip> <-d./> Firstarg=true; pp=-d./ firstarg: <-d./> End of unzipping. Setting database description ... Setting up checkpointing ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _U8X7X_00001 Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_1 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_2 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_1 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_2 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_3 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_4 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_5 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_6 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_7 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_8 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_9 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000001_ClassicAbinitio__stage_3_iter1_10 ... success! Starting work on structure: _U8X7X_00002 BOINC:: Initializing ... ok. [2009- 3-10 1:38:17:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. Registering options.. Registered extra options. Initializing core... Initializing options.... ok Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev26003.zip <unzip> <-oq> <../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev26003.zip> <-d./> Firstarg=true; pp=-d./ firstarg: <-d./> End of unzipping. Setting database description ... Setting up checkpointing ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _U8X7X_00002 Continuing computation from checkpoint: chk_S_U8X7X_00000002_ClassicAbinitio__stage_1 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000002_ClassicAbinitio__stage_2 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000002_ClassicAbinitio__stage_3_iter1_1 ... success! Continuing computation from checkpoint: chk_S_U8X7X_00000002_ClassicAbinitio__stage_3_iter1_2 ... success! ====================================================== DONE :: 1 starting structures 9401.06 cpu seconds This process generated 2 decoys from 2 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down... called boinc_finish </stderr_txt> ]]> Would someone here be able to explain to me what all of the above meant? (not in detail, just a general overview). I have noticed similar lines of text (although some shorter than others) on my other completed work units. Or is the above data, just the textual representation of the proteins we see on the screensaver? So yeah, any help in clarifying the above would be great. Finally (while I am here), I noticed that the homepage of Rosetta@home says that R@home is not for profit. But I then read on Dr David Bakers journal (which I skimmed and some parts are a great read!) and he mentioned something about manuscripts (which I assume means, publishing articles in scientific journals). Dont those articles go on to be published for a profit (correct me if I am wrong here)? Or does the heading mean that all the data is released in the public domain, and then you can use the data however way you wish (i.e. publish the data into results, make money etc etc?) Cheers!