Posts by Morten Starkeby

1) Message boards : Rosetta@home Science : Types of WU's and Their Nomenclature (Message 63607) Posted 5 Oct 2009 by Morten Starkeby Post: This thread should help you a bit on the way: http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1453
2) Message boards : Cafe Rosetta : Personal Milestones (Message 19122) Posted 22 Jun 2006 by Morten Starkeby Post: <--- User of the day: 22/06-2006
3) Message boards : Rosetta@home Science : Science News (Message 12600) Posted 24 Mar 2006 by Morten Starkeby Post: There are tons of great ideas on this page! I put the clickable links that you guys suggested to the EBI database pages (with cartoons, biological descriptions, etc.) from the news page and the top predictions page. We're looking into setting up a page for "What's next". And also a guide to what the cryptic "HBLR_1.0" stuff means... stay tuned for explanations of these new scientific strategies. And please keep making suggestions! Thanks for the links you added. You probably have this in the pipeline, but the Results link under Returning Participants on the main page is a bit outdated. It should be brought up to date in some way. Cheers, Morten
4) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 12014) Posted 14 Mar 2006 by Morten Starkeby Post: We are now posting these in the "news" section of the homepage! As David mentioned in his journal, we are looking into pritable certificates. We are also looking into adding "top predictions" to people's profiles. I'd appreciate any feedback on the format of the daily top predictions posts! I like it already. Not sure if this is feasible, but everytime I notice a new protein being issued, I look it up in RCSB. Would it be possible to include the name of the protein as a link to some protein database where more information about the protein can be studied, e.g. RCSB, your own Robetta-server or something similar?
5) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 11931) Posted 12 Mar 2006 by Morten Starkeby Post: Hi James, we have been trying to do something along these lines-- every evening we are posting a new result in the "top predictions" section, with an acknowledgement of the finder, which I then explain in the journal. do you think we should instead post the prediction on the main page where it is more visible? A rotating daily Top Prediction of the Day (TPD), similar to user of the day, would probably be neat. (I would not be opposed to replacing user of the day with top prediction of the day, but I am not sure how others would feel about that) From these, you could select the Top Prediction of the Month (TPM). If I somehow got the top prediction of the day, I would appreciate it being available to me forever in my result or profile page. e.g. Awarded the Top Prediction of the Day on DD-MM-YY for [protein name and link to graphics]
6) Message boards : Number crunching : Help us solve the 1% bug! (Message 11785) Posted 8 Mar 2006 by Morten Starkeby Post: Got my first 1% stuck bug. The work unit is stuck at 1% for 1 hour and 54 minutes at the time of this writing. It is stuck at model 1, step 20880, in the Ab initio stage. Name of work unit: HB_BARCODE_30_1a32__351_1964 I supended boinc, and ran the following command from the command prompt: rosetta_4.82_windows_intelx86.exe cc 1a32 _ -abrelax -stringent_relax -more_relax_cycles -output_chi_silent -vary_omega -rand_envpair_res_wt -rand_SS_wt -farlx -ex1 -ex2 -silent -barcode_from_fragments -new_centroid_packing -barcode_from_fragments_length 30 -ssblocks -barcode_mode 3 -omega_weight 0.5 -jitter_frag -jitter_variation gauss -output_silent_gz -nstruct 10 -paths ccfrags200.txt -relax_score_filter -filter1 -115 -filter2 -130 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -increase_cycles 10 -cpu_run_time 7200 -constant_seed -jran 3046839 The command executed perfectly, and proceeded quickly beyond 1% (at the time of writing it is at model 3, 20.9%). I then aborted the stand alone rosetta execution. I am using the 5.3.24 version of Boinc (beta version)
7) Message boards : Rosetta@home Science : Science News (Message 11566) Posted 2 Mar 2006 by Morten Starkeby Post: A simple suggestion that could be rather fast to implement if you guys want to. On our results we see the name of the protein as: Name: HBLR_1.0_1dtj_323_3093_1 Name: HBLR_1.0_1hz6_323_1593_0 which is not very informative for the average user, unless you know that the letters in the middle is the pdb id, and that you can look it up in protein databases. What if you made the name a clickable link that linked to your robetta server? E.g for my examples: Name: HBLR_1.0_1dtj_323_3093_1 Name: HBLR_1.0_1hz6_323_1593_0 You then get a quick overview over what the protein/domain does, and can click on further links to get more information.
8) Message boards : Rosetta@home Science : Science News (Message 11553) Posted 2 Mar 2006 by Morten Starkeby Post: Some suggestions: * screensaver should be updated to show the rmsd and the lowest energy found so far during the WU, in addition to the latest accepted ones. * Regular updates and feedback from the team is important, both on the science part and the tech part is important * I think it also would help retain users if you could get the Top predictions to be more or less automated each month, and that users on their result page could access their current top prediction at any time. Maybe even have a Java-applet where you can navigate inside your protein structure(s) and have various options for display. * More information about the various proteins we run WU on. Provide link to various databases on proteins for example. It looks like several of your users like to learn about the science, so it would be nice to know in what biological processes the proteins participate in, what class/family of protein do they belong to and so on. I am sure some of this could be automated with lookups to current protein databases.
9) Message boards : Number crunching : Miscellaneous Work Unit Errors (Message 11227) Posted 22 Feb 2006 by Morten Starkeby Post: Received another client error: Result ID: 11875565 <core_client_version>5.3.19</core_client_version> <message> - exit code -1073741811 (0xc000000d) </message> <stderr_txt> # random seed: 1054947 # cpu_run_time_pref: 28800 </stderr_txt>
10) Message boards : Number crunching : Miscellaneous Work Unit Errors (Message 11203) Posted 22 Feb 2006 by Morten Starkeby Post: I got the following error today: 22/02/2006 07:40:42\|rosetta@home\|Unrecoverable error for result PRODUCTION_ABINITIO_INCREASECYCLES50_1opd__317_273_0 ( - exit code -1073741811 (0xc000000d)) http://boinc.bakerlab.org/rosetta/result.php?resultid=11852924 on computer http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=167418 Leave in memory is set to YES Application switch time: 120 min Client version: 5.3.19 (BBC CCE version)