Posts by Ray Wang

1) Message boards : Rosetta@home Science : CASP 10 (Message 74731) Posted 14 Dec 2012 by Ray Wang Post: Can anyone tell me what the results were? Hi ALL ROSETTA@HOME participants, Good new from CASP10 meeting, which just ended yesterday at Italy!!! Having your contribution to Rosetta@Home project, the Baker lab did really good this time. With a lot of exceptional scientists' effort, in CASP10 we have improved our template-based modeling (TBM) method. And here are those results: Let's focus on TBM easy/hard using "best model" (best out of five submission) as the criterion. 1. Baker Lab is ranked first in Server Prediction (fully automated structure prediction) --------------------------------------------------- [1] [2] [3] [4] [5] --------------------------------------------------- 1. 330 s BAKER-ROSETTASERVER 111 79.614 2. 035 s Zhang-Server 111 79.365 [1] rank [2] server id [3] server name [4] proteins count [5] Z-score (how well you did compared to others using GDT-TS as metrics) website: http://www.predictioncenter.org/casp10/groups_analysis_best.cgi?type=server&tbm=on&tbm_hard=on&submit=Filter 2. Baker Lab is ranked second in Human Prediction (manually structure prediction): --------------------------------- [1] [2] [3] [4] [5] --------------------------------- 1. 237 zhang 56 56.832 2. 477 BAKER 56 54.482 [1] rank [2] server id [3] server name [4] proteins count [5] Z-score (how well you did compared to others using GDT-TS as metrics) website: http://www.predictioncenter.org/casp10/groups_analysis_best.cgi?type=all&tbm=on&tbm_hard=on&submit=Filter 3. Baker Lab is ranked first in Human Contact-assisted Prediction (given few native contacts, to predict protein structure) with a tremendous distance to the group ranked second: Here is the preliminary results the CASP organizer posted on website: http://predictioncenter.org/casp10/results.cgi?view=targets&model=all&tr_type=others&groups_id=4 , where for each graph with orange-color lines into it, you need to compare the black line to the rest- that's us. The main predictor, David Kim, will come here, explaining it clearly to you all with a summary table. With the help and contribution to Rosetta@HOME from you all, we are able to make significantly progress to predict more accurate protein structures, which ends up would impact the real world by tackling human deseases, like, therapeutics protein design. Please let me know if I said something unclear. Again, thank you so much for the support. We will keep you updated about our triumph in contact-assisted protein structure prediction in CASP10. Sincerely, Baker Lab CASP10 Team
2) Message boards : Rosetta@home Science : CASP 10 (Message 73411) Posted 9 Jul 2012 by Ray Wang Post: Hello everyone!! Apologies! I am Ray Wang, one of the protein structures predictors of Baker Lab CASP10 team. Few days ago, there were massive error submissions which caused the success rates to be zero. That was due to a remiss update of the CASP working pipeline. We were very sorry about causing the inconvenience for you all, and for sure will be doing more meticulous checking before we trigger the pipeline! Again Sorry about this, and THANKS you all for the contribution to the Rosetta@home! We couldn't accomplish these scientific feats without your participation!!!!! Sincerely yours, Baker Lab CASP10 team
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 70295) Posted 9 May 2011 by Ray Wang Post: out of memory error codes on these tasks, that is not possible as I have 3.24GB of RAM. FOLD_N_DOCK_2kqt_D2symm_SAVE_ALL_OUT_IGNORE_THE_REST_26674_9746_0 FOLD_N_DOCK_2kqt_D2symm_SAVE_ALL_OUT_IGNORE_THE_REST_26674_1528_0 FOLD_N_DOCK_dagk_D2symm_SAVE_ALL_OUT_IGNORE_THE_REST_26520_9259_1 Error message: - Unhandled Exception Record - Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x7C812AFB Hi Speedy and Greg_BE, I am Ray, a graduate student in the Baker lab. I will be taking care of the issues caused by "FOLD_N_DOCK" related jobs. As Greg_BE said, this is really not likely that these jobs could run out of all those 3.24GB of RAM. Thank you all for letting us know the problems, as well as your contribution to Rosetta@home!!!