Posts by noelia

1) Message boards : News : Noelia's PhD defence and departure (Message 43026) Posted 17 Mar 2016 by noelia Post: Dear all, I have defended my doctoral thesis very recently, on March 4th, and it would have been impossible without your support. My thesis focused on the understanding of ligand-receptor interactions on a different set of systems, in all cases by running simulations in GPUGRID. The thesis itself will be publicly available after an embargo period (here is the link in any case: http://hdl.handle.net/10803/363212) due to the still-unpublished works it contains. In summary, with the support of GPUGRID we have produced works on seven systems, three are already published, two under review and the two left will be submitted very soon (so expect new badges soon!!). I must also say that I will be no longer working in GPUGRID. I have already moved to Boston where I will apply the methods that I have learned working on here to drug discovery programs. Many thanks again, Noelia
2) Message boards : News : Badges ready for the last paper! (Message 42404) Posted 16 Dec 2015 by noelia Post: Hello guys! We recently published a paper which used a considerable amount of GPUgrid simulations. It would not have been possible without your contributions. The paper is: N. Ferruz, M. J. Harvey, J. Mestres and G. De Fabritiis, Insights from Fragment Hit Binding Assays by Molecular Simulations, J. Chem. Inf. Model., 2015, 55, pp 2200-2205 You can also browse ranking positions ;) : https://www.gpugrid.net/science.php?topic=methods Thanks to all! Noelia
3) Message boards : Number crunching : NOELIA Error (Message 42159) Posted 13 Nov 2015 by noelia Post: Hi KSUMatt, Sorry to hear your about your error. Just tried in a local machine and worked fine, we're having a look at it. Please report if this error pops again. Thanks for your time! Noelia
4) Message boards : Number crunching : Short runs (Message 41250) Posted 4 Jun 2015 by noelia Post: Hi Speedy, This short tasks are based in the Dopamine 3 receptor. It is a target for treating schizophrenia, Parkinson's, drug abuse and other neurological disorders. This receptor is involved in many complex pathways in the central nervous system and its dysfunction affects in a variety of neuropsychiatric disorders which are not yet well understood. With this experiments, we are trying to understand how eticlopride (ETQ) interacts with it and exerts its action. This molecule is known to bind and block the receptor, and therefore it is mainly used for the schizophrenia treatment. It's mechanism of binding, although would be very interesting for the design of other similar molecules, it is yet not known and that's what we are trying to understand with this simulations. Many thanks for your time!
5) Message boards : News : WU: THROMBIN (Message 37133) Posted 23 Jun 2014 by noelia Post: Hi guys, There was a bug for some unexpected reason in this batch and we apologize. As you were having problems validating i've cancelled those WUs that still were unsent and resend them -THROMBIN1-. Those which were running can still be completed and you won't lose any credit. Theoretically minimum quorum should be now 1, but please report if you notice any problem. Noelia
6) Message boards : News : WU: THROMBIN (Message 37079) Posted 19 Jun 2014 by noelia Post: Hi guys!! There's a new project in the long queue ( NOELIA_THROMBIN ) . It consists of the binding of 6 different inhibitors to the protease thrombin, a protein in the coagulation cascade. With these, we are trying to demonstrate that molecular simulations can be as useful as X-Ray crystallography predicting binding modes. Thanks to all, P.D: Report any problems please! Noelia
7) Message boards : News : WU: TRPS1S4 (Message 37042) Posted 12 Jun 2014 by noelia Post: Hi Jeremy, Yes, there was a problem in the configuration file of those batches - which made they had no charm in windows indeed! - I tested the WUs in a linux workstation so didn't notice any issues. Stopped and fixed those ones and all the series TRPXXX and SH2XX should not have any problem now. Thanks!
8) Message boards : News : WU: TRPS1S4 (Message 37036) Posted 11 Jun 2014 by noelia Post: Dear all, Just sent 1000 WUs under the group name TRPS1S4. This is probably the last batch of a project you've been crunching for more than one year now (WUs: FXA, FXArep.. and similar names) for thrombosis disease. This last batch is particularly important, since will allow us to see if these simulations can predict experimental outcomes. Please report any problems. Thanks to all and happy crunching! Noelia
9) Message boards : News : WU: BI_3 (Message 36866) Posted 19 May 2014 by noelia Post: Hi all! Just sent a new project to the long queue, around 2500WUs, ~100,000 credits each. In particular, this project will help us to understand how antidiabetic drugs block its target, but also to develop a better general method for other targets and drugs involved in different diseases. Thanks to all!!
10) Message boards : News : WU: FXArep (Message 34601) Posted 8 Jan 2014 by noelia Post: We realized we needed one last bunch of WUs to finish the project. We've already started writing, so should be able to post final results sometime soon, hopefully :) thanks!!
11) Message boards : News : WU: RL1_run (Message 33616) Posted 25 Oct 2013 by noelia Post: Hi all, Just sent a bunch of ~1600 WU to the short queue. It won't last very long, only one step. Thanks!!! Noelia
12) Message boards : News : WU: FXArep (Message 33461) Posted 11 Oct 2013 by noelia Post: Hi all, I have just sent a good bunch of WU (4000) to the long queue. Only two steps, 90000 credits each. With the analysis of this last batch, we will be able to finish a project on drug discovery for the thrombosis disease. Please let me know if you find any problem, although these simulations were already on the long queue some moths ago and should run fine. Noelia
13) Message boards : News : WU: NOELIA_INS1P (Message 32663) Posted 3 Sep 2013 by noelia Post: Hi all, New WUs in the long queue, big-box size, 120000 credits each. The batch has been previously tested and should not report any issues, but please comment any problems you might have. Noelia
14) Message boards : News : WU: NOELIA_KLEBEs (Message 32444) Posted 29 Aug 2013 by noelia Post: Hi, for some reason some of you are having problems with this WUs in the new application and we've moved them to the beta queue to have a proper look. I've also just sent 50 WU under the name KLEBEbeta with a much simpler configuration file. These simulations are really important, and fixing this bug will also help for future similar projects in drug discovery. Please report any problems you might have on groups KLEBEs and KLEBEbeta.
15) Message boards : News : New project in long queue (Message 28895) Posted 1 Mar 2013 by noelia Post: Hello all, After testing the new application, it is time to send a new project. I'm sending at the moment around 6000WUs to the long queue. Credits will be around 100000. Let me know if you have any issues, since is the first big thing we submit to the recently updated long queue and these WUs include new features. Noelia
16) Message boards : Server and website : GPU Results ready to send - number dwindling (Message 28786) Posted 26 Feb 2013 by noelia Post: We'll send a new big project to the long queue very soon.
17) Message boards : News : βeta and short queue jobs (Message 28440) Posted 7 Feb 2013 by noelia Post: Hi guys!! I will be sending a good bunch of WUs to the short queue during the following days. Group names "RC1_run" and "RL1_run". A total of 13624 jobs will be submitted in total, once the first step -currently ongoing in the betaqueue- is finished for each of them. Around 1200 already submitted. Thanks a lot!!!!
18) Message boards : News : Beta testing starting soon (Message 28436) Posted 7 Feb 2013 by noelia Post: Actually yes, WUs in betaqueue right now are the first step of the simulations which will be sent to short queue. So this is already the real thing.
19) Message boards : News : New systems in Long queue (Message 27733) Posted 19 Dec 2012 by noelia Post: Hi all! A good amount of new WUs will be around for the next weeks in the long queue. The systems are called hfXA_long and will provide around 90000 credits each. Thanks and Merry Christmas to all!! Noelia
20) Message boards : News : New systems in long queue (Message 27672) Posted 12 Dec 2012 by noelia Post: Dear volunteers, Batch group "sh2forces" requires extensive CPU usage and that's why some of you have noticed a big slow down. Same problem as we were having with previous systems: http://www.gpugrid.org/forum_thread.php?id=3116 but we won't send any of this kind anymore. The group had 100 WUs, but it is aborted now. Noelia

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