Unfortunately within the Gna! infrastructure (http://gna.org/) or open source hosting infrastructure in general, there is no support for wikis. Or any dynamic content for that matter. The Gna! website infrastructure behind http://www.nmr-relax.com is quite simple, the most advanced it does is SSI. But the PHP required for a wiki implementation is not there (https://gna.org/cookbook/?func=detailitem&item_id=108). I pay for the http://www.nmr-relax.com domain name myself, so could create the http://wiki.nmr-relax.com/ URL, but I have no fixed IP address server at home or at work to point this to. Would you know any solutions to such problems?
Regards, Edward On 30 May 2013 23:47, Troels Emtekær Linnet <[email protected]> wrote: > By the way. > > Would it be possible to implement a wiki? > > It would be beneficial, for a little "loser" user control, to write up > some scratches, how to for example script up some analysis, > of for example CPMG. > > I have looked into making a page at "http://nmrwiki.org/"; > But they seem to have problems (for a long time now), so > you can't edit anything. > > Best > Troels > > > > Troels Emtekær Linnet > > > 2013/5/30 Troels Emtekær Linnet <[email protected]>: >> Uhhh, that is great. :-) >> >> Looking forward to try! >> >> Troels Emtekær Linnet >> >> >> 2013/5/30 Edward d'Auvergne <[email protected]> >>> >>> Hi Troels, >>> >>> The relaxation dispersion GUI in relax is now fully debugged and >>> functional. Well as far as I can tell anyway. Enjoy! >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 30 May 2013 17:34, Edward d'Auvergne <[email protected]> wrote: >>> >> You are very productive! and I am stunned to see the development >>> >> so fast. :-) >>> > >>> > Well, I'm sorting out the code for myself specifically for my own >>> > R1rho analyses. I'm guessing you are interested in the CPMG side of >>> > things. >>> > >>> > >>> >> I think you are hitting "the nail" with the current development of relax. >>> > >>> > There's not much left to finish with the base infrastructure. As for >>> > adding new models, that's a different, but relatively easy story. The >>> > numerical integration of the Block-McConnell equations might take more >>> > effort to add but, as all the infrastructure is in place, it shouldn't >>> > be too hard. Integrating with the other softwares (input file >>> > creation, execution, and reading of results - for NESSY, CPMGFit, >>> > ShereKhan, Catia, Chemex, etc.) will be a continual work in progress. >>> > It will be advanced when someone needs it, this is currently myself to >>> > fully automate the comparison between all the different dispersion >>> > programs simply for sanity purposes. >>> > >>> > >>> >> At the moment the "hardest/time consuming" part for students in our lab, >>> >> is >>> >> the analysis of the >>> >> results. We have a good workflow from recording and peak assignment. >>> >> But from there, it gets more tricky. >>> > >>> > I know this problem well :) >>> > >>> > >>> >> Most of our analysis part is based on "home made" scripts for Igor >>> >> Pro/Matlab. >>> > >>> > Ah, the code for the dispersion models shouldn't be too difficult to >>> > port into relax if you already have Matlab code in place! >>> > >>> > >>> >> They come a long way for most of our analysis. >>> >> The problem is that for a "beginner" there can be a "high energy >>> >> barrier" to >>> >> start >>> >> using these scripts. Not mentioning "license problems", installation and >>> >> such. >>> >> And if you have to make some peak adjustments, then the whole analysis >>> >> should be performed again. >>> >> For a "trained" this takes some hours, but for un-trained, it can take a >>> >> day >>> >> or two. >>> > >>> > I understand this, and this is one useful advantage of a GUI. I don't >>> > know how you would avoid having to redo a full analysis if the input >>> > data is changed though, except that maybe you could have a relax save >>> > file for the GUI analysis and slightly tweak the data already within >>> > relax, and the rerun the full analysis. >>> > >>> > >>> >> We have been looking for other software for CPMG. >>> >> At least to "quickly" try to match our scripts values. (Here Nessy >>> >> seemed >>> >> very interesting, but very buggy) >>> > >>> > I am now the maintainer of NESSY so I can fix some of the trivial >>> > bugs. I have been doing this for a few annoying bugs, for example >>> > see: >>> > >>> > https://mail.gna.org/public/nessy-commits/2013-05/threads.html >>> > >>> > However finding the big bugs and improving the optimisation will not >>> > be possible for me at the moment. >>> > >>> > >>> >> But concerns about installation, development, and even a "harder" >>> >> interface >>> >> than Igor Pro/Matlab, stopped us. >>> >> We(as in me) are at the moment matching some test results at the >>> >> Sherekhan >>> >> server, after making >>> >> a input converter to Sherekhan. That seems to be very easy, and >>> >> promising. >>> > >>> > relax now has this as well in the relax_disp.sherekhan_input user >>> > function. You can access this from both the prompt/script mode and >>> > the GUI. I've noticed though that the ShereKhan numerical integration >>> > of the Block-McConnell equations is currently problematic and the poor >>> > little tiger just runs forever! >>> > >>> > >>> >> I am very impressed with relax. Mostly because the GUI can take care of >>> >> novices, and there exist the possibility to >>> >> script it all up for extensive analysis. >>> >> It's free, and I was able to install it on Windows/Linux without to much >>> >> fuss. >>> > >>> > Cheers! That is exactly what the relax developers have tried to create: >>> > >>> > - the GUI is really for those who don't have much interest in the >>> > theory and just want quick, idiot-proof results from a blackbox (i.e. >>> > perfect for undergrads), >>> > - the prompt/script mode is for power users with interest in the NMR >>> > theory and analysis, >>> > - the prompt/script mode in combination with the relax library >>> > functions is to be a replacement for Mathematica/Matlab for those who >>> > want to live on the cutting edge. >>> > >>> > >>> >> If I want to try some of our data, is the GUI ready for trying? >>> > >>> > There are a few minor bugs I have to sort out first. For example with >>> > the error analysis for peak heights. It should be ready for the >>> > 'R2eff' and 'LM63' models soon though. Still, right now you can do >>> > everything except for clicking on the 'Execute analysis' button. I >>> > hope it won't take too long. >>> > >>> > Regards, >>> > >>> > Edward >>> > >>> > >>> > >>> > >>> >> 2013/5/29 Edward d'Auvergne <[email protected]> >>> >>> >>> >>> Hi, >>> >>> >>> >>> Troels, you might be interested in the following comparison. The >>> >>> reviving Sebastien Morin's relaxation dispersion branch in relax is >>> >>> now complete. The relax_disp branch can now correctly optimise one of >>> >>> the dispersion models, that of Luz and Meiboom 1963 for 2-site fast >>> >>> exchange for CPMG-type experiments. This does not implement the >>> >>> gradients or Hessians yet, and parameter constraints are still to be >>> >>> added. But nevertheless relax can find the correct parameter values. >>> >>> This should be a good test of the dispersion code in relax as the >>> >>> addition of other models - such as that for R1rho data, more >>> >>> complicated models for CPMG-type data, and numerical integration of >>> >>> the Bloch-McConnell equations - should be trivial after that >>> >>> (requiring only 20-50 lines of new code, not counting comments and >>> >>> docstrings). >>> >>> >>> >>> Through relax user functions, I can now generate the input for CPMGFit >>> >>> and NESSY. These are the relax_disp.cpmgfit_input and >>> >>> relax_disp.nessy_input user functions. We can now also execute >>> >>> CPMGFit within relax using relax_disp.cpmgfit_execute. This can be >>> >>> completed later, but the idea is to follow the concept of model-free >>> >>> user functions: >>> >>> >>> >>> dasha.create >>> >>> dasha.execute >>> >>> dasha.extract >>> >>> palmer.create >>> >>> palmer.execute >>> >>> palmer.extract >>> >>> >>> >>> These are for the Dasha and Modelfree4 programs respectively. >>> >>> Implementing the 3 user functions for creating input files, executing >>> >>> the program in-line, and extracting the results from the program's >>> >>> output will allow relax to use external programs as optimisation >>> >>> engines. This is useful for comparing the results from different >>> >>> programs and really eliminating all bugs from the dispersion field. >>> >>> >>> >>> Back to the comparison, I have used Flemming Hansen's 500 and 800 MHz >>> >>> CPMG data from: >>> >>> >>> >>> Hansen, Vallurupalli & Kay, 2008, JPhysChemB, 112: 5898-5904. >>> >>> >>> >>> which he donated to Seb to be added to relax (located in >>> >>> test_suite/shared_data/dispersion/Hansen/). Looking at a single >>> >>> randomly chosen residue (number 70), I see different results from the >>> >>> 3 programs: >>> >>> >>> >>> Param relax NESSY CPMGFit >>> >>> R2 (500) 6.806 7.639 6.866 >>> >>> R2 (800) 6.679 7.387 6.866 >>> >>> phi 1.259e-13 0.259 1.226e-13 >>> >>> phi (500) 31464.605 26292.031 30644.496 >>> >>> phi (800) 80549.390 67307.598 78449.180 >>> >>> kex 4763.249 3906.180 4.683 >>> >>> tau 4.199e-05 5.120e-05 0.427 >>> >>> chi2 106.393 156.446 106.471 >>> >>> >>> >>> tau = 2/kex (I think that CPMGFit works with ms units). >>> >>> >>> >>> Obviously NESSY is not doing so well (likely due to using the horribly >>> >>> buggy scipy optimisation code) and relax and CPMGFit find the same >>> >>> result for this model. The slight difference between relax and >>> >>> CPMGFit is that it looks like CPMGFit assumes the same R2 value for >>> >>> all static fields - which I think would be a little strange, >>> >>> especially if fast internal motions are also present for that spin >>> >>> system. >>> >>> >>> >>> Therefore I believe that this relax branch is in a state to accept >>> >>> code for the other models. The backends for the >>> >>> relax_disp.cpmgfit_input and relax_disp.nessy_input could be also >>> >>> modified to handle these new models to allow for rigorous comparisons >>> >>> and debugging. The dispersion infrastructure should no longer have >>> >>> any large changes, so feel free to start playing. >>> >>> >>> >>> Regards, >>> >>> >>> >>> Edward >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> relax (http://www.nmr-relax.com) >>> >> >>> >> This is the relax-devel mailing list >>> >> [email protected] >>> >> >>> >> To unsubscribe from this list, get a password >>> >> reminder, or change your subscription options, >>> >> visit the list information page at >>> >> https://mail.gna.org/listinfo/relax-devel >>> >> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
