Oh, the current solution for relax for such an idea is that users submit scripts for inclusion in the sample_scripts/ directory. These have the format of:
- Copyright header using the GPL3+. This tells other users who wrote the script and when, and if it was modified by anyone else. The licence itself is needed for redistribution with relax. - A verbose docstring which describes the problem and the solution of the script. - The code of the script. For example see http://svn.gna.org/viewcvs/%2Acheckout%2A/relax/trunk/sample_scripts/consistency_tests.py?content-type=text%2Fplain. It's not quite the same as a wiki, but it is the best we can do at the moment. Regards, Edward On 31 May 2013 08:58, Edward d'Auvergne <[email protected]> wrote: > 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
