Order swapped.
On Oct 30, 2010, at 11:36 AM, Keren Lasker wrote: > > My suggestion is: > module/example - simple examples of specific code as now > module/bin - utilities to run functionalities of the module that > produce meaningful output (basically what that is in applications now > and javi's 2dem/bin is a great example) > applications/method - subdirectory for each complete method (paper) + > tutorial if written > applications/systems - subdirectory for each biological system (such > as Nup84 This is the current organization, there is just a shortage of things in all of the categories, especially as one gets further down the list :-) We also don't have a way to specify for an application whether the code is intended to be read or not (so it should be include in the list of examples).
> i am not completely sure how to best divide application module/bin, > module/example. > To my understanding applications was suppose to be a complete protocol > for a specific complex (such as Nup84). > I added simple scripts like resampling / simulating density maps to > applications/em, but they should probably move to em/bin. > the problems with the current system are: > 1. when someone opens IMP and looks for where to start, it would be > good to direct to clear and simple tutorials. This is not the case now. Sure, there should be more tutorials/examples in a easy to find place, but I don't see that an example module vs a tutorial module is a clean divide to have both.
> 2. each application in application/module and tutorials uses more > than one module, so users that want to look for application of modeling > +em should go to atom / modeller / em / 2dem / multifit - its not > clear.
Yeah, it would be nice to automatically generate links from a module to all example code which uses it. I'm not sure how to do things, but I haven't looked. Just scanning the example files from other places for "import IMP.modulename" and "#include <IMP/modulename" and including this list in the example page for the module would be pretty easy to implement.
> > > On Oct 30, 2010, at 11:13 AM, Dina Schneidman wrote: > >> we also have applications... >> >> On Sat, Oct 30, 2010 at 10:47 AM, Keren Lasker kerenl@salilab.org >> wrote: >>> because they are a set of scripts that should be run together. >>> so it more of a protocol then an example of a specific functionality. >>> On Oct 30, 2010, at 12:49 AM, Daniel Russel wrote: >>> >>>> How are tutorials different from examples? >>>> >>>> On Oct 29, 2010, at 11:15 PM, Keren Lasker wrote: >>>> >>>>> >>>>> We have few sets of tutorial scripts that are currently scattered >>>>> in >>>>> various modules within imp and outside of imp. >>>>> I think it would make sense to have a module named tutorials and >>>>> then >>>>> subdirectories for the different tutorials. For example, our recent >>>>> book chapter on assembly modeling by comparative modeling and em >>>>> can >>>>> go there. >>>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev