Re: [IMP-dev] tutorials module in IMP?

[Keren Lasker <kerenl@salilab.org>]

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.
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.
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)
I do not have strong preferences either way so what ever decided is ok  
with me, as long as we will decide on a clear definition for what  
should go where.

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.
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