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.
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