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

As an IMP user I cannot help but jump into that conversation.

Maybe it's because I am a mathematician, but I think setting the terminology is an important prior work, and I have the feeling all terms are not well specified yet, though there seem to be a slow convergence towards the following semantics :

 - Examples : a very short piece of code solely intended to highlight the very specific aspect it exemplifies (e.g. the sample code on the ConnectivityRestraint html page).
If I understand it well, examples are actually found in modules/example subdirectories only in the svn source dir (i.e. not in the installed dir), and automatically included in the manual pages. I think it is OK like that, though it might be useful to let the user install examples as well, maybe in a distinct directory (share/examples/modules/ ?).

 - Applications : utility scripts and binaries developed on top of IMP (fox application, multifit scripts, scripts to transform coordinates of atoms in a PDB file)
I am not sure I like the term 'application' because it is somehow ambiguous and could be read as 'application of IMP', thus biasing expectations towards 'examples', 'tutorials', 'exercises', or 'biological applications'. As a replacement I would suggest softwares, binaries, utilities, executables… Anyway, this is probably a matter of taste, and any choice is good as long as the definitions are documented (for instance on the first page of the manual).
I don't know also if it would not make sense to discriminate between 'utilities' (isolated scripts or binaries that can be used to achieve useful tasks in various situations, such as the transformations of coods for ATOMS in a PDB file) and plain 'software' (more connoted to a dedicated application : fox and multifit binaries), and maybe sort scripts in subdirectories for each distinct softwares so as to make clear for instance what belongs to the multifit protocol etc…

 - biological_systems : all scripts and data that where used in a published paper
Once again, I am not really keen on the term, but this time because I think it is not descriptive enough. Maybe biological applications would suit better. Also, it would be worth making clear the goals of this directory : providing examples of IMP usage in real life applications ? Providing base scripts that can be modified by users for testings/understanding how IMP works ? Providing a repository to ease re-run and verification of published works ? ...

I would also add tutorials :

 - Tutorials : A fully step by step documented script or series of scripts, intended to fully explain the usage of one or several IMP aspects. Writing tutorials is probably time consuming and notw gratifying at all, it is nonetheless critical to help people find their way among the main directions of a tentacular project such as IMP. I'll try and make my first "groping and discovering" scripts into a first tutorial that I'll place in the IMP wiki.

Le 5 nov. 2010 à 22:54, Daniel Russel a écrit :

Next version of the proposal:
- mudulename/bin becomes internal, undocumented, utility executables (eg the benchmarks). They will not get installed in build/bin or installed at all with imp. protein_ligand_score gets moved to

- applications which has executables that users are supposed to see (we will add facility to document the applications in a similar manner to how modules are currently documented). The code is not expected to be read by random users and the applications will get build into build/bin and installed in bin.

- a new directory, biological_systems will be added. In there will be scripts with data that have been published in separate papers about the biological system in question, The scripts should be written so as to be readable and modifiable by others.