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presentaBALL
by Stefan Nickels, Daniel Stöckel, Sabine C. Mueller, Hans-Peter Lenhof, Andreas Hildebrandt, Anna Katharina Hildebrandt
If you want to understand function, study structure! (Crick 1988)
Image(presentaball-structure.jpg, 30%)
Easy yet powerful dissemination of structure based research results at conferences or trade fairs, the preparation of lectures, or the development of massive open online courses (MOOCs)
A presentation in PresentaBALL is made up from two kinds of information: on the one side, we have molecular systems, on the other, '''text and images describing''' the structures and their features, such as their function or other scientific findings.
A web interface is embedded into BALL's graphical frontend BALLView, and provides complete, interactive '''access to loaded molecular data'''.
PresentaBALL uses established web technology standards to provide a freely configurable browser-based interface into the extensive modeling and visualization capabilities of our Biochemical Algorithms Library (BALL).
Image(Presentaball_workflow.png, 40%)
The molecular scenes can be pre-arranged in BALLView, made persistent using our BALLView project file format (.bvp), and all non-molecular content of the presentation can be developed using standard tools for web design.
The textual content, illustrative images or movies, or interactions with the user, are then combined into HTML pages. For this task, the designer can choose from a variety of powerful intuitive tools for web content creation. To then bridge web page and molecular visualization, he includes hyperlinks of the form
{{{ Computer-aided Drug Design }}} Activation of this link will call the loadProject - function implemented in the predefined python module common_functions provided by PresentaBALL. The filename-argument is passed to the function, which then proceeds to locate the BALLView project file 1mah_o_ligand.bvp in a subdirectory projects of BALL's search path (BALL_DATA_PATH). The project is then loaded, all molecular content and visual representations are added to BALLView, and visualization options such as lighting or material settings are restored.
During content creation, the designer can choose from many pre-defined actions. Exemplary functionality offered by our common_functions python module are:
- loadProject - loads a BALLView project file, e.g., representation models, camera and light settings
- setViewPoint - move the camera to a predefined position and orientation, e.g., to peak into a binding pocket
- selectByExpression - highlight parts of a molecule using BALL's molecular expression syntax, e.g., ligands, chains, or binding pockets, to focus the user's attention
- showOnlyRepresentationsByNames - limit representations to the list of given ones, e.g., to provide a more detailed view of a binding pocket
- toggleRepresentationsByNames - show/hide representations, e.g., to add representations of ligands or to display mutation variants
- toggleSelectionByExpression - turn highlighting of regions of interest on/off
You can download and install a pre-release version of BALLView (Windows x86-64) including the PresentaBALL plugin here. Officially, PresentaBALL will be part of the upcoming BALL/BALLView release (1.5).
PresentaBALL is a Plugin of BALLView and as such needs to be activated.
This can be done via the Menu Edit-> Preferences ->Plugins (not the menu entry PresentaBALL_PLUGIN). Click on the green plus button and a dialog for chosing the plugin directory opens. Chose the bin folder within the folder where BALL was installed (probably something like C:Programme\ball-1.4.79\bin). Then activate the plugin and confirm.
Now, within BALLView the PresentaBALL widget was added.
For trying a lesson the windows "Structures" und "Representations" can be closed (via the "x" symbols or the menu Windows). If you plan to show the lessons on fairs etc. you should switch off everything but Scene and PresentaBALL via the menu Windows, kids love to click on everything and providing them with full modelling functionality is not what you want :-)
A number of lessons are already provided, e.g. Headache, HIV etc. Just check it out or create your own lessons.
=== Create your own lesson ===
- Prepare a molecular scene and store as bvp file (default is BALL\share\BALL\data\projects)
- Prepare the textual content, e.g. copy one of our html files (e.g. BALL\share\BALL\data\HTMLBasedInterface\html_eng\aspirin.html)
- Pass your lesson page to the plugin via Edit->Preferences->Plugin->PresentaBALL_PLUGIN as user defined start page