Presentations in Protein Explorer (PiPEs)
Last updated February, 2005

At long last, Protein Explorer (PE) now supports presentations. For examples, full documentation, and a template with instructions for creating your own Presentations in PE (PiPEs), go to proteinexplorer.org and look for the version supporting presentations.

Two categories of PiPEs exist, each aimed at different audiences. In both cases, the advantage is that any image in the presentation can be explored with the full power of Protein Explorer.

  1. Research and Database Communication
  2. Educational Tutorials


Presentations in Protein Explorer I:
Research and Database Communication

Several bioinformatics research groups have expressed interest, but so far only one has implemented a working server. Because PIPE support and documentation are still under development, implementation required a close collaboration between Eric Martz (working on PE) and the research group in Tel-Aviv. Once full support and documentation for PIPE have been released, it should be possible to author such resources with little or no assistance from Martz.


Presentations in Protein Explorer II: Educational Tutorials

The presentations below were prepared before the public release of PE supported presentations. They employ a now-obsolete format. They remain here for the historical record, and for those interested in their subject matter. The publically released and supported format for new PiPEs, along with example PiPEs, full documentation, and a template for creating new PiPEs can be found at proteinexplorer.org.


These presentations were created by students in Macromolecular Visualization Lab (Microbiology 597V).

These tutorials are presented within Protein Explorer. This means that any image in the presentation can be explored with the full power of Protein Explorer if desired. The presentation interface within Protein Explorer is currently under development. It will not be generally available until it is completed, at which time a link to the documentation and download site will be placed here. Because it was in a partially developed state when the tutorials below were developed, they have some instability and limitations. It is best to allow plenty of time after pressing a button for the javascript to catch up before pressing another button. If it crashes, close it, start again and be more patient between buttons!


2000 version of Protein Explorer with latest (fall 2000) under-development version of Presentations in Protein Explorer (PIPE).
This version of PIPE adds pop-up details, presentation controls for details, font size, and documentation for the controls. It has 3 modes: one person, audience (for projection), and development. It operates in PE 1.72-beta. An alpha-test version of a script recorder was used by the students in authoring their presentations, but because it is in a rough state, the script recorder is not included in the copies here. Unless otherwise indicated, these require an older version of Chime, (2.0.3 for Windows), which is available from MDL.)


The presentations below are offered primarily for their top-quality content. Both of the presentations below have benefited from a great deal of effort by these students beyond what was required in the course.
(These operate in PE 1.1-beta, fall 1999, in the fall 1999 under-development version of Presentations in Protein Explorer. Unless otherwise indicated, these require an older version of Chime, (2.0.3 for Windows), which is available from MDL.)