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Proteopedia: A Powerful Tool for Biomolecular Communication and a 3D Web Encyclopedia of Biomolecules
Proteopedia is an interactive resource that facilitates understanding the role of 3D protein structures have in their biological function http://proteopedia.org (Fig. 1). Proteopedia is widely used in scientific research, in the preparation of papers for publication and teaching from secondary level to post-graduate.
Two main facts explain the popularity of Proteopedia in the teaching community: pages specifically designed for and by educators (Teaching Scenes, Tutorials, and Educators' Pages) and the exclusive Proteopedia’s Scene Authoring Tool that enables the creation of rich Jmol 3D scenes with zero learning effort.
Teaching Strategies Using Proteopedia:
Use Existing Pages
Of course, you can use existing pages in Proteopedia. Be sure to consider those specifically designed for and by educators, which are listed at Teaching Scenes, Tutorials, and Educators' Pages.
Proteopedia pages can be projected during lectures (if you Export them in advance or have an Internet connection in the classroom), and/or assigned to students as homework.
Author Your Own Pages
If you create your own pages, you will have scenes of the molecules that you are emphasizing in your teaching -- scenes that show exactly the structural features you wish to emphasize. See the Main Page (Fig. 1) for links to videos that show you how to author pages in Proteopedia. Customizing molecular scenes is amazingly easy with Proteopedia's Scene Authoring Tool.
Again, see some examples at Teaching Scenes, Tutorials, and Educators' Pages.
Fig. 1. Main Page of Proteopedia showing the green hyperlinks that when clicked result in a change in the 3D Jmol figure to reflect what is described in the text.
Worksheets
A low tech, but quick-to-prepare lesson plan involves distributing worksheets of questions regarding the molecular scenes on a particular Proteopedia page. These worksheets can be on paper, a web page (which could be on a page in Proteopedia), or within your local courseware system. Students in a computer lab can do such worksheets in class, concurrently, perhaps in pairs, which fosters discussion. The questions can be purposefully vague, to encourage discussion -- in which case completion could be simply "checked off" rather than graded in detail. Such worksheets give focus and a finite completion goal to each student. In contrast, simply assigning students to read a Proteopedia page may leave them less focused and perhaps uncertain about whether they have absorbed what you intend from the page.
Quizzes
Proteopedia has a mechanism to include quizzes on pages you prepare for your students. See Help:Quiz.
Student Authoring of Projects as Permanent Proteopedia Pages
Upper level undergraduates, e.g. biochemistry majors, or graduate students may be assigned to complete a project in the form of a permanent Proteopedia page. A particularly outstanding example, Photosystem II (Fig. 2), was authored by Emily Forschler while she was a senior biochemistry major at Messiah College (Grantham PA US) in a class taught by Karl Oberholser. Professor Oberholser reported "I think that Emily's work on Photosystem II shows that Proteopedia is a system that a Jmol novice can use with good effect. Emily had no experience with using Jmol. The other students in the class ... [made] PowerPoint presentations of their chosen proteins, and after seeing Emily's Proteopedia presentation one student's response was all of us should have used Proteopedia. Thank you for a great product!" Another strategy for a small, upper level class is to have individuals or small groups author pages that address a particular topic. Ann Taylor has used this at Wabash College to create pages on Glycolysis Enzymes, Citric Acid Cycle and Proteins involved in cancer. Any student planning to author a permanent page should request a personal user account in their own real name, identifying themselves as a student, and their college. See, for example, Emily Forschler. The pages for the project can then be created as subpages of an individual’s user page (find out how to do that at Help:Protected_Pages). The use of the protected pages insures that the page will be editable only by the student and not subject to alterations possible for typical sandbox pages. The project could then later always be copied to standard Proteopedia page so others can improve it.
Fig. 2. Photosystem II page of Proteopedia was authored by Emily Forschler while she was a senior biochemistry major at Messiah College (Grantham PA US) in a class taught by Karl Oberholser.
Student Authoring of Temporary Proteopedia Pages: Sandboxes
Some educators have assigned their students to try out authoring a Proteopedia molecular scene or two, just to learn the process, without making permanent pages in Proteopedia. Proteopedia has Sandbox pages where you or your students are invited to try authoring. The contents of these pages are not permanent, and will be erased or replaced at a later time.
Molecular Structure: FirstGlance in Jmol
Every page in Proteopedia that is titled with a 4-character PDB code has a link to FirstGlance in Jmol. FirstGlance makes it easy to explore the molecular structure in more detail (and, like Proteopedia, it can use Java but also works without Java). FirstGlance reports the number of chains of protein, DNA, RNA, and lists all ligands and non-standard residues with their full names. You can click on any of these to find them. Sequences can be displayed and short sequences can be found. With one click each you can see secondary structure, amino and carboxyl termini, hydrophobic cores (two clicks, one to slice through the center with "Slab"), positive and negative charges, and much more. Tools locate disulfide bonds, salt bridges, cation-pi interactions, and non covalent bonds to any moiety you specify. Help and color keys appear automatically.
When students are given a worksheet or a list of suitable questions, FirstGlance provides an easy way to see answers. Here are 20 questions assigned to students in a workshop. These questions apply to any protein; each student chose a different protein to investigate. Jaswal, O'Hara, Williamson and Springer (2013)[1] describe in detail how they use Proteopedia, FirstGlance in Jmol and student-authored presentations about their structure-function analysis projects in a one-semester biochemistry course at Amherst College (Amherst, Massachusetts, USA).
Who’s using Proteopedia?:
High School:
- as live support for lectures
- as live support for student’s self-paced learning
Universities:
- as live support for lectures
- as live support for student’s self-paced learning
- as media for Final Projects/Thesis
- as driving topic for Student’s Clubs
Researchers:
- as a source of information
- as a shared secure shared collaboration site
Journals:
- as an Interactive 3D Complement
Current modes for pages in Proteopedia:
Community domain:
Open read access, registered users write access
/Ribosomal_protein_S13
User domain:
Open read access, owner write access
/User:Eric_Martz/Resolution
User workbench:
Selected users read access, owner write access
/User:Eric_Martz/Workbench/Movements
Sandbox:
Scratch testing open pages
/Sandbox_prueba
Special Areas in Proteopedia:
Group domain:
Open read and write access
/Group:MUZIC:Interactome
/Group:SMART:Teams
Journal domain:
before paper publication: Restricted read and write access
after publication: Open read access, restricted write access
/Journal:PLoS_ONE:2
Studio domain:
Selected users read and write access
/Studio:G1SecL01
Proteopedia off-line:
Exported pages:
Off-line, self-contained, active Proteopedia pages
References:
1. Jaswal SS, O'Hara PB, Williamson PL, Springer AL. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course. Biochem Mol Biol Educ. 2013 Sep-Oct;41(5):351-9. doi: 10.1002/bmb.20718. Epub, 2013 Sep 10. PMID:24019219 doi:http://dx.doi.org/10.1002/bmb.20718
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Comments
DOIs and Wikis
Dear Jaime and Joel,
Thank you for contributing this paper. How you have used hypertext to connect the narrative of a text to a visualization is really something worth discussing and thinking about. But I am going to ask a simple question. You have connected a DOI to a Wiki. Could you discuss this? Both philosophically (a Wiki is ephemeral, changing over time, while a DOI is supposed to be static (I think) and not change - you may want to discuss what a DOI is), and who is responsible for the maintenance of the DOI? But I think you have an interesting publishing paradigm here. (Actually, I think you have done more than that, and changed the actual layout of the textbook, effectively merging the caption of an image with the text proper, with the image changing as one reads the text).
Thank you for sharing your work with us.
Cheers,
Bob
DOIs and Wikis
Dear Bob,
Good point. Thank you for bringing this up. Proteopedia introduces here a new publication model.
It's correct that Wiki pages are dynamic, allowing for the continuous improvement by multiple collaborators. This is the basic essence of the Wiki and of Proteopedia itself.
At the same time, Proteopedia keeps a complete history of each version of a given page, enabling at any time to retrieve the page as it was on a particular date and time. The link "Permanent link" located at the bottom of the left hand side toolbar of Proteopedia, provides a URL to a version of a Proteopedia page that remains static, despite any further modification. A Proteopedia DOI points to one of these Permanent links, i.e. a frozen in time version of a page, and not to the latest default available version.
When Proteopedia's Editorial Board rules that a page reaches a mature state, that page is granted a DOI, a unique identifier that will permanently point to that state of the page frozen in time. At this stage, the content of the page is equivalent to a paper publication. The page remains open for additions and further improvement, as expected in a collaborative wiki dynamic environment. When the new information and accumulated changes represent a significative improvement in the page, it can effectively be considered as a revised version of the previous published paper and will be granted a new DOI.
A complete explanation is available at http://proteopedia.org/w/DOI .
Jaim
How to reserve Proteopedia pages for your students?
It is possible to reserve a group of Proteopedia pages for your students to practice during your course. These pages enable your students to try out authoring a Proteopedia molecular scene or two, just to learn the process, without making permanent pages in Proteopedia.
To reserve a block of pages for your course go to http://proteopedia.org/w/Special:SandboxReservation
For additional information and other Teaching Strategies with Proteopedia go to http://proteopedia.org/w/Teaching_Strategies_Using_Proteopedia
Jmol and JSmol
Jaime and Joel,
Thank you for sharing this valuable project with us. A couple of years ago I registered as a user on Proteopedia with the intent to set up some pages to help my research students get up to speed with the protein that we study computationally. At that time the site was using Jmol exclusively, since JSmol did not yet exist. I notice that all the pages I have seen recently use JSmol instead. I appreciate the conversion to JSmol, because I've had my share of troubles with Java. Is the conversion to JSmol complete? Or is the site responsive, using JSmol when users do not have Java enabled in their browsers?
Jennifer
Jmol and JSmol
Proteopedia in full defaults now to the HMTL5/Javascript mode, called JSmol. This is also true for Proteopedia's Scene Authoring Tool (SAT), allowing the authoring of molecular scenes even on a Tablet.
Jmol has evolved a lot and performance of the HMTL5/Javascript mode is very good and improving every day, thanks to the continuous work of Robert 'Bob' Hanson and the Jmol Development Team.
However, as today Java remains the best for performance when rendering large structures, Proteopedia provides a couple of ways for choosing Java over the default HTML5/JavaScript described at http://proteopedia.org/w/Using_Java_for_Rendering_Structures
Jmol and JSmol
Hi Jennifer
About the "responsive" idea, the issue is that currently there is no reliable way to detect whether Java is installed and enabled in the browser. Added to that, the strong security imposed by Java puts the user through diverse dialogs before the applet is loaded. So an automatic decision on whether to use Jmol-Java or JSmol-HTML5 cannot be implemented. That's why a default may be coded in the page (JSmol in the case of Proteopedia) but the switch to the other must be left to the user.
Apart from the configuration options that Jaime has mentioned, in many pages that use a current version of Jmol/JSmol you can force the modality by appending a parameter in the URL; the JSmol Javascript library takes care of checking for that. For details, see http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Setting_parameters_from_the_URL
Proteopedia technologies, uses in and out of proteomics
Dear Joel and Jaime,
Please forgive me if these questions can be answered by navigating the Proteopedia site. I went and created an account, but am travelling and will not have the chance to thoroughly investigate things before the discussion is over.
My first question deals with coupling audio to the Jmol visualizations. I understand from dual coding information processing theories that by coupling audio to visual modes of information acquisition you effectively use less working memory, making it is easier to process information for long term memory. It seems that an audio narrative option for the Jmol visualization could be of great value. I am not saying “speak the script” of the text with the green links, but a second script about the objects of the green links that sort of juxtapositions the object to the narrative, bringing forth the salient features the author wishes to emphasize. This could be activity/project oriented, like what is the distance between these two atoms-where the student interacts with the Jmol to determine the answer. This second audio-script could also end with leading questions or statements, that transition back to the original narrative. A sort of audio based guided inquiry approach.
Do you have any other types of objects which are placed into these frames (other than Jmol), like spectra, tables, simulations, figures, …..?
Please pardon my ignorance, but are there other resources that provide this type of activity in chemistry, or other disciplines? I do not mean just mean coupling Jmol to the text, but the coupling of any digital object to the text by continually directing links to a dynamic text-dependent object hosting frame, or whatever it is that you host the Jmol in. But you have sort of placed the text into the caption of an image that changes as the text changes. Are there other sites that are doing similar things? Are your authoring tools limited to Jmol? Are they open source? Can they be repurposed outside of proteomics and into other areas of chemical education, like freshmen chemistry?
This really is fascinating work, and thank you ever so much for sharing it.
Sincerely,
Bob Belford