Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching

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This is the online version of Part C of a book chapter entitled Publishing in Proteopedia: The Guide by Jaime Prilusky, Wayne Decatur, and Eric Martz."

Reference: Jaime Prilusky, Wayne Decatur, Eric Martz. Publishing in Proteopedia: The Guide, Advancing Methods for Biomolecular Crystallography. In NATO Science for Peace and Security Series A: Chemistry and Biology 2013, pp 277-295 [doi:10.1007/978-94-007-6232-9_24]



Advanced Authoring and Uses

There are myriad ways to further your skills in authoring Proteopedia content; however, none is probably more helpful than just further exploring the site. Here we will briefly list here a few routes we hope you’ll consider.

  • You can incorporate scrollable sections to your pages, for an example see Glutamate receptor (GluA2).
  • Having earlier in this guide learned to cite references from PubMed using the PMID shortcut, you could learn to efficiently handle using the same citation multiple times on your page, see for example Help:Editing#Repeat citations.
  • Develop a page for presenting a structural paper in journal club, class presentation, or a lab group meeting. Using a restricted access workbench for development might be suitable for such efforts because collaborative development is allowed via this mechanism, which is not possible when authoring in one’s own user space, see Workbenches. As you can develop in private and then make the page public, workbenches are also useful for developing interactive 3D content in Proteopedia that complements published research work or review articles, see for examples Interactive 3D Complement in Proteopedia.

Advanced efforts in authoring are also possible via the Scene Authoring Tools.

  • You could alter the transition between your scene views, see Scene_authoring_tools.
  • You could add custom interfaces for controlling the Jmol structure scene window using templates and Jmol commands, see for example Template:Button Toggle AnimationOnPause used on the Citrate Synthase page. Related methods allow you to develop very complex animations that can be triggered via green scene link, see a list of morphs at Jmol#Complex Animations. An advanced scene that can be developed is a morph. These show as the transition between two structural states as rotatable, interactive 3D structures and are particularly good for illustrating conformational changes, such as those involved in ligand binding; see Morphs#Morphing Methods.

Practical Guide for Teachers and Educators: Publishing pages that your students will use to explore structural biology

Consider protected namespaces for publishing class related content

As a registered user you have a protected namespace for publishing within as was covered earlier in this primer when discussing personal sandboxes. Only the user owning that space can edit pages there while any user can view the page. Most likely anything you want to be available for a class should be authored in your protected user space. Otherwise you may find your page edited to form not suitable for your purposes if you choose to leave it solely in the public space. Ultimately this would not be too problematic because your content as you wrote it would still exist in the page’s history; however, placing it in your protected user space from the outset may save you from having to ponder which version as you stand before a audience of students and make it easier to direct students to the page when outside of class. Much of the earlier parts of this guide, particularly the first section, will be applicable for steps in making such a protected page. Instead of making a person sandbox though, you’d title the page as you see fit with a descriptive title that is preceded by ‘User:’ followed by your username. See Eric Martz’s Nucleosomes page for example (User:Eric_Martz/Nucleosomes). Keep in mind that you can author quizzes like those described earlier in this guide on your page.

Publish a version of your class-related content to the public space as well

Unless much of the content is already present in Proteopedia in some form, any content you produce may be useful to others outside of your class as well. Please consider publishing any content to the public user space in addition. Most often these pages are more readily found relevant in searches. Additionally, you will be attributed with your contribution at the bottom of the page and the page can serve as resource for others for learning or for further development. And others can edit the public version and improve the content. The version in your protected user space will still remain untouched though.

Copying a protected page into a public page is done by copying the entire wikitext of the protected page (from the wikitext box in edit mode), and then pasting it into the wikitext box of a newly-created public page. For example, the above page on nucleosomes, protected for class use, was copied into Nucleosomes. Subsequently many other people contributed to this page.

Practical Guide for Teachers and Educators: Choosing the right pages for your students to work on in Proteopedia


Beyond a way to convey structural biology to your students in a visually informative way, Proteopedia offers options for involving students at a wide-range of levels actively in educational ways. For example very advanced projects have emerged at both the University (see CBI_Molecules) and high school level (see Group:SMART:Teams). These are the exceptions rather than the rule. Most teachers use Proteopedia as a resource and engagement tool with the majority of content being produced meant to be temporary starting point if the students wish to take their efforts farther. Some have done so with tremendous outcomes, see Student_Projects and News#Adoptions in University Classes.

Considering the scope of this guide, we will be discussing using Proteopedia for teaching in this manner with an emphasis on students authoring and publishing pages. We will only be able to cover the basics here. We suggest Proteopedia’s Teaching Strategies page as a resource for additional information. Going beyond being passive users of Proteopedia can empower students to be more knowledgeable about structural biology and also be better scientific communicators. Regardless of whether ultimately students produce anything of reasonable substance and quality that would add to Proteopedia, attempts at producing any sort of content, no matter how ephemeral, within Proteopedia often engages students in a manner that makes them think differently about how to consider structural data, extract meaningful insights, and share structural information productively with others. As with any class, the goals for an individual module of a course have to be factored against the overall pedagogical goals for the course and considered against the major limiting factors. Generally time of both the instructor and students is the major limiting factor. We hope that by outlining a few of the basic considerations here we will obviate many of the technical hurdles an educator might come across when using Proteopedia for teaching. Account type and namespace for your students to use within Proteopedia are some of the primary issues faced. As these two actually turn out to be linked by the permissions system built in to Proteopedia we will first touch upon accounts and then outline a number of page types suitable for places to have students author content within Proteopedia. We suggest exploring Proteopedia in order to familiarize yourself with them. To aid in this endeavor, after we discuss types of accounts we outline many of the types of pages in order to hopefully aid considering which of the possibilities best match with your pedagogical goals.

Individual users or a shared student account?

In order to publish, ultimately users need an individual account, and encouraging students to register as Proteopedia users sooner, rather than later, is in the best interest overall. However, as part of the efforts to control quality and prevent abuse, registrations are not handled in an automated manner; each registration is considered by a Proteopedia staff member and upon approval accounts are set up, which takes time. Typically, accounts are approved within 24 hours of application. In a class this can often hamper efforts to smoothly transition from being a passive user of Proteopedia to being an author. If possible, encouraging your students to register well in advance of any class in which authoring may be involved and contacting the staff of Proteopedia ahead of such a class so they are expecting registrations can help mitigate such minor hiccups. Keep in mind though Proteopedia is an international, voluntary effort and sometimes delays cannot be avoided.

Importantly, educators who plan accordingly can contact Proteopedia staff () to request special shared student accounts that can be used in classes to get students quickly authoring without having to wait for the registration process. A shared, student access account is not as fully privileged as an individual user account and only allows editing in the student userspace or sandboxes, either reserved or basic. In fact, if teaching using Proteopedia it is best to at least obtain the credentials for shared account access, as it may become useful to keep class moving productively. If using a shared account, be sure to keep in mind its limitations and you’d be well advised to use it ahead of the class to perform any planned exercises.

Teachers should point out that those students that are registered users are best served by signing in and working in their own account even if the shared account is available. As touched upon earlier in this guide, Proteopedia has mechanisms for tracking contributions and efforts by which the student will benefit by being logged into their own account.

Basic Sandboxes

Basic personal sandboxes were covered earlier in this guide from the point of view of someone beginning authoring in Proteopedia. While this type of page would be suitable for students work, a basic sandbox requires the users be logged in (either in a shared or a personal account) in order to edit pages. Additionally, for any assessment of the student’s work the educator is required to learn the name of the particular page the student edited.

Reserved Sandboxes

A solution that avoids the issues associated with basic personal sandboxes is for the educator to set up a number of Reserved Sandboxes for students’ work. In conjunction with reserving these sandboxes, an educator can contact Proteopedia staff () and request a student login account that can be shared with the class as described earlier. There is a page on Proteopedia (Special:SandboxReservation) where Reserved Sandboxes can be set up and populated with text at the time of set up. Because of this latter issue, it is best for the educator to have the content with which to seed the pages chosen at the time of request. This will save the educator from possibly needing to edit a lot of pages. It is suggested to look at examples of Reserved Sandboxes set up by other educators, preferably those not subsequently altered by students, when designing the seed content. It is suggested links to the individual pages in the block of reserved sandboxes be placed on a page where students are directed. As reserved sandboxes are numbered, a student or group of students can be assigned a specific page number by the Educator. It is suggested students be directed to add their name into the page proper as part of the editing process for the class, or else the specific assignments need to be recorded. Integrating the student’s name into the text of the sandbox is especially important if using the option of the shared student account; unlike normal registered users, users logged into the shared student account do not have their individual names added to the contributors list at the bottom of every page in Proteopedia. Furthermore, it is suggested educators caution students to be careful to edit their own page; however, remind them that if issues should arise in the course of editing that most can be sorted out easily given the page history component of the Wiki. For example, if one student accidentally saves their page over another student’s assigned page, there remains a record of the first student’s page among the history of the page and the student or instructor can restore the content by copying and pasting if needed. At the time the sandboxes are reserved, an expiration date is set and the pages may be cleaned out some time after that. If you or your students are planning to publish the content elsewhere (see below), they should at least copy the content to somewhere else in a reasonable time frame, prior to the agreed-upon expiration date.


Workbenches are pages that can be developed while hidden from the public. Only the author, and specified other account holders, can read Workbench pages. They are intended for development of pages that complement journal articles.

Eventually they can be converted to the public namespace, typically when the journal article is published, see Proteopedia:Workbench. Because their set-up borders on being an advanced authoring task and relies on your students allowing you access for grading, Workbench pages are not suitable for teaching and are mainly included here to illustrate the logical progression between the concepts of Sandboxes and Studios.

Studios for supervised, private group collaboration and page development A modified form of a Workbench, a Studio is a restricted access namespace where authorized users can work. In the current implementation, there's a landlord that creates the Studio page, for example Studio:G5SecL04 and grants access to a group of tenants, who can be students, TA's, and/or a mix of other registered Proteopedia users. Users that are either landlords or tenants. Each tenant can be given read only, or read and write privileges.

Studio shares with a Workbench the privacy properties, however, Studio tenants cannot grant access to the page to other users. The credits area at the bottom area of a Studio page will list all those tenants that actually did some editing, like a regular page. This is a nice complement to the workbench environment. And similar to the workbench environment, the studio can be converted to the public namespace at a later point and maintain the list of contributors to the page.

Where to go next?

Finally, you may wish that your students publish the content they have authored in Proteopedia. This can either be a requirement for a component of the grade or an option suggested as follow-up to particularly motivated students. In the latter case you may wish to direct the students to the earlier parts of this primer within Proteopedia to start thinking about best practices and publishing. If publishing is a requirement, we suggest significant involvement of the instructor at each step of the work to insure production of content meeting expectations, especially if this is to be published to the public user space. Excitingly, student users who have developed pages have even had articles published describing their efforts in a peer-reviewed journal, see for example Citrate Synthase. This possibility is related to the joint effort between the journal Biochemistry and Molecular Biology Education (BAMBED) and Proteopedia to publish high-quality Proteopedia articles in BAMBED as features in a section titled 'Multimedia in Biochemistry and Molecular Biology Education', see Proteopedia:BAMBED (Decatur, 2010; Oberholser, 2010; Canner, 2011; Decatur & Eddelman, 2011; Dornfeld et al., 2012; Sagar & Oberholser, 2012; Prilusky & Hodis, 2012).

For additional ideas for where to proceed next, we also suggest exploring more within Proteopedia in order to maximize your use of Proteopedia as a component of teaching in the future. Moreover, we suggest Proteopedia’s Teaching Strategies page as a next step for additional information.

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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