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<big>This page presents some ideas for how educators/teachers/professors might use Proteopedia in their teaching. For specific lesson plans, consult [[Journal:BAMBEd:A practical guide to teaching with Proteopedia]]<ref>DOI:10.1002/bmb.21548</ref>.</big>
This page presents some ideas for how educators/teachers/professors might use Proteopedia in their teaching.


==Use Existing Pages==
==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%27 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%27 Pages]]. Specifically for biochemistry courses, [[Proteopedia:Biochemistry in 3D]] list pages that fit a one-semester course.


Proteopedia pages can be '''projected''' during lectures (if you have an Internet connection in the classroom), and/or '''assigned''' to students as homework.
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==
==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]] 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''.
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]] 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''. You can protect your pages against unwanted editing by others: see [[Help:Protected Pages]].
 
Again, see some examples at [[Teaching Scenes, Tutorials, and Educators%27 Pages]].


==Worksheets==
==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 Protopedia), 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.
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.
 
Examples of questions/worksheets on specific molecules:
* On the [[Lac Repressor]].
* On DNA in a tutorial available in a dozen languages: [http://dna.molviz.org DNA.MolviZ.Org]
* On [http://biomodel.uah.es/en/water/p2.htm Liquid Water and its hydrogen bonds].
 
Examples of vague/open-ended questions about [[antibody]] (IgG):
* What is the function of the thinnest part of the intact (whole) IgG molecule?
* What fills the hole between the chains of Fab?
* What important antibody function is not visible in images of the antibody molecule?


==Student Authoring of Temporary Proteopedia Pages: Sandboxes==
==Quizzes==


Some educators have assigned their students to try out authoring a Proteopedia page 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 is not permanent, and may be erased or replaced at a later time.
Proteopedia has a mechanism to include quizzes on pages you prepare for your students. See [[Help:Quiz]].


One strategy is to assign a number to each student. For example, if a student is assigned number 17, that student uses the page titled [[Sandbox 17]]. The student should enter ''Sandbox 17'' in the search slot at the upper left of any Proteopedia page, and click on Go. If the page does not exist, there will be a red link on the resulting page. Clicking on the red link will create the page, which can then be edited.
==Molecular Structure: FirstGlance in Jmol==


If you want to protect a range of Sandbox page numbers for a specified number of weeks, so that your students need not worry about other Proteopedia users changing their pages, please contact <email>eran.hodis@weizmann.ac.il</email> in advance. There is always a safety net: the History tab on each page allows you to revert to an earlier version, even if the entire content was deleted and replaced.
[[Image:Firstglance-resource-link.png|right]]
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. ''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 locate them in the 3D image. 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.


A single generic login account and password are available for use by every member of a class of students. Please contact <email>eran.hodis@weizmann.ac.il</email> for details.
When students are given a worksheet or an assignment of suitable questions, ''FirstGlance'' provides an easy way to discover answers.
* [[User:Eric Martz/Introduction to Structural Bioinformatics 2016|Here are 11 questions]] for upper level bio-science major undergraduates taking three 3-hour lab sessions.
*[https://www.umass.edu/molvis/workshop/challeng/2015/ppslides.htm Here are 20 questions] assigned to M.S. students in a [http://workshops.molviz.org 5-day workshop].
*These questions apply to any protein; each student chose a different protein to investigate, for example from the [http://atlas.molviz.org Atlas of Macromolecules].
 
Jaswal, O'Hara, Williamson and Springer (2013)<ref>PMID: 24019219</ref> 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).
 
==Capturing Molecular Scenes in Presentation Slides==
Slides in ''Powerpoint'' (&reg; Microsoft) or free presentation software ([http://slides.google.com Google Slides], [https://www.libreoffice.org/ Libre Office]) are a good place to put snapshots or animations from Proteopedia or ''FirstGlance'', and to record answers to questions. The resulting file can be presented in class and/or emailed to the teacher/professor for grading.
 
It is easy to make snapshots or presentation-ready animations of macromolecules:
* In FirstGlance it is super-easy (just a few mouse clicks) to make a hi-res static image, or an animation: [http://bioinformatics.org/firstglance/fgij/slides.htm Instructions]. You are limited to the color schemes and renderings offered, but you can zoom in and/or isolate portions of the structure.
* In Proteopedia, it is also very easy. Use the link below the molecule ''Export Animated Image'' (it also exports static images). If you author your own molecular scenes (easy!), you can customize the colors and renderings.
* A customized scene can be exported as a static image or animation in [[PyMOL]] using free [[Polyview-3D]].
 
[http://www.umass.edu/molvis/workshop/ppt/kane-demo-report-2014.ppt Here is a sample report in Powerpoint] showing answers to these [http://www.umass.edu/molvis/workshop/challeng/2014/pps-um14.htm 20 questions].
 
==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 is not permanent, and will be erased or replaced at a later time.
 
One strategy is to '''assign a number to each student'''. For example, if a student is assigned number 17, that student uses the page titled [[Sandbox 17]]. A student assigned number N should enter ''Sandbox N'' in the search slot at the upper left of any Proteopedia page, and click on Go. If the page does not exist, there will be a red link on the resulting page. Clicking on the red link will create the page, which can then be edited.
 
If you want to '''protect a range of Sandbox page numbers for a specified number of months''', so that your students need not worry about other Proteopedia users changing their pages, please use the [[Special:SandboxReservation|Sandbox Reservation]] form. See [[Help:Sandboxes]] for more information. There is always a safety net: the History tab on each page allows you to revert to an earlier version, even if the entire content was deleted and replaced.
 
===Studios===
 
Proteopedia provides a mechanism called ''Studios'' for supervised student collaborations. Each Studio has a landlord (who could be a professor, instructor, TA, etc.) and a number of tenants (students) which work together on a page. Studios are designed for private development, so they are not readable by the public. If a completed Studio project has sufficient quality, it can be converted to a permanent page. For more information, see [[Proteopedia:Studio]].
 
===Assessment===
 
How to '''assess completion of this assignment'''? One method is to require students to take a screenshot of their Sandbox N page, and convey it electronically to their professor (via email, in a Powerpoint presentation .ppt file, via courseware, etc.). If the block of Sandbox page numbers is still reserved, the professor can simply view each page directly. Putting the screenshot in e.g. a Powerpoint presentation has the advantage of making something tangible that the student can keep.
 
===Generic Student Login===
 
A single generic login account and password are available for use by every member of a class of students. Please contact {{Template:Contact}} for details.


==Student Authoring of Projects as Permanent Proteopedia Pages==
==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]], was authored by [[User:Emily Forschler|Emily Forschler]] while she was a senior biochemistry major at Messiah College (Grantham PA US) in a class taught by [[User:Karl Oberholser|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.  [[User:Ann Taylor|Ann Taylor]] has used this at Wabash College to create pages on [[Glycolysis Enzymes]], [[Citric Acid Cycle]], [[Proteins involved in cancer]] and [[DNA-protein_interactions]].
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, [[User:Emily Forschler|Emily Forschler]].
The pages for the project can then be created as subpages of an individuals user p|age (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.
==See Also==
===Ready To Use Resources===
*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]
* [[High school teachers' resources]]
* [http://undsci.berkeley.edu/teaching/index.php Understanding Science]
===How To Use Proteopedia===
*[[Proteopedia:Primer]] for teachers.
*[[Help:Getting Started in Proteopedia]]
*[[Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching]]
*[[Help:Quiz]]: how to create quizzes in Proteopedia.
*[[Help:Editing|How to Author Proteopedia Pages]]
*[[Scene authoring tools|Molecular Scene Authoring Tools]]
*[[Proteopedia:Video Guide|Movies Showing How to Author Proteopedia Pages]]
*[[Help:Protected_Pages]]
*[[Help:Contents|Help]], a list of all Help pages within Proteopedia.
===Use in Education===
*List of Completed [[Student Projects]]
* [[Proteopedia:News#Adoptions in College and University Classes|Adoptions in College and University Classes]]
==References==
<references />

Latest revision as of 15:53, 22 December 2021

This page presents some ideas for how educators/teachers/professors might use Proteopedia in their teaching. For specific lesson plans, consult Journal:BAMBEd:A practical guide to teaching with Proteopedia[1].

Use Existing PagesUse 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. Specifically for biochemistry courses, Proteopedia:Biochemistry in 3D list pages that fit a one-semester course.

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 PagesAuthor 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 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. You can protect your pages against unwanted editing by others: see Help:Protected Pages.

Again, see some examples at Teaching Scenes, Tutorials, and Educators' Pages.

WorksheetsWorksheets

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.

Examples of questions/worksheets on specific molecules:

Examples of vague/open-ended questions about antibody (IgG):

  • What is the function of the thinnest part of the intact (whole) IgG molecule?
  • What fills the hole between the chains of Fab?
  • What important antibody function is not visible in images of the antibody molecule?

QuizzesQuizzes

Proteopedia has a mechanism to include quizzes on pages you prepare for your students. See Help:Quiz.

Molecular Structure: FirstGlance in JmolMolecular 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. 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 locate them in the 3D image. 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 an assignment of suitable questions, FirstGlance provides an easy way to discover answers.

Jaswal, O'Hara, Williamson and Springer (2013)[2] 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).

Capturing Molecular Scenes in Presentation SlidesCapturing Molecular Scenes in Presentation Slides

Slides in Powerpoint (® Microsoft) or free presentation software (Google Slides, Libre Office) are a good place to put snapshots or animations from Proteopedia or FirstGlance, and to record answers to questions. The resulting file can be presented in class and/or emailed to the teacher/professor for grading.

It is easy to make snapshots or presentation-ready animations of macromolecules:

  • In FirstGlance it is super-easy (just a few mouse clicks) to make a hi-res static image, or an animation: Instructions. You are limited to the color schemes and renderings offered, but you can zoom in and/or isolate portions of the structure.
  • In Proteopedia, it is also very easy. Use the link below the molecule Export Animated Image (it also exports static images). If you author your own molecular scenes (easy!), you can customize the colors and renderings.
  • A customized scene can be exported as a static image or animation in PyMOL using free Polyview-3D.

Here is a sample report in Powerpoint showing answers to these 20 questions.

Student Authoring of Temporary Proteopedia PagesStudent Authoring of Temporary Proteopedia Pages

SandboxesSandboxes

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 is not permanent, and will be erased or replaced at a later time.

One strategy is to assign a number to each student. For example, if a student is assigned number 17, that student uses the page titled Sandbox 17. A student assigned number N should enter Sandbox N in the search slot at the upper left of any Proteopedia page, and click on Go. If the page does not exist, there will be a red link on the resulting page. Clicking on the red link will create the page, which can then be edited.

If you want to protect a range of Sandbox page numbers for a specified number of months, so that your students need not worry about other Proteopedia users changing their pages, please use the Sandbox Reservation form. See Help:Sandboxes for more information. There is always a safety net: the History tab on each page allows you to revert to an earlier version, even if the entire content was deleted and replaced.

StudiosStudios

Proteopedia provides a mechanism called Studios for supervised student collaborations. Each Studio has a landlord (who could be a professor, instructor, TA, etc.) and a number of tenants (students) which work together on a page. Studios are designed for private development, so they are not readable by the public. If a completed Studio project has sufficient quality, it can be converted to a permanent page. For more information, see Proteopedia:Studio.

AssessmentAssessment

How to assess completion of this assignment? One method is to require students to take a screenshot of their Sandbox N page, and convey it electronically to their professor (via email, in a Powerpoint presentation .ppt file, via courseware, etc.). If the block of Sandbox page numbers is still reserved, the professor can simply view each page directly. Putting the screenshot in e.g. a Powerpoint presentation has the advantage of making something tangible that the student can keep.

Generic Student LoginGeneric Student Login

A single generic login account and password are available for use by every member of a class of students. Please contact for details.

Student Authoring of Projects as Permanent Proteopedia PagesStudent 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, 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, Proteins involved in cancer and DNA-protein_interactions.

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 individuals user p|age (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.

See AlsoSee Also

Ready To Use ResourcesReady To Use Resources

How To Use ProteopediaHow To Use Proteopedia

Use in EducationUse in Education

ReferencesReferences

  1. ↑ Castro C, Johnson RJ, Kieffer B, Means JA, Taylor A, Telford J, Thompson LK, Sussman JL, Prilusky J, Theis K. A practical guide to teaching with Proteopedia. Biochem Mol Biol Educ. 2021 Jun 3. doi: 10.1002/bmb.21548. PMID:34080750 doi:http://dx.doi.org/10.1002/bmb.21548
  2. ↑ 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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Eran Hodis, Jaime Prilusky, Ann Taylor, Karsten Theis
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