By Cody Taylor

Biochemical Methods Lab Manual Accomodations

In addition to the Thermodynamics project, we also recreated a Biochemical Methods lab manual for Dr. Paul Sims and his graduate assistant, Alyssa Hill.  The manual had already been created using iBooks Author, it is a beautiful book and is probably preferred by those who have the devices to view it.  That is; however, the problem.  The iBooks version of the Lab Manual is only accessible by students who have iOS devices.  This means that those without these devices must use university computers to access their lab manual.  Fortunately, the university library does have iPad and Macbooks for students to check out as well as computers labs full of iMacs, but doing so regularly for class might be a hassle for some students.  Dr. Sims requested that we assist he and is graduate assistant in converting the iBook into a more accessible format.  We searched for a while looking for authoring platforms that best suited the needs of Dr. Sims.  We found several nice platforms, but each was lacking in some way and because of that we chose to develop another website using the same template that was developed for the Thermodynamics textbook.

There were a couple solutions needed to be developed for the Biochem project.  Like the Thermo. book, it contained a lot of equations and special symbols that required the use of LaTeX markup and MathJax.  Having already had experience in this area, this was no problem at all; however, the iBook version of the manual has some interactive content that needed to be duplicated in the manual’s web-based form.  The first interactive content to be recreated was the reading quizzes at the end of each chapter.  These are quizzes, a few multiple choice questions each that are intended to let the reader know how well they understand the material.  Stacy and I looked into a few embedable quizzing applications, but were most satisfied by the flexibility of Google Forms.

biochem_quiz_flowchartGoogle Forms turned out to be a nice solution for our purpose.  It provides a fair amount of structure while remaining flexible enough to serve as a platform for creating and hosting surveys, general purpose feedback form, and as a quizzing platform.  Using Google Forms presented its own challenge at first, but with a bit of work we were able to make the tool do exactly as we originally intended.  The problem with using Google Forms as a multiple choice quiz is not that it is incapable of the task or even intended for the task, because I think it is; however, how to use it as such was not obvious to me the first time I tried to build a quiz.  From a creation perspective, Google Forms seems to be designed with those creating surveys in mind.  Each form is made up of multiple pages that can be linked to from other pages. Utilizing this functionality, each radio button that corresponds to a choice can point to its own corresponding page within the form.  For this, there needs to be a dedicated page that informs the user of a correct response and another for an incorrect response.  The incorrect responses will point to the same page, the incorrect page, and the one correct response will point to its own page informing the user that their choice was indeed correct.

The most difficult part of the Biochem lab manual to recreate was its 3D interactivity.  This interactivity allows the user to rotate a few relevant 3D protein models such that the user is able to examine their structure.  Jmol is a Java-based platform that is designed specifically to implement this functionality in a webpage.  I am; however, not a professional web developer and struggled while trying to implement Jmol on the Biochem site.  I even tried to implement JSmol, Jmol’s Javascript counterpart, and could not make it work on the site.  I am positive that it can be done, and am quite frustrated still that I was not able to fully implement this feature into the Biochem book.  Persistent, I spent far too much time trying to make these implementations work before pursuing other, perhaps equivalent, methods of displaying these models.  In the end, the solution that we delivered to Dr. Sims and Alyssa turned out to be an animated GIF of the rotating proteins.  Which from what I understand about the purpose of these animations is acceptable way to view these models.


To produce these, I used a piece of software called PyMOL which is a molecular visualization tool for rendering images of molecular structures.  PyMOL allows its users to import the data file that makes up what will be rendered as a 3D model directly from the Protein Data Bank.  Once the structure was loaded into PyMOL, I sought out a script that I could use to rotate and render each frame of what would become the animation.  Although PyMOL supports rotating models in a number of complicated ways, I chose to only spin the protein about its vertical axis.  I found that 100 frames was the smallest number of frames that could be used while still preserving the fluid motion.  It took several tens of minutes to render all of the 100 frames.  Once they had all been rendered, I loaded them into Photoshop and stitched together what turned out to be a fair substitution for what was initially so difficult.



Another feature of the iBook lab manual that needed to be recreated was its integrated slideshows.  The lecture slides applicable to each exercise within the manual are included for the convenience of those using the book.  In order to include these in the website realization of the manual we decided to use SlideShare.  SlideShare is an online collection of user-submitted slideshows that allows users to search among its contents for slides pertaining to specific subjects or search for keywords within the slides themselves.  Users are able to comment on slides, download them, and most importantly embed them.  My favorite feature that Slide Share offers is that which allows users to label each item that is uploaded with a license.  Of course it gives you the option to reserve all rights to your content, and likewise it gives you the option to choose from all of the Creative Commons licenses.  So not only does Slide Share provide us the capability to embed slides directly into the webpages of the Biochemical Methods lab manual, it also allows us to contribute those slides to the Slide Share community under a CC BY-NC-SA license.