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Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL - PLoS Comput. Biol. (2014)

Bottom Line: This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules.In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework.In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.

ABSTRACT
This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

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The file upload page of CHARMMing version 0.10.A drop-down menu allowing the user to select a lesson that the new structure is to be used for has been added.
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pcbi-1003719-g001: The file upload page of CHARMMing version 0.10.A drop-down menu allowing the user to select a lesson that the new structure is to be used for has been added.

Mentions: A lesson in CHARMMing is a list of tasks that a user must perform, beginning with creating a structure. Each lesson is independent and has an HTML page within CHARMMing that updates the user's progress as they complete tasks. Initially, the page for a particular lesson will contain instructions for submitting the structure that is to be used. Once each step is done, new text is added to the lesson page describing the next step that is to be performed. Once all steps are completed, the user is informed that the lesson is over. If a task is performed incorrectly at any time, an error message is displayed on the lesson page, and the step must be repeated until it is done correctly. All of the lesson pages are accessed under the “Lessons” subheader of CHARMMing's main menu. A drop down box was also added to the Submit Structure page that lets the user select with which, if any, lesson the structure is associated (see Figure 1). This allows users to start multiple lessons and even multiple copies of the same lesson. When a lesson is started, an additional status window is shown on the left-hand sidebar following the user's progress (Figure 2).


Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL - PLoS Comput. Biol. (2014)

The file upload page of CHARMMing version 0.10.A drop-down menu allowing the user to select a lesson that the new structure is to be used for has been added.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109840&req=5

pcbi-1003719-g001: The file upload page of CHARMMing version 0.10.A drop-down menu allowing the user to select a lesson that the new structure is to be used for has been added.
Mentions: A lesson in CHARMMing is a list of tasks that a user must perform, beginning with creating a structure. Each lesson is independent and has an HTML page within CHARMMing that updates the user's progress as they complete tasks. Initially, the page for a particular lesson will contain instructions for submitting the structure that is to be used. Once each step is done, new text is added to the lesson page describing the next step that is to be performed. Once all steps are completed, the user is informed that the lesson is over. If a task is performed incorrectly at any time, an error message is displayed on the lesson page, and the step must be repeated until it is done correctly. All of the lesson pages are accessed under the “Lessons” subheader of CHARMMing's main menu. A drop down box was also added to the Submit Structure page that lets the user select with which, if any, lesson the structure is associated (see Figure 1). This allows users to start multiple lessons and even multiple copies of the same lesson. When a lesson is started, an additional status window is shown on the left-hand sidebar following the user's progress (Figure 2).

Bottom Line: This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules.In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework.In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America.

ABSTRACT
This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

Show MeSH