Molecular Workbench
From Proteopedia
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What Is Molecular Workbench?
The Molecular Workbench (MW) project offers free, ready-to-use educational activities as well as software for authoring such educational activities. The existing activities are primarily targeted to the middle and high school levels. College-level activities are under development. MW is the product of the Concord Consortium:
"The Concord Consortium is a nonprofit educational research and development organization based in Concord, Massachusetts. We create interactive materials that exploit the power of information technologies. Our primary goal in all our work is digital equity — improving learning opportunities for all students." (Concord.Org)
The MW home page is mw.concord.org. All software available from the Concord Consortium is free and open-source.
Molecular Workbench activities are stand-alone programs (in java). They run automatically and quickly from the MW website, and work equally well on Windows and Mac OS X.
What Can Molecular Workbench Do For Me?
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One of the newest parts of Molecular Workbench (MW) is the Science of Atoms and Molecules (SAM.Concord.Org). It includes:
  Protein folding simulations. Click image for Movie. |
- Simulations of biochemical, chemical and physical processes are featured. Often students can experiment by controlling parameters of the simulation.
- Protein and DNA molecules can be rendered as interactive, 3D rotating structures in Jmol. Controls can highlight structural features, zoom in, and even play movie-like molecular animations.
  Molecular Rover. Click image for Movie. |
- Students can pilot a Molecular Rover to explore the molecular structure structures of hemoglobin or immune system molecules (histocompatibility) to accomplish mission objectives. Some students find the Rover fun and engaging, while for others, learning how to pilot it is frustrating. Enthusiastic pilots could group with those who would rather not pilot. Only a handful of Activities utilize the Rover and these are optional -- most Activities do not use the Rover. Watch the movie here, then try out the Rover yourself at Rover.Concord.Org.
- Students capture snapshots of simulations, interactive molecules, or Rover explorations to document their achievements.
- Snapshot images can be annotated with balloons, and described in open response text notes.
- SAM activities end by generating a report that includes answers to multiple choice questions, annotated snapshots, and the text of open responses. These reports are emailed to the teacher. Students have a chance to edit reports before they are submitted.
- Activities often include multiple choice questions that give immediate feedback to students. Encouraging or thought-provoking hints can be given in response to incorrect answers.
- All activities can be downloaded for offline use, in case your Internet connection is problematic. See Running MW without an Internet connection.
| Assessment
The immediate feedback and report-generating functions mentioned above provide assessment mechanisms for students and teachers. |
How Do I Get Started?
Problems Running Molecular Workbench?
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Here are direct links to start a few MW SAM Activities that involve macromolecules (click Trust to permit each to start):
- Four Levels of Protein Structure
- Molecular Recognition & Protein Function
- Proteins and Nucleic Acids
- From DNA to Proteins
Here is a direct link to see the entire list of dozens of SAM activities:
SAM is only a small part of MW. A good place to find other MW activities is workbench.concord.org/database.
Movies of Molecular Workbench
Below are a few short movies that illustrate some capabilities of Molecular Workbench.
Balloon Annotation
| Snapshots of simulations and interactive molecules enable students to report their findings. Balloons can be used to label snapshot images.
This movie has sound. |
Simulations: Protein Folding
This movie file is large (3 Mb) and may take a few minutes to download. The movie will appear on the right below once download is complete.
| Students conduct experiments with simulations, record their findings in snapshots, and make reports.
This movie has sound. |
Molecular Rover
This movie file is large (10 Mb) and may take a few minutes to download. The movie will appear on the right below once download is complete.
| The Molecular Rover is a vehicle that you can pilot to explore molecular structures. Here we are guiding it towards a virus peptide (mostly green and blue) attached to a histocompatibility protein on the surface of a cell. To try out the Rover, go to Rover.Concord.Org.
This movie is silent. |
Pros and Cons
Advantages
Many of the advantages of Molecular Workbench have been introduced above. Generally, the Activities support and encourage effective, discovery-based pedagogy, and provide built-in assessment tools including feedback to teachers.
Disadvantages
- As mentioned above, some students find the Molecular Rover frustrating to pilot, which distracts from their learning about molecular structure. However, there are only three Rover-based activities (rover.concord.org). None of the 20-some Science of Atoms and Molecules activities (SAM List) are Rover-based.
- Concord Consortium staff state that the time commitment threshold for authoring simple Activities is low. However, authoring sophisticated Molecular Workbench Activities (such as the SAM Activities linked above) requires a substantial time commitment. This is not surprising given the powerful and diverse capabilities and responses that are built into such Activities.
