User:Frieda Reichsman/PALM: Difference between revisions

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==PALM Workshop presentation links==
== The Science of Atoms & Molecules Project: Guided Inquiry with The Molecular Workbench  ==
*[http://concord.org Concord.org]
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/proteinfolding/index.cml Four Levels of Protein Structure]


==Download the presentation==
'''This page links resources presented at the [http://www.rpc.msoe.edu/cbm/currentprograms/nsfpalm.php Proteins in Active Learning Modules (PALM) Workshop] held at the Center for Biomolecular Modeling at the Milwaukee School of Engineering on June 17-19, 2009.'''
How do I do this?


==SAM: How Do I Get Started?==
 
{| class="wikitable" align="right" style="background-color:#ffff80"
<big> Web sites</big>
*[http://concord.org The Concord Consortium]
*[http://moleculesinmotion.com Molecules in Motion]
*[http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/protein_dna/protein_dna.htm Protein-DNA Interactions]
*[http://sam.concord.org/ The Science of Atoms and Molecules Project]
* Also see this <b>Proteopedia</b> page highlighting [[Molecular_Workbench|features of Molecular Workbench]]
 
 
<big> Molecular Workbench </big>
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/index.cml The Molecular Workbench Home Page]
SAM Activities:
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/proteinfolding/index.cml Four Levels of Protein Structure] SAM Activity
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/diffat/page2.cml Net Flow from Low to High] Simulation
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/proteinfolding/page6.cml Protein Folding (2D)] Simulation
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/proteinfolding/page9.cml Secondary Structure Stabilization] Embedded Jmol
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part1/index.cml Science of Atoms and Molecules (SAM) Activity Center]
 
Rover Activity:
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/missimmu/index.cml Mission Immunity (Molecular Rover)]
 
Teaching with Molecular Workbench:
*[http://molecularmodelingbasics.blogspot.com/2009/06/do-i-have-to-draw-you-phase-diagram.html Jan Jensen (Univ. of Copenhagen) 2 min screencast on phase change]
*[http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/student/gaslaws/cool.cml Neocles Leontis (Bowling Green State Univ.) student models - gas law example]
 
 
 
SAM is only a small part of MW. A good place to find '''other MW activities''' is [http://workbench.concord.org/database workbench.concord.org/database].
 
'''Questions?''' Contact me at freichsman at concord dot org!
 
{| class="wikitable" align="left"
|-
|-
| <big>Problems Running Molecular Workbench?</big>
| <big>Problems Running Molecular Workbench?</big>
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* Firewall problems? You can [http://mw.concord.org/modeler/faq.html#cdmode run MW offline].
* Firewall problems? You can [http://mw.concord.org/modeler/faq.html#cdmode run MW offline].
|}
|}
Here are direct links to start a few MW SAM Activities that involve macromolecules (click '''Trust''' to permit each to start):
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/proteinfolding/index.cml Four Levels of Protein Structure]
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part1/protein3/index.cml Molecular Recognition & Protein Function]
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/pna/index.cml Proteins and Nucleic Acids]
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part2/dna/index.cml From DNA to Proteins]
Here is a direct link to see the entire list of dozens of SAM activities:
* [http://mw2.concord.org/tmp.jnlp?address=http://mw2.concord.org/public/part1/index.cml Science of Atoms and Molecules Activity Center]
SAM is only a small part of MW. A good place to find '''other MW activities''' is [http://workbench.concord.org/database workbench.concord.org/database]. <!--
To find the above list of SAM Activities from the Concord Consortium website:
# Start at [http://workbench.concord.org Workbench.Concord.Org], then
# Click on MW Curriculum.
# At the MW Database, click on SAM. (You can go here directly with [http://sam.concord.org SAM.Concord.Org].)
# At SAM, click on Activities, and '''Trust''' the java application.
# The MW application (a stand-alone java program) will start. Teachers who want to receive reports, and students who want to be able to send reports to their teacher, must register. If you just want to try the Activities '''without registering''', click on the link '''&quot;the public main page&quot;''' near the bottom.
# At the next MW page, click on '''Activity Center'''. -->
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