Tutorial should have energy-based challenge

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  • Idea
  • Updated 8 years ago
In order to prepare the user to create more stable RNA, the tutorial should prepare them to pay attention to the energy. A puzzle or two to get the user above or below a certain range would be sufficient.
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seth.thygesen

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Posted 9 years ago

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Alex Limpaecher, Alum

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That's a cool idea for a tutorial Seth! I think I'd learn a lot from that myself. I put it on our task list at #170

Thanks for the input!
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Matt Baumgartner [mpb21], Alum

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Yes it should include the G in the adjacent position of the loop aspect as well.
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Adrien Treuille, Alum

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Seth: but one important thing to note is that lower energies are not necessarily better. In fact, one of the thing which we're trying to figure out in the lab is what are the right criteria to predict if an RNA will synthesize properly.
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seth.thygesen

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Good point! Perhaps having challenges within a certain range would be best, i.e. both above and below a certain number. A target energy.
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Alex Limpaecher, Alum

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Hey Seth,
So for reasons that Adrien listed we are probably not going to implement this. Thanks for the suggestion though!

Alex
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alan.robot

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I agree with the points above, however, when the upcoming improvements regarding ensemble readouts are implemented (such as dot-plots, MFE frequency, and ensemble diversity), a tutorial contrasting these measures with MFE would be awesome.