Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments: Difference between revisions
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(X - Y) indicates that strand X and strand Y bind to form a complex. | (X - Y) indicates that strand X and strand Y bind to form a complex. | ||
===Block 1: Walker Binding to track=== | ===Block 1: Walker Binding to track=== | ||
====Experiment 1-1==== | ====Experiment Design 1-1==== | ||
'''Gel Identity:''' 1-6<br> | '''Gel Identity:''' 1-6<br> | ||
'''Equation:''' W + TR<sub>1</sub> → (W - TR<sub>1</sub>)<br> | '''Equation:''' W + TR<sub>1</sub> → (W - TR<sub>1</sub>)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 1-2==== | ====Experiment Design 1-2==== | ||
'''Gel Identity:''' 1-7<br> | '''Gel Identity:''' 1-7<br> | ||
'''Equation:''' W + TR<sub>2</sub> → (W - TR<sub>2</sub>)<br> | '''Equation:''' W + TR<sub>2</sub> → (W - TR<sub>2</sub>)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 1-3==== | ====Experiment Design 1-3==== | ||
'''Gel Identity:''' 1-12<br> | '''Gel Identity:''' 1-12<br> | ||
'''Equation:''' TR<sub>1</sub> + TR<sub>2</sub> → TR<sub>1</sub> + TR<sub>2</sub><br> | '''Equation:''' TR<sub>1</sub> + TR<sub>2</sub> → TR<sub>1</sub> + TR<sub>2</sub><br> | ||
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===Block 2: Walker Triggering Mechanism=== | ===Block 2: Walker Triggering Mechanism=== | ||
====Experiment 2-1==== | ====Experiment Design 2-1==== | ||
'''Gel Identity:''' 1-8<br> | '''Gel Identity:''' 1-8<br> | ||
'''Equation:''' W + WI → (W - WI)<br> | '''Equation:''' W + WI → (W - WI)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 2-2==== | ====Experiment Design 2-2==== | ||
'''Gel Identity:''' 1-9<br> | '''Gel Identity:''' 1-9<br> | ||
'''Equation:''' WI + WT → (WI - WT)<br> | '''Equation:''' WI + WT → (WI - WT)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 2-3==== | ====Experiment Design 2-3==== | ||
'''Gel Identity:''' 1-10<br> | '''Gel Identity:''' 1-10<br> | ||
'''Equation:''' W + WI + TR<sub>1</sub> → (W - WI - TR<sub>1</sub>)<br> | '''Equation:''' W + WI + TR<sub>1</sub> → (W - WI - TR<sub>1</sub>)<br> | ||
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'''Negative Result:''' We should not see dark bands corresponding to any of the control lanes. This indicates that the strands did not bind as intended. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | '''Negative Result:''' We should not see dark bands corresponding to any of the control lanes. This indicates that the strands did not bind as intended. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | ||
<br> | <br> | ||
====Experiment 2-4==== | ====Experiment Design 2-4==== | ||
'''Gel Identity:''' 1-11<br> | '''Gel Identity:''' 1-11<br> | ||
'''Equation:''' (W - WI - TR<sub>1</sub>) + WT → (W - TR<sub>1</sub>) + (WI - WT)<br> | '''Equation:''' (W - WI - TR<sub>1</sub>) + WT → (W - TR<sub>1</sub>) + (WI - WT)<br> | ||
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===Block 3: Random Walking Mechanism=== | ===Block 3: Random Walking Mechanism=== | ||
====Experiment 3-1==== | ====Experiment Design 3-1==== | ||
'''Gel Identity:''' 2-5<br> | '''Gel Identity:''' 2-5<br> | ||
'''Equation:''' TR<sub>2</sub> + PTR<sub>2</sub> → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | '''Equation:''' TR<sub>2</sub> + PTR<sub>2</sub> → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | ||
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'''Negative Result:''' We should not see dark bands corresponding to either of the controls. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see dark bands corresponding to either of the controls. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 3-2==== | ====Experiment Design 3-2==== | ||
'''Gel Identity:''' 2-6<br> | '''Gel Identity:''' 2-6<br> | ||
'''Equation:''' W + (TR<sub>2</sub> - PTR<sub>2</sub>) → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | '''Equation:''' W + (TR<sub>2</sub> - PTR<sub>2</sub>) → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | ||
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'''Negative Result:''' We should not see dark bands corresponding to any of the control lanes. This indicates that the strands did not bind as intended. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | '''Negative Result:''' We should not see dark bands corresponding to any of the control lanes. This indicates that the strands did not bind as intended. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | ||
<br> | <br> | ||
====Experiment 3-3==== | ====Experiment Design 3-3==== | ||
'''Gel Identity:''' 2-8<br> | '''Gel Identity:''' 2-8<br> | ||
'''Equation:''' (W - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) ↔ (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | '''Equation:''' (W - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) ↔ (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | ||
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'''Negative Result:''' We should not see any other dark bands. These would indicate that This indicates that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | '''Negative Result:''' We should not see any other dark bands. These would indicate that This indicates that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | ||
<br> | <br> | ||
====Experiment 3-4==== | ====Experiment Design 3-4==== | ||
'''Gel Identity:''' 2-9<br> | '''Gel Identity:''' 2-9<br> | ||
'''Equation:''' TR<sub>1</sub> + (W - TR<sub>2</sub> - PTR<sub>2</sub>) ↔ (TR<sub>2</sub> - PTR<sub>2</sub>) + (W - TR<sub>1</sub>)<br> | '''Equation:''' TR<sub>1</sub> + (W - TR<sub>2</sub> - PTR<sub>2</sub>) ↔ (TR<sub>2</sub> - PTR<sub>2</sub>) + (W - TR<sub>1</sub>)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. These would indicate that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | '''Negative Result:''' We should not see any other dark bands. These would indicate that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | ||
<br> | <br> | ||
====Experiment 3-5==== | ====Experiment Design 3-5==== | ||
'''Gel Identity:''' 2-12<br> | '''Gel Identity:''' 2-12<br> | ||
'''Equation:''' (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) → (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | '''Equation:''' (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) → (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | ||
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<br> | <br> | ||
====Experiment 3-6==== | ====Experiment Design 3-6==== | ||
'''Gel Identity:''' 2-13<br> | '''Gel Identity:''' 2-13<br> | ||
'''Equation:''' (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) + WT → (WI - WT) + (TR<sub>2</sub> - PTR<sub>2</sub>) + (W - TR<sub>1</sub>) + (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | '''Equation:''' (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) + WT → (WI - WT) + (TR<sub>2</sub> - PTR<sub>2</sub>) + (W - TR<sub>1</sub>) + (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | ||
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===Block 4: Cargo Pickup Mechanism=== | ===Block 4: Cargo Pickup Mechanism=== | ||
====Experiment 4-1==== | ====Experiment Design 4-1==== | ||
'''Gel Identity:''' 4-4<br> | '''Gel Identity:''' 4-4<br> | ||
'''Equation:''' C<sub>1</sub> + CA → (C<sub>1</sub> - CA)<br> | '''Equation:''' C<sub>1</sub> + CA → (C<sub>1</sub> - CA)<br> | ||
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<br> | <br> | ||
====Experiment 4-2==== | ====Experiment Design 4-2==== | ||
'''Gel Identity:''' 4-5<br> | '''Gel Identity:''' 4-5<br> | ||
'''Equation:''' W + C<sub>1</sub> → (W - C<sub>1</sub>)<br> | '''Equation:''' W + C<sub>1</sub> → (W - C<sub>1</sub>)<br> | ||
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<br> | <br> | ||
====Experiment 4-3==== | ====Experiment Design 4-3==== | ||
'''Gel Identity:''' 4-6<br> | '''Gel Identity:''' 4-6<br> | ||
'''Equation:''' W + (C<sub>1</sub> - CA) → (W - C<sub>1</sub>) + CA<br> | '''Equation:''' W + (C<sub>1</sub> - CA) → (W - C<sub>1</sub>) + CA<br> | ||
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<br> | <br> | ||
====Experiment 4-4==== | ====Experiment Design 4-4==== | ||
'''Gel Identity:''' 4-8<br> | '''Gel Identity:''' 4-8<br> | ||
'''Equation:''' W + C<sub>1</sub> + TR<sub>1</sub> → (W - C<sub>1</sub> - TR<sub>1</sub>)<br> | '''Equation:''' W + C<sub>1</sub> + TR<sub>1</sub> → (W - C<sub>1</sub> - TR<sub>1</sub>)<br> | ||
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<br> | <br> | ||
====Experiment 4-5==== | ====Experiment Design 4-5==== | ||
'''Gel Identity:''' 4-9<br> | '''Gel Identity:''' 4-9<br> | ||
'''Equation:''' W + C<sub>1</sub> + TR<sub>2</sub> → (W - C<sub>1</sub> - TR<sub>2</sub>)<br> | '''Equation:''' W + C<sub>1</sub> + TR<sub>2</sub> → (W - C<sub>1</sub> - TR<sub>2</sub>)<br> | ||
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<br> | <br> | ||
====Experiment 4-6==== | ====Experiment Design 4-6==== | ||
'''Gel Identity:''' 4-10<br> | '''Gel Identity:''' 4-10<br> | ||
'''Equation:''' (W - TR<sub>1</sub>) + (C<sub>1</sub> - CA) → (W - C<sub>1</sub> - TR<sub>1</sub>) + CA<br> | '''Equation:''' (W - TR<sub>1</sub>) + (C<sub>1</sub> - CA) → (W - C<sub>1</sub> - TR<sub>1</sub>) + CA<br> | ||
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<br> | <br> | ||
====Experiment 4-7==== | ====Experiment Design 4-7==== | ||
'''Gel Identity:''' 4-11<br> | '''Gel Identity:''' 4-11<br> | ||
'''Equation:''' (W - TR<sub>2</sub>) + (C<sub>1</sub> - CA) → (W - C<sub>1</sub> - TR<sub>2</sub>) + CA<br> | '''Equation:''' (W - TR<sub>2</sub>) + (C<sub>1</sub> - CA) → (W - C<sub>1</sub> - TR<sub>2</sub>) + CA<br> | ||
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===Block 5: Goal Triggering Mechanism=== | ===Block 5: Goal Triggering Mechanism=== | ||
====Experiment 5-1==== | ====Experiment Design 5-1==== | ||
'''Gel Identity:''' 3-4<br> | '''Gel Identity:''' 3-4<br> | ||
'''Equation:''' CG<sub>1</sub> + CGI → (CG<sub>1</sub> - CGI)<br> | '''Equation:''' CG<sub>1</sub> + CGI → (CG<sub>1</sub> - CGI)<br> | ||
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<br> | <br> | ||
====Experiment 5-2==== | ====Experiment Design 5-2==== | ||
'''Gel Identity:''' 3-5<br> | '''Gel Identity:''' 3-5<br> | ||
'''Equation:''' CGI + CGT → (CGI - CGT)<br> | '''Equation:''' CGI + CGT → (CGI - CGT)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the inhibitor does not bind with the goal.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the inhibitor does not bind with the goal.<br> | ||
<br> | <br> | ||
====Experiment 5-3==== | ====Experiment Design 5-3==== | ||
'''Gel Identity:''' 3-6<br> | '''Gel Identity:''' 3-6<br> | ||
'''Equation:''' (CG<sub>1</sub> - CGI) + CGT → CG<sub>1</sub> + (CGI - CGT)<br> | '''Equation:''' (CG<sub>1</sub> - CGI) + CGT → CG<sub>1</sub> + (CGI - CGT)<br> | ||
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===Block 6: Cargo Drop Off Mechanism=== | ===Block 6: Cargo Drop Off Mechanism=== | ||
====Experiment 6-1==== | ====Experiment Design 6-1==== | ||
'''Gel Identity:''' 6-7<br> | '''Gel Identity:''' 6-7<br> | ||
'''Equation:''' C1 + CG1 → (C1 - CG1)<br> | '''Equation:''' C1 + CG1 → (C1 - CG1)<br> | ||
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===Block 7: Time-based Tests=== | ===Block 7: Time-based Tests=== | ||
====Experiment 7-1==== | ====Experiment Design 7-1==== | ||
'''Gel Identity:''' 3-6<br> | '''Gel Identity:''' 3-6<br> | ||
'''Equation:''' (W - C1) + (CG1 - CGI) → (C1 - CG1) + W + CGI<br> | '''Equation:''' (W - C1) + (CG1 - CGI) → (C1 - CG1) + W + CGI<br> | ||
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===Block 8: Walker Goal Functionality=== | ===Block 8: Walker Goal Functionality=== | ||
====Experiment 8-1==== | ====Experiment Design 8-1==== | ||
'''Gel Identity:''' 8-6<br> | '''Gel Identity:''' 8-6<br> | ||
'''Equation:''' W + WG → (W - WG)<br> | '''Equation:''' W + WG → (W - WG)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker does not bind to the goal.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Walker does not bind to the goal.<br> | ||
<br> | <br> | ||
====Experiment 8-2==== | ====Experiment Design 8-2==== | ||
'''Gel Identity:''' 8-7<br> | '''Gel Identity:''' 8-7<br> | ||
'''Equation:''' WG + PWG → (WG - PWG)<br> | '''Equation:''' WG + PWG → (WG - PWG)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker does not bind to the goal.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Walker does not bind to the goal.<br> | ||
<br> | <br> | ||
====Experiment 8-3==== | ====Experiment Design 8-3==== | ||
'''Gel Identity:''' 8-6<br> | '''Gel Identity:''' 8-6<br> | ||
'''Equation:''' W + (WG - PWG) → (W - WG - PWG)<br> | '''Equation:''' W + (WG - PWG) → (W - WG - PWG)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal Probe interferes with the Walker and Walker Goal bond.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal Probe interferes with the Walker and Walker Goal bond.<br> | ||
<br> | <br> | ||
====Experiment 8-4==== | ====Experiment Design 8-4==== | ||
'''Gel Identity:''' 8-10<br> | '''Gel Identity:''' 8-10<br> | ||
'''Equation:''' (W - TR<sub>1</sub>) + (WG - PWG) → TR<sub>1</sub> + (W - WG - PWG)<br> | '''Equation:''' (W - TR<sub>1</sub>) + (WG - PWG) → TR<sub>1</sub> + (W - WG - PWG)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 1.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 1.<br> | ||
<br> | <br> | ||
====Experiment 8-5==== | ====Experiment Design 8-5==== | ||
'''Gel Identity:''' 8-11<br> | '''Gel Identity:''' 8-11<br> | ||
'''Equation:''' (W - TR<sub>2</sub>) + (WG - PWG) → TR<sub>2</sub> + (W - WG - PWG)<br> | '''Equation:''' (W - TR<sub>2</sub>) + (WG - PWG) → TR<sub>2</sub> + (W - WG - PWG)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 2.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 2.<br> | ||
<br> | <br> | ||
====Experiment 8-6==== | ====Experiment Design 8-6==== | ||
'''Gel Identity:''' 8-12<br> | '''Gel Identity:''' 8-12<br> | ||
'''Equation:''' TR<sub>1</sub> + (W - WG - PWG) → TR<sub>1</sub> + (W - WG - PWG)<br> | '''Equation:''' TR<sub>1</sub> + (W - WG - PWG) → TR<sub>1</sub> + (W - WG - PWG)<br> | ||
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'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker is capable of leaving the walker goal.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Walker is capable of leaving the walker goal.<br> | ||
<br> | <br> | ||
====Experiment 8-7==== | ====Experiment Design 8-7==== | ||
'''Gel Identity:''' 8-13<br> | '''Gel Identity:''' 8-13<br> | ||
'''Equation:''' (W - TR<sub>2</sub>) + (WG - PWG) → TR<sub>2</sub> + (W - WG - PWG)<br> | '''Equation:''' (W - TR<sub>2</sub>) + (WG - PWG) → TR<sub>2</sub> + (W - WG - PWG)<br> |
Revision as of 22:28, 2 November 2011
Saturday, April 27, 2024
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Design for the Gel Experiments
ExampleExperiment 0-1The number to the left of the dash in the title represents which block of tests it belongs to, and the number to the right of the dash represents it's identity within the block List of ExperimentsX + Y indicates strand X and strand Y exist independently in the same solution. Block 1: Walker Binding to trackExperiment Design 1-1Gel Identity: 1-6 Experiment Design 1-2Gel Identity: 1-7 Experiment Design 1-3Gel Identity: 1-12 Block 2: Walker Triggering MechanismExperiment Design 2-1Gel Identity: 1-8 Experiment Design 2-2Gel Identity: 1-9 Experiment Design 2-3Gel Identity: 1-10 Experiment Design 2-4Gel Identity: 1-11 Block 3: Random Walking MechanismExperiment Design 3-1Gel Identity: 2-5 Experiment Design 3-2Gel Identity: 2-6 Experiment Design 3-3Gel Identity: 2-8 Experiment Design 3-4Gel Identity: 2-9 Experiment Design 3-5Gel Identity: 2-12 Experiment Design 3-6Gel Identity: 2-13 Block 4: Cargo Pickup MechanismExperiment Design 4-1Gel Identity: 4-4 Experiment Design 4-2Gel Identity: 4-5 Experiment Design 4-3Gel Identity: 4-6 Experiment Design 4-4Gel Identity: 4-8 Experiment Design 4-5Gel Identity: 4-9 Experiment Design 4-6Gel Identity: 4-10 Experiment Design 4-7Gel Identity: 4-11 Block 5: Goal Triggering MechanismExperiment Design 5-1Gel Identity: 3-4 Experiment Design 5-2Gel Identity: 3-5 Experiment Design 5-3Gel Identity: 3-6 Block 6: Cargo Drop Off MechanismExperiment Design 6-1Gel Identity: 6-7 Block 7: Time-based TestsExperiment Design 7-1Gel Identity: 3-6 Block 8: Walker Goal FunctionalityExperiment Design 8-1Gel Identity: 8-6 Experiment Design 8-2Gel Identity: 8-7 Experiment Design 8-3Gel Identity: 8-6 Experiment Design 8-4Gel Identity: 8-10 Experiment Design 8-5Gel Identity: 8-11 Experiment Design 8-6Gel Identity: 8-12 Experiment Design 8-7Gel Identity: 8-13
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