Difference between revisions of "20.309 Main Page"
From Course Wiki
MAXINE JONAS (Talk | contribs) (→20.309 Master Schedule) |
MAXINE JONAS (Talk | contribs) (→20.309 Master schedule) |
||
(19 intermediate revisions by 3 users not shown) | |||
Line 7: | Line 7: | ||
== 20.309 course information== | == 20.309 course information== | ||
− | * [[20.309:Course Information]] | + | * [[20.309:Course Information| 20.309 course information]] |
− | * [[20.309:Safety]] | + | * [[20.309:Safety| lab safety]] |
* Reserve a lab station here: [http://measurebiology.org/reservations/Web/schedule.php Bioinstrumentation Lab reservation system] | * Reserve a lab station here: [http://measurebiology.org/reservations/Web/schedule.php Bioinstrumentation Lab reservation system] | ||
− | == 20.309 | + | == 20.309 master schedule== |
<div style="padding: 10px; width: 740px; border: 5px solid #000FFF;"> | <div style="padding: 10px; width: 740px; border: 5px solid #000FFF;"> | ||
Line 40: | Line 40: | ||
| Assignment 2 | | Assignment 2 | ||
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]] | | [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]] | ||
− | * [[Assignment 2 Part 1: Noise in images]] | + | * [[Assignment 2 Part 1: Noise in images|Part 1: Noise in images]] |
− | * [[Assignment 2 Part 2: Fluorescence microscopy]] | + | * [[Assignment 2 Part 2: Fluorescence microscopy|Part 2: Fluorescence microscopy]] |
− | * [[Assignment 2 Part 3: Build an epi-illuminator for your microscope]] | + | * [[Assignment 2 Part 3: Build an epi-illuminator for your microscope|Part 3: Build an epi-illuminator for your microscope]] |
| | | | ||
+ | * [[Geometrical optics and ray tracing]] | ||
* [[Physical optics and resolution]] | * [[Physical optics and resolution]] | ||
+ | * [[Optical aberrations]] | ||
+ | * [[Aperture and field stops]] | ||
+ | * [[Optical detectors, noise, and the limit of detection]] | ||
+ | * [[Manta G032 camera measurements]] | ||
|- | |- | ||
| <font color=#04B45F>9/28/17</font color> | | <font color=#04B45F>9/28/17</font color> | ||
Line 57: | Line 62: | ||
| | | | ||
*[[Flat-field correction|Flat-field correction of non-uniform illumination]] | *[[Flat-field correction|Flat-field correction of non-uniform illumination]] | ||
+ | *[[Matlab: Scalebars]] | ||
|- | |- | ||
| <font color=#04B45F>10/8/17</font color> | | <font color=#04B45F>10/8/17</font color> | ||
| Assignment 4 | | Assignment 4 | ||
− | | | + | |{{Template:Assignment 4 navigation}} |
| | | | ||
+ | * [[Physical optics and resolution]] | ||
|- | |- | ||
| <font color=#04B45F>10/15/17</font color> | | <font color=#04B45F>10/15/17</font color> | ||
Line 80: | Line 87: | ||
|- | |- | ||
|} | |} | ||
− | + | <br /> | |
− | <br | + | |
− | + | ||
===Module 2: Signals and Systems=== | ===Module 2: Signals and Systems=== | ||
Line 96: | Line 101: | ||
* [[Assignment 6, Part 1: Pre-lab questions|Part 1: Pre-lab questions]] | * [[Assignment 6, Part 1: Pre-lab questions|Part 1: Pre-lab questions]] | ||
* [[Assignment 6, Part 2: Electronics bootcamp|Part 2: Build circuits and measure them]] | * [[Assignment 6, Part 2: Electronics bootcamp|Part 2: Build circuits and measure them]] | ||
− | |||
| | | | ||
+ | * [[Electronics primer]] | ||
+ | * [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"] | ||
+ | * [[Real electronics]] | ||
+ | * [[Impedance Analysis|Impedance analysis]] | ||
+ | * [[Bode plots|Transfer functions and Bode plots]] | ||
+ | * [[Complex Number Review|Complex number review]] | ||
+ | * [[Input and output impedance]] | ||
+ | |||
|- | |- | ||
| <font color=#04B45F>11/2/17</font color> | | <font color=#04B45F>11/2/17</font color> | ||
Line 112: | Line 124: | ||
| | | | ||
− | * [[DNA Melting | + | * [[DNA Melting Thermodynamics]] |
* [[Real electronics]] | * [[Real electronics]] | ||
* [[Impedance Analysis|Impedance analysis]] | * [[Impedance Analysis|Impedance analysis]] | ||
Line 125: | Line 137: | ||
* [[Assignment 8, Part 2: lock-in amplifier and temperature control| Part 2: modify your instrument]] | * [[Assignment 8, Part 2: lock-in amplifier and temperature control| Part 2: modify your instrument]] | ||
| | | | ||
− | |||
− | |||
− | |||
* [http://mfold.rna.albany.edu/?q=DINAMelt/Hybrid2 DINAMelt Web Server] | * [http://mfold.rna.albany.edu/?q=DINAMelt/Hybrid2 DINAMelt Web Server] | ||
|- | |- | ||
Line 134: | Line 143: | ||
| [[Assignment 9 Overview]] | | [[Assignment 9 Overview]] | ||
* [[Assignment 9, Part 1: model function|Part 1: writing the model function]] | * [[Assignment 9, Part 1: model function|Part 1: writing the model function]] | ||
− | * [[Assignment 9, Part 2: Simulating DNA melting data and testing the model function| | + | * [[Assignment 9, Part 2: Simulating DNA melting data and testing the model function|Part 2: test your code with simulated data]] |
+ | * [[Assignment 9, Part 3: Fitting your data|Part 3: fitting your data]] | ||
| | | | ||
+ | * [[DNA Melting: Model function and parameter estimation by nonlinear regression]] | ||
+ | * [[DNA Melting Thermodynamics]] | ||
+ | * [[DNA melting: Identifying the unknown sample]] | ||
|- | |- | ||
| <font color=#04B45F>12/3/17</font color> | | <font color=#04B45F>12/3/17</font color> | ||
| Assignment 10 | | Assignment 10 | ||
− | | | + | | [[Assignment 10 Overview|Assignment 10: measure DNA melting curves and identify your unknown sample.]] |
+ | |||
| | | | ||
+ | * [[DNA melting: Identifying the unknown sample]] | ||
+ | * [[DNA Melting: DNA Sequences]] | ||
+ | * [[DNA Melting: Model function and parameter estimation by nonlinear regression]] | ||
|- | |- | ||
| <font color=#04B45F>12/7/17</font color> | | <font color=#04B45F>12/7/17</font color> |
Revision as of 23:41, 13 November 2017
Bioinstrumentation scholars: you are welcome to edit and improve this course wiki. Correct, helpful, exquisitely-expressed changes will increase your class participation grade. Alterations not meeting those critera may have the opposite effect.
If you would like to contribute to this site, please request an account.
20.309 course information
- 20.309 course information
- lab safety
- Reserve a lab station here: Bioinstrumentation Lab reservation system
20.309 master schedule
Module 1: Optics & Microscopy
Important dates | Assignment due | Assignment page links | Useful resources |
9/17/17 | Assignment 1 |
| |
9/24/17 | Assignment 2 | Assignment 2 Overview | |
9/28/17 | Quiz 1 (in lecture) | ||
10/1/17 | Assignment 3 | Assignment 3 Overview | |
10/8/17 | Assignment 4 | ||
10/15/17 | Assignment 5 | Assignment 5 Overview | |
10/19/17 | Exam 1 (at 7:30pm in 4-163) |
Module 2: Signals and Systems
Important dates | Assignment due | Assignment page links | Useful resources |
10/29/17 | Assignment 6 | Assignment 6 Overview | |
11/2/17 | Quiz 2 (in lecture) | ||
11/5/17 | Assignment 7 | Assignment 7 Overview | |
11/12/17 | Assignment 8 | Assignment 8 Overview | |
11/19/17 | Assignment 9 | Assignment 9 Overview | |
12/3/17 | Assignment 10 | Assignment 10: measure DNA melting curves and identify your unknown sample. | |
12/7/17 | Exam 2 (at 7:30pm in 4-163) | ||
12/13/17 | Assignment 11 |
Optics and microscopy resources
Background reading
- Geometrical optics and ray tracing
- Physical optics and resolution
- Optical aberrations
- Aperture and field stops
- Optical detectors, noise, and the limit of detection
- Manta G032 camera measurements
- Understanding log plots
Code examples and simulations
- Converting Gaussian fit to Rayleigh resolution
- MATLAB: Estimating resolution from a PSF slide image
- Matlab: Scalebars
- Calculating MSD and Diffusion Coefficients
Electronics resources
Background reading
- Electronics primer
- Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"
- Real electronics
- Impedance analysis
- Transfer functions and Bode plots
- Complex number review
- Input and output impedance
Code examples and simulations
- DNA Melting: Simulating DNA Melting - Basics
- DNA Melting: Simulating DNA Melting - Intermediate Topics
- DNA Melting: Model function and parameter estimation by nonlinear regression
Reference materials
Limits of detection mini-lab
- Lab Manual: Limits of Detection
- Lab Manual: Atomic Force Microscopy (AFM)
- Limits of Detection: Data Sessions