Difference between revisions of "20.309 Main Page"

From Course Wiki
Jump to: navigation, search
(→‎20.309 Master schedule)
 
(77 intermediate revisions by 3 users not shown)
Line 3: Line 3:
 
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.
 
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 [[Special:RequestAccount|request an account]].
+
If you would like to contribute to this site, please [[Special:RequestAccount|request an account]]. ()
  
 
== 20.309 course information==
 
== 20.309 course information==
  
 +
* [https://accessibility.mit.edu/ Accessibility]
 
* [[20.309:Course Information| 20.309 course information]]
 
* [[20.309:Course Information| 20.309 course information]]
 
* [[20.309:Safety| lab safety]]
 
* [[20.309:Safety| lab safety]]
Line 21: Line 22:
 
|style="width: 45%;"|'''Useful resources'''
 
|style="width: 45%;"|'''Useful resources'''
 
|--  
 
|--  
−
|  <font color=#04B45F>9/17/17</font color>
+
|  <font color=#04B45F>2/16/20</font color>
 
| Assignment 1
 
| Assignment 1
 
|  
 
|  
Line 30: Line 31:
 
* [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: Measure stuff]]
 
* [[Assignment 1, Part 4: Building your transilluminated microscope|Part 4: Measure stuff]]
 
|  
 
|  
−
* [https://stellar.mit.edu/S/course/20/fa13/20.309/materials.html Lectures 1 through 9 of the 20.309 class]
+
* [https://stellar.mit.edu/S/course/20/sp20/20.309/materials.html Lectures 1 through 9 of the 20.309 class]
−
* From [http://www.microscopyu.com Nikon MicroscopyU]
+
* [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
−
** [http://www.microscopyu.com/articles/formulas/formulasconjugate.html Conjugate planes in optical microscopy] (includes transmitted and reflected (epi) illumination)
+
−
** [http://www.microscopyu.com/articles/formulas/formulasri.html Snell's law]
+
−
** [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
+
 
*  [[Understanding log plots]]
 
*  [[Understanding log plots]]
 
|-
 
|-
−
| <font color=#04B45F>9/24/17</font color>
+
| <font color=#04B45F>2/23/20</font color>
 
| Assignment 2
 
| Assignment 2
 
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]]
 
| [[Assignment 2: fluorescence microscopy| Assignment 2 Overview]]
Line 51: Line 49:
 
* [[Manta G032 camera measurements]]
 
* [[Manta G032 camera measurements]]
 
|-
 
|-
−
| <font color=#04B45F>9/28/17</font color>
+
| <font color=#04B45F>2/25/20</font color>
 
| Quiz 1 (in lecture)
 
| Quiz 1 (in lecture)
 
| ||
 
| ||
 
|-
 
|-
−
|  <font color=#04B45F>10/1/17</font color>
+
|  <font color=#04B45F>3/1/20</font color>
 
| Assignment 3
 
| Assignment 3
 
| [[Assignment 3 Overview|Assignment 3 Overview]]
 
| [[Assignment 3 Overview|Assignment 3 Overview]]
Line 64: Line 62:
 
*[[Matlab: Scalebars]]
 
*[[Matlab: Scalebars]]
 
|-
 
|-
−
|  <font color=#04B45F>10/8/17</font color>
+
|  <font color=#04B45F>3/8/20</font color>
 
| Assignment 4
 
| Assignment 4
 
|{{Template:Assignment 4 navigation}}
 
|{{Template:Assignment 4 navigation}}
 
|
 
|
 +
* [http://www.microscopyu.com/articles/formulas/formulasresolution.html Resolution]
 
* [[Physical optics and resolution]]
 
* [[Physical optics and resolution]]
 +
* [[Converting Gaussian fit to Rayleigh resolution]]
 +
* [[MATLAB: Estimating resolution from a PSF slide image]]
 +
* [[Matlab: Scalebars]]
 +
* [[Calculating MSD and Diffusion Coefficients]]
 
|-
 
|-
−
|  <font color=#04B45F>10/15/17</font color>
+
|  <font color=#04B45F>4/3/20</font color>
 
| Assignment 5
 
| Assignment 5
−
| [[Assignment 5 Overview|Assignment 5 Overview]]
+
| [[Assignment 5: Spring 2020|Assignment 5 Overview (Spring 2020)]]
−
* [[Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures|Part 1: Estimating the diffusion coefficient by tracking suspended microspheres]]  
+
* [[Assignment 5, Part 1: MSD difference tracking and microscope stability|Part 1: MSD difference tracking and microscope stability]]  
 
* [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]]
 
* [[Assignment 5, Part 2: live cell particle tracking of endocytosed beads| Part 2: Live cell particle tracking of endocytosed beads]]
 
|
 
|
−
* [[Converting Gaussian fit to Rayleigh resolution]]
 
−
* [[MATLAB: Estimating resolution from a PSF slide image]]
 
 
* [[Matlab: Scalebars]]
 
* [[Matlab: Scalebars]]
 
* [[Calculating MSD and Diffusion Coefficients]]
 
* [[Calculating MSD and Diffusion Coefficients]]
 
|-
 
|-
−
|  <font color=#04B45F>10/19/17</font color>
+
|  <font color=#04B45F>4/7/20</font color>
−
| Exam 1 (at 7:30pm in 4-163)
+
| Exam 1  
 
|  
 
|  
 
|
 
|
Line 89: Line 90:
 
<br />
 
<br />
  
−
===Module 2: Signals and Systems===
+
===Module 2: electronics, signals and systems===
 
{| border=1px
 
{| border=1px
 
|style="width: 10%;"|'''Important dates'''  
 
|style="width: 10%;"|'''Important dates'''  
Line 96: Line 97:
 
|style="width: 45%;"|'''Useful resources'''
 
|style="width: 45%;"|'''Useful resources'''
 
|--  
 
|--  
−
|  <font color=#04B45F>10/29/17</font color>
+
|  <font color=#04B45F>4/13/20</font color>
 
| Assignment 6
 
| Assignment 6
−
| [[Assignment 6 Overview]]
+
| [[Spring 2020 Assignment 6]]
−
* [[Assignment 6, Part 1: Pre-lab questions|Part 1: Pre-lab questions]]
+
* (Previous semesters' assignment 6 for reference)
−
* [[Assignment 6, Part 2: Electronics bootcamp|Part 2: Build circuits and measure them]]
+
* [[Assignment 6 Overview: two color microscope|Assignment 6 overview]]
 +
* [[Assignment 6, Part 1: build a two-color microscope]]
 +
* [[Assignment 6, Part 2: electronics written problems]]
 
|
 
|
 
* [[Electronics primer]]
 
* [[Electronics primer]]
 
* [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"]
 
* [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]]
 
* [[Impedance Analysis|Impedance analysis]]
−
* [[Bode plots|Transfer functions and Bode plots]]
 
−
* [[Complex Number Review|Complex number review]]
 
 
* [[Input and output impedance]]
 
* [[Input and output impedance]]
−
 
−
|-
 
−
|  <font color=#04B45F>11/2/17</font color>
 
−
| Quiz 2 (in lecture)
 
−
|
 
−
|
 
 
|-
 
|-
−
|  <font color=#04B45F>11/5/17</font color>
+
|  <font color=#04B45F>4/20/20</font color>
 
| Assignment 7
 
| Assignment 7
−
| [[Assignment 7 Overview]]
+
| [[Spring 2020 Assignment 7]]
−
* [[Assignment 7, Part 1: op amp golden rules questions|Part 1: Op amps]]  
+
* (Previous semesters' assignment 7 for reference)
−
* [[Assignment 7, Part 2: measure temperature and fluorescence| Part 2: measure temperature and fluorescence]]  
+
* [[Electronics boot camp I: passive circuits and transfer functions|Assignment 7 overview]]
−
* [[Assignment 7, Part 3: testing your instrument and measuring a DNA melting curve| Part 3: test your instrument and measure a preliminary melting curve]]
+
* [[Electronics written problems II|Assignment 7, Part 1: more electronics written problems]]
 +
* [[Electronics boot camp lab part 1|Assignment 7, Part 2: Electronics bootcamp I]]
  
−
|
+
|  
−
* [[DNA Melting Thermodynamics]]
+
−
* [[Real electronics]]
+
 
* [[Impedance Analysis|Impedance analysis]]
 
* [[Impedance Analysis|Impedance analysis]]
 
* [[Bode plots|Transfer functions and Bode plots]]
 
* [[Bode plots|Transfer functions and Bode plots]]
Line 131: Line 124:
 
* [[Input and output impedance]]
 
* [[Input and output impedance]]
 
|-
 
|-
−
|  <font color=#04B45F>11/12/17</font color>
+
|  <font color=#04B45F>4/21/20</font color>
−
| Assignment 8
+
| Quiz 2 (60 min)
−
| [[Assignment 8 Overview]]
+
|  
−
* [[Assignment 8, Part 1: convolution|Part 1: convolution and lock-in amplifiers]]
+
−
* [[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]
 
 
|-
 
|-
−
|  <font color=#04B45F>11/19/17</font color>
+
|  <font color=#04B45F>4/27/20</font color>
 +
| Assignment 8
 +
| [[Spring 2020 Assignment 8]]
 +
*(Previous semester's assignment 8 for reference)
 +
*[[Assignment 8 Overview: flow channel & two-color microscope|Assignment 8 Overview]]
 +
* [[Electronics bootcamp II: feedback systems|Part 1: feedback systems]]
 +
* [[Assignment 8, Part 2: fabricate a microfluidic device| Part 2: fabricate a microfluidic device]]
 +
* [[Assignment 8, Part 3: add flow control and test your device| Part 3: add flow control and test your device]]
 +
|[http://science.sciencemag.org/content/319/5862/482 *The* yeast paper: Mettelal ''et al.'', ''Science'' (2008)]
 +
|-
 +
|  <font color=#04B45F>5/4/20</font color>
 
| Assignment 9
 
| Assignment 9
−
| [[Assignment 9 Overview]]
+
| [[Spring 2020 Assignment 9]]
−
* [[Assignment 9, Part 1: model function|Part 1: writing the model function]]
+
*(Previous semester's assignment 9 for reference)
−
* [[Assignment 9, Part 2: Simulating DNA melting data and testing the model function|Part 2: test your code with simulated data]]
+
* [[Assignment 9 Overview: Analyzing yeast images]]
−
* [[Assignment 9, Part 3: Fitting your data|Part 3: fitting your data]]
+
* [[Assignment 8, Part 0: convolution practice| Part 0: convolution practice]]
−
 
+
* [[Assignment 9, Part 1: Analyze two-color yeast images| Part 1: Analyze two-color yeast images]]
 +
* [[Assignment 10, Part 1: Measuring the osmotic shock response of yeast| A10: Measure the osmotic shock response of yeast]]
 
|
 
|
−
* [[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>5/8/20</font color>
−
| Assignment 10
+
| Exam 2 (90 min)
−
| [[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>5/12/20</font color>
−
| Exam 2 (at 7:30pm in 4-163)
+
| Assignment 10
−
|  
+
| [[Spring 2020 Assignment 10]]
 +
*(Previous semester's assignment 10 was combined with assignment 9)
 
|
 
|
 
|-
 
|-
−
|  <font color=#04B45F>12/13/17</font color>
+
|  cancelled
 
| Assignment 11
 
| Assignment 11
 +
| [[Assignment 11: Tell us about your lab visit]]
 
|  
 
|  
−
|
 
 
|-
 
|-
−
 
 
|}
 
|}
 
</div>
 
</div>
Line 194: Line 188:
 
* [[Electronics primer]]
 
* [[Electronics primer]]
 
* [https://www.khanacademy.org/science/electrical-engineering/ee-circuit-analysis-topic Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"]
 
* [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]]
 
* [[Impedance Analysis|Impedance analysis]]
 
* [[Bode plots|Transfer functions and Bode plots]]
 
* [[Bode plots|Transfer functions and Bode plots]]
 
* [[Complex Number Review|Complex number review]]
 
* [[Complex Number Review|Complex number review]]
 
* [[Input and output impedance]]
 
* [[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===
 
−
* [[DNA Melting Thermodynamics]]
 
−
* [[DNA Melting: DNA Sequences]]
 
−
* [http://mfold.rna.albany.edu/?q=DINAMelt/Hybrid2 DINAMelt Web Server]
 
  
 
==Limits of detection mini-lab==
 
==Limits of detection mini-lab==

Latest revision as of 20:47, 16 October 2020

20.309: Biological Instrumentation and Measurement

ImageBar 774.jpg


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 master schedule

Module 1: Optics & Microscopy

Important dates Assignment due Assignment page links Useful resources
2/16/20 Assignment 1

Assignment 1 Overview

2/23/20 Assignment 2 Assignment 2 Overview
2/25/20 Quiz 1 (in lecture)
3/1/20 Assignment 3 Assignment 3 Overview
3/8/20 Assignment 4
4/3/20 Assignment 5 Assignment 5 Overview (Spring 2020)
4/7/20 Exam 1


Module 2: electronics, signals and systems

Important dates Assignment due Assignment page links Useful resources
4/13/20 Assignment 6 Spring 2020 Assignment 6
4/20/20 Assignment 7 Spring 2020 Assignment 7
4/21/20 Quiz 2 (60 min)
4/27/20 Assignment 8 Spring 2020 Assignment 8 *The* yeast paper: Mettelal et al., Science (2008)
5/4/20 Assignment 9 Spring 2020 Assignment 9
5/8/20 Exam 2 (90 min)
5/12/20 Assignment 10 Spring 2020 Assignment 10
  • (Previous semester's assignment 10 was combined with assignment 9)
cancelled Assignment 11 Assignment 11: Tell us about your lab visit

Optics and microscopy resources

Background reading

Code examples and simulations

Electronics resources

Background reading

Limits of detection mini-lab

MRI mini-lab

(Kept for historical reasons.)
Retrieved from "http://measurebiology.org/w/index.php?title=20.309_Main_Page&oldid=45842"