20.309: Difference between revisions

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==Announcements==
==Announcements==  
*Make sure to select your presentation by September 23 by signing up on the [[20.309:Presentations|wiki]]
 
*For lab demo tomorrow, we will meet on the 2nd floor of NE47 (500 Technology Square) across the street from the McGovern Center (Brain and Cog building).  We will divide the class into two groups.  People with last names from A-L, please come at 12:00 and people with last names from M-Z please come at 12:30.
*Lecture notes for 3D Microscopy II: Multiphoton Microscopy posted.
*Lecture notes for 3D Microscopy I: Confocal Microscopy posted.
*Thank you for reminding me that I have forgotten to give you the images to process for the Fourier problem in HW8.  They are now posted in MATLAB file format.  I have also included the Perlman paper that I mentioned in the homework and hopefully it makes the last problem clearer.  Good luck.
*Lecture note for Advanced Fluorescence Microscopy II posted.
*Lecture note for Advanced Fluorescence Microscopy I posted.
*Homework 8 posted, due right before Thanksgiving.
 
 
[[Old Announcement| Announcement Archives]]
 
<!--
*Lecture notes for Fluorescence Spectroscopy II & III are posted.
*Office Hours Monday from 2:00-4:00 PM to answer questions about PSET #7
*Lecture note for Fluorescence Spectroscopy I is posted.
*A corrected, updated schedule is posted again:  [http://openwetware.org/wiki/Image:Schedule_v6.pdf schedule].  There may be an additional homework 9 for extra credit.
*Lectures notes for ImageProcessing I & II are posted
*Lecture notes for Fluorescence spectroscopy I is posted.
*Note that we have updated the course [http://www.openwetware.org/images/8/84/Schedule_v5.pdf schedule].
*Lecture Note for Optoelectronics III posted. 
*Lecture Note for Optoelectronics II posted.  Reminder: Quiz tomorrow (focus only on Optics & Microscopy lectures)
*Lecture Note for Optoelectronics I posted.  Homework 7 posted.
*Fluorescence microscopy starts today. This week: build your microscope and characterize the white light path.
*'''Preliminary''' lab manual for fluorescence microscopy is [http://scripts.mit.edu/~20.309/wiki/index.php?title=20.309/Labs/Fluorescence_Optical_Microscope here]. Please note there will be changes.
*Lecture Note for Optics & Microscopy IV is now online.  Please note that there will be a quiz tomorrow.
*Lecture Note for Optics & Microscopy III is now online.
*Lecture Notes for Optics & Microscopy I & II and Problem Set #6 are now online.  Due to some posting problems, Problem Set #6 is due on October 28.  See updated schedule.
*Problem Set #5 will be extended to October 24, part (e): 10ms (not 10us)
*[[Media:Thermal Noise Lecture.pdf|DNA melting report and thermal noise lab slides from Friday 10/04 lecture]]
*DNA data analysis slides from Tuesday 9/30 lecture are now posted [[Media:DNA Analysis Advice v2.pdf|here]]
*Slides for Friday 9/26 lecture are now posted [[Media:Sampling Lecture.pdf|here]]
*Sign up for your presentation (with [[20.309:Presentations|this link]]) by September 23 to avoid being randomly assigned.
*[[20.309:Updates for DNA Melting Module|Updates for the DNA melting module]]
*[[20.309:Updates for DNA Melting Module|Updates for the DNA melting module]]
-->
*New lab hours:
*New lab hours:
{|border="1"
{| class="wikitable" border="1" style="margin: 1em auto 1em auto"
|+'''Lab Opening Hours'''
|-
|-
|Monday||10:00-7:00
|Monday||10:00-7:00
Line 20: Line 55:
|}
|}


*Welcome to 20.309!
==Course Documents==
*Download ''[[Media:packet.pdf|this file]]'' containing course information, including schedule, reading assignments, lab modules, and homework (3.5 MB)
[[Documents]] This includes documents related to psets, quizes, labs, and lectures
*Readings for the first half of 20.309 are available in a single (32 MB) pdf file. You can find the file in the ''readings'' folder of the course locker. To access the locker from a Project Athena machine, type: <code>attach 20.309</code> and then <code>cd ~20.309</code>. The full path to the readings folder is: <code>\\afs\athena.mit.edu\course\20\20.309\Students\Readings</code>.  You can also download the file directly at [http://www.media.mit.edu/nanoscale/courses/BE309/private/reading.pdf this link].  The login and password will be provided in lecture.
 
==Deadlines Update==
*Student presentations Tuesday 11/25
*PSET #8 DUE Monday, 12/1 at 12:00 PM. No exceptions. (note change ONCE again)
*Thanksgiving holiday 11/27-28
*12/9 will be the last day to work in the lab on your final project
*Final project poster will be due at 4:59 PM on 12/10
*Very informal poster session and class party at 5:00 PM on 12/10
 
 
==Course packet and readings==
===Course packet===
''[[Media:packet.pdf|20.309 course packet]]'' (schedule, reading assignments, lab modules, and homework: 3.5 MB pdf file)
 
===Readings===
Readings for the first half of the course are available in a single (32 MB pdf) file, located in the ''readings'' folder of the course locker. The course locker is available on all lab machines, Project Athena machines, and via AFS.
 
To access the locker from a Project Athena machine, type: <code>attach 20.309</code> and then <code>cd ~20.309</code>.  


The full AFS path to the readings folder is: <code>\\afs\athena.mit.edu\course\20\20.30\Students\Readings</code>. 
You can also download the file directly at [http://www.media.mit.edu/nanoscale/courses/BE309/private/reading.pdf this link]. The login and password will be provided in lecture.
(Due to copyright restrictions, this file cannot be posted on Openwetware.)
==This Week==
==This Week==
{{Template:20.309Week
|StartDate=10/6
|EndDate=10/10
|Lecture1=Mechanical Systems
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_15.pdf Ultimate limits of force and position detection]
|Recitation=[[20.309:Presentations|Student Presentations]]
|Optional reading=
|Lab=
*DNA Melting lab
|Homework=
*Homework #5 due on Oct 24 at noon
|Lab=
*Module 2: Thermal noise measurement
}}
==Week 4==
{{Template:20.309Week
|StartDate=9/29
|EndDate=10/3
|Lecture1=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_9.pdf Convolution]
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_10.pdf Application of Convolution Theorem]
|Recitation=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_dna.pdf Lab 1 Requirements and Intro to Lab 2]
|Optional reading=
|Lab=
*DNA Melting lab
|Homework=
*Homework #4 due on Oct 7  [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw4.pdf SOLUTIONS]
|Lab=
*Module 1: [[20.309:Measuring_DNA_Melting_Curves|DNA Melting Lab]] FINAL WEEK
}}
==Week 3==
{{Template:20.309Week
|StartDate=9/15
|EndDate=9/20
|Lecture1=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_8.pdf Intro to Fourier Analysis]    [http://www.media.mit.edu/nanoscale/courses/BE309/private/quizzes/quiz_2_sol.pdf  Quiz #2 Solutions]
|Lecture2=Power Spectral Density, Noise and Bandwidth (blackboard)
|Recitation=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/samp.pdf Sampling and Discrete Analysis]
|Optional reading=
|Lab=
*DNA Melting lab
|Homework=
*Homework #3 due on Sept 30  [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw3.pdf SOLUTIONS]
|Lab=
*Module 1: [[20.309:Measuring_DNA_Melting_Curves|DNA Melting Lab]]
}}
==Week 2==
{{Template:20.309Week
|StartDate=9/15
|EndDate=9/20
|Lecture1=Op-amps and negative feedback (blackboard)  [http://www.media.mit.edu/nanoscale/courses/BE309/private/quizzes/quiz_1_sol.pdf  Quiz #1 Solutions]
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_7.pdf Op-amp applications]
|Recitation=The reality of op-amps
|Optional reading=
|Lab=
*DNA Melting lab
|Homework=
*Homework #2 due on Sept 23  [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw2.pdf SOLUTIONS]
|Lab=
*Module 1: [[20.309:Measuring_DNA_Melting_Curves|DNA Melting Lab]]
}}
==Week 1==
{{Template:20.309Week
{{Template:20.309Week
|StartDate=9/8
|StartDate=9/8
Line 36: Line 157:
*Lab opens 9/8
*Lab opens 9/8
|Homework=
|Homework=
*[[20.309:Homeworks/Homework1|Homework #1]] (also available in the course [[Media:packet.pdf|PDF file]]) <font color=#aa0000>'''due 9/16'''</font>
*[[20.309:Homeworks/Homework1|Homework #1]] (also available in the course [[Media:packet.pdf|PDF file]])   [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw1.pdf SOLUTIONS]
|Lab=
|Lab=
*Module 0: Introduction to Electronics
*Module 0: Introduction to Electronics

Latest revision as of 14:34, 4 December 2008

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       


Announcements

  • For lab demo tomorrow, we will meet on the 2nd floor of NE47 (500 Technology Square) across the street from the McGovern Center (Brain and Cog building). We will divide the class into two groups. People with last names from A-L, please come at 12:00 and people with last names from M-Z please come at 12:30.
  • Lecture notes for 3D Microscopy II: Multiphoton Microscopy posted.
  • Lecture notes for 3D Microscopy I: Confocal Microscopy posted.
  • Thank you for reminding me that I have forgotten to give you the images to process for the Fourier problem in HW8. They are now posted in MATLAB file format. I have also included the Perlman paper that I mentioned in the homework and hopefully it makes the last problem clearer. Good luck.
  • Lecture note for Advanced Fluorescence Microscopy II posted.
  • Lecture note for Advanced Fluorescence Microscopy I posted.
  • Homework 8 posted, due right before Thanksgiving.


Announcement Archives


  • New lab hours:
Lab Opening Hours
Monday 10:00-7:00
Tuesday 1:00-11:00
Wednesday 10:00-9:00
Thursday 1:00-9:00
Friday 1:00-7:00

Course Documents

Documents This includes documents related to psets, quizes, labs, and lectures

Deadlines Update

  • Student presentations Tuesday 11/25
  • PSET #8 DUE Monday, 12/1 at 12:00 PM. No exceptions. (note change ONCE again)
  • Thanksgiving holiday 11/27-28
  • 12/9 will be the last day to work in the lab on your final project
  • Final project poster will be due at 4:59 PM on 12/10
  • Very informal poster session and class party at 5:00 PM on 12/10


Course packet and readings

Course packet

20.309 course packet (schedule, reading assignments, lab modules, and homework: 3.5 MB pdf file)

Readings

Readings for the first half of the course are available in a single (32 MB pdf) file, located in the readings folder of the course locker. The course locker is available on all lab machines, Project Athena machines, and via AFS.

To access the locker from a Project Athena machine, type: attach 20.309 and then cd ~20.309.

The full AFS path to the readings folder is: \\afs\athena.mit.edu\course\20\20.30\Students\Readings.

You can also download the file directly at this link. The login and password will be provided in lecture.

(Due to copyright restrictions, this file cannot be posted on Openwetware.)

This Week

10/6-10/10
Lecture & Recitation
Tuesday

Mechanical Systems

Thursday

Ultimate limits of force and position detection

Friday

Student Presentations

Optional reading
Homework
  • Homework #5 due on Oct 24 at noon
Lab
  • Module 2: Thermal noise measurement

Week 4

9/29-10/3
Lecture & Recitation
Tuesday

Convolution

Thursday

Application of Convolution Theorem

Friday

Lab 1 Requirements and Intro to Lab 2

Optional reading
Homework
Lab

Week 3

9/15-9/20
Lecture & Recitation
Tuesday

Intro to Fourier Analysis Quiz #2 Solutions

Thursday

Power Spectral Density, Noise and Bandwidth (blackboard)

Friday

Sampling and Discrete Analysis

Optional reading
Homework
Lab

Week 2

9/15-9/20
Lecture & Recitation
Tuesday

Op-amps and negative feedback (blackboard) Quiz #1 Solutions

Thursday

Op-amp applications

Friday

The reality of op-amps

Optional reading
Homework
Lab

Week 1

9/8-9/12
Lecture & Recitation
Tuesday

RC Circuits

Thursday

Filters

Friday

Thermodynamics of DNA melting

Optional reading
Homework
Lab
  • Module 0: Introduction to Electronics

Week 0

9/4-9/5
Lecture & Recitation
Tuesday
  • No lecture
Thursday
Friday
Optional reading
  • No optional readings this week
Homework
  • None assigned
Lab
  • Lab opens 9/8



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