20.309:Course Information - Revision history

Steven Wasserman: /* Present data properly */

Steven Wasserman — Tue, 07 Oct 2008 14:34:10 GMT

Present data properly

←Older revision		Revision as of 14:34, 7 October 2008
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	*Pictures must have a scale. (Pictures of your apparatus are an exception.)		*Pictures must have a scale. (Pictures of your apparatus are an exception.)
	*[http://en.wikipedia.org/wiki/Chartjunk Chartjunk] is forbidden.		*[http://en.wikipedia.org/wiki/Chartjunk Chartjunk] is forbidden.
-	*Use tables appropriately~~. If a table can be replaced by one or two sentences, do so~~.	+	*Use tables appropriately.
	*Try not to use screen captures.		*Try not to use screen captures.

Steven Wasserman at 14:32, 7 October 2008

Steven Wasserman — Tue, 07 Oct 2008 14:32:46 GMT

←Older revision		Revision as of 14:32, 7 October 2008
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	There are four laboratory modules that require a written report: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.		There are four laboratory modules that require a written report: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.
		+
		+	===Homework===
		+
		+	We will have weekly problem sets until the project labs begin. The problem sets are designed to help you solidify concepts presented in lecture and also to prepare for upcoming labs.
		+
		+	===Class Presentation===
		+	Presentations will be on a research paper (in some cases two related papers) from the list under ‘Student Presentations’. You should look through these papers and enter your name next to paper that interests you the most (edit the wiki page to do this). This should be done by Tuesday, September 23 to avoid being randomly assigned by the instructors. It is also an option to present on your own research experience (e.g. a fruitful UROP) or a paper that is not on the list (but related to the overall themes of 20.309). If you’re interested in this option, make sure to discus this with an instructor before Sept 23.
		+
		+	Your presentation time is 10 minutes and it's very important that you do not go over this time. We will have a few minutes for questions and discussion. It's also important that all non-presenters read the papers carefully before the session as this will make the discussion much more interesting.
		+
		+	Your presentation should provide background to motivate why the research was conducted, describe the key results of the paper (not necessarily all of the results) and the essence of the measurement method, and explain the significance of the results to the general field. Remember that 10 minutes will not be nearly enough time to discuss every aspect of the paper so you will need to identify the most important aspects to include in your presentation.
		+
		+	Make sure to upload a Powerpoint or PDF file of your presentation to the wiki site 12 hours in advance of your presentation so that all files can be launched from a single laptop. Individual laptops will not be allowed since there is no time allotted for connecting between talks.
		+
		+	Feel free to see 20.309 staff outside of class to discuss any questions or ideas that you might have about the paper.

	==Lab report guidelines==		==Lab report guidelines==
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	Manuscripts not meeting the above criteria will be graded accordingly.		Manuscripts not meeting the above criteria will be graded accordingly.
-
-	~~===Homework===~~
-
-	~~We will have weekly problem sets until the project labs begin. The problem sets are designed to help you solidify concepts presented in lecture and also to prepare for upcoming labs.~~
-
-	~~===Class Presentation===~~
-	Presentations will be on a research paper (in some cases two related papers) from the list under ‘Student Presentations’. You should look through these papers and enter your name next to paper that interests you the most (edit the wiki page to do this). This should be done by Tuesday, September 23 to avoid being randomly assigned by the instructors. It is also an option to present on your own research experience (e.g. a fruitful UROP) or a paper that is not on the list (but related to the overall themes of 20.309). If you’re interested in this option, make sure to discus this with an instructor before Sept 23.
-
-	Your presentation time is 10 minutes and it's very important that you do not go over this time. We will have a few minutes for questions and discussion. It's also important that all non-presenters read the papers carefully before the session as this will make the discussion much more interesting.
-
-	Your presentation should provide background to motivate why the research was conducted, describe the key results of the paper (not necessarily all of the results) and the essence of the measurement method, and explain the significance of the results to the general field. Remember that 10 minutes will not be nearly enough time to discuss every aspect of the paper so you will need to identify the most important aspects to include in your presentation.
-
-	Make sure to upload a Powerpoint or PDF file of your presentation to the wiki site 12 hours in advance of your presentation so that all files can be launched from a single laptop. Individual laptops will not be allowed since there is no time allotted for connecting between talks.
-
-	~~Feel free to see 20.309 staff outside of class to discuss any questions or ideas that you might have about the paper.~~


	</div>		</div>

Steven Wasserman at 14:31, 7 October 2008

Steven Wasserman — Tue, 07 Oct 2008 14:31:53 GMT

←Older revision		Revision as of 14:31, 7 October 2008
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	There are four laboratory modules that require a written report: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.		There are four laboratory modules that require a written report: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.

-	It is ~~important~~ that data is ~~presented~~ properly. ~~This includes:~~	+	==Lab report guidelines==
-	*Plots must have a brief, informative title. Axes must be labeled with a description, including units~~, and be legible when printed~~.	+
-	*~~Images~~ must have a scale.	+	The purpose of your report is to convey as clearly as possible which physical phenomena you examined in the lab, the means you employed, and what you learned. The report should be brief. Consider each pixel you choose to darken on the page in the context of the information it conveys. Ideally (but not practically), erasing a single pixel would diminish the content. Focus on the essentials.
		+
		+	Imagine that you are writing the report for a classmate. The intended audience for your report has a deep understanding of the subject. As such, lengthy derivations and explanations are not necessary. The reader would very much like to understand what you did in the lab, what sort of problems you ran into, how you analyzed your data, and what you concluded.
		+
		+	Your report does not have to be written like a formal scientific paper. Feel free to use whatever organization works for you so long as it includes all of the information. Bullet points are often more effective than flowing text. Follow the content and style guidelines below.
		+
		+	===Introduce the subject===
		+
		+	Begin with a paragraph explaining why you went to the lab. What were the key questions you set out to answer? What techniques did you apply to the problem?
		+
		+	===Explain the apparatus and procedure===
		+
		+	Some lab exercises involve significant design and construction work. Others utilize complex systems that were built by others. In either case, the apparatus you used in the lab must be documented in your report. Block diagrams, schematics, photographs, and text descriptions, and citations of sources are all excellent ways to describe an apparatus.
		+
		+	Design documentation should be sufficiently detailed to enable another person to build a functionally similar piece of equipment. Include component values and reference designators (R<sub>l</sub>, C<sub>f</sub>, L<sub>1</sub>, etc…) on schematics. Explain why you chose the values you did. If you chose to implement a portion of your apparatus differently than the lab manual suggested, explain why. If you wrote a program, explain what it did in the body of your report and include the source code in an appendix.
		+
		+	Detailed documentation is available for the predesigned pieces of equipment in the lab (such as the AFM and the optical trap). In these cases, focus on the aspects of the machine that are essential to understanding your data analysis. A simple block diagram and a few bullet points will meet the requirements.
		+
		+	Once you have documented the apparatus, explain how you used it and what measurements you took.
		+
		+	===Explain your analysis===
		+
		+	Tell what steps you took to analyze your data. As in the other parts of your report, focus on what is important. It is not necessary to reproduce each step of every calculation. Make sure the reader understands what you did, though.
		+
		+	===Say what would you do differently next time===
		+
		+	The instruments and procedures you will use in the lab are not perfect. Explain what factors limited your measurements how you could improve the results.
		+
		+	===Answer questions posed in the lab manual===
		+
		+	Ensure that your report addresses all the questions posed in the lab manual and by instructors. If there is not a natural place to do this in the body your report, put the answers in a section of their own.
		+
		+	===Present data properly===
		+
		+	*Figures must be numbered, descriptively captioned, and discussed in the text.
		+	*Plots must have a brief, informative title. Axes must be labeled with a description, including units.
		+	*Pictures must have a scale. (Pictures of your apparatus are an exception.)
		+	*[http://en.wikipedia.org/wiki/Chartjunk Chartjunk] is forbidden.
	*Use tables appropriately. If a table can be replaced by one or two sentences, do so.		*Use tables appropriately. If a table can be replaced by one or two sentences, do so.
-	*Do not use screen captures for ~~line plots~~ and avoid ~~screen captures~~ for images. ~~Instead, plot~~ the data ~~files~~ with ~~your own scripts (using Matlab~~ or ~~your favorite plotting program)~~.	+	*Try not to use screen captures.
		+
		+	Do not present every piece of raw data you gathered. Put in only things that are important, in a clear and concise format. If for some reason you have a large body of extremely interesting data to present, put it in an appendix and refer to it in your report. If you have a large body of uninteresting data, leave it out.
		+
		+	===Write tight prose===
		+
		+	*Use bullet points.
		+	*Avoid the first person.
		+	*Use active verbs.
		+	*Eliminate unnecessary words.
		+
		+	It is common practice in scientific writing to avoid using the pronouns I and we. This is changing slowly; however, it is an excellent habit to minimize the first person in your scientific writing. The author of a first person sentence in a scientific paper has frequently misidentified the true subject of a sentence. Consider the following 4 versions of a sentence:
		+
		+	#''I ran the experiment three times and calculated an average power of 1.21 GW.''
		+	#''The experiment was run three times and an average power of 1.21 GW was calculated.''
		+	#''Three experimental runs yielded a calculated average power of 1.21 GW.''
		+	#''Three experimental runs yielded an average power of 1.21 GW.''
		+
		+	In this example, substituting the subject “The experiment” for “I” eliminated the first person pronoun in sentence number 1, resulting in somewhat preferable sentence 2. The second sentence, though, is undesirable because it contains the passive verb forms "was run" and "was calculated." Passive voice is common in scientific writing; however, that does not mean you are required repeat the offense.
		+
		+	It is impossible to completely eliminate passive sentences from scientific writing. But that doesn’t mean you can’t try. See if you can limit your use of the passive voice to fewer than tweny percent of the verbs in your report.
		+
		+	Sentence 3 is preferable to number 2 because it uses an active verb. But it still could be tighter. Average values are necesarily calculated. Unless required to differentiate between several possible averages, remove the redundant verbiage.
		+
		+	===Write your ''own'' report===
		+
		+	In 20.309, you will work collaboratively in the lab. '''''The report you submit must be entirely your own work'''''. Any words, data, images, code, or other intellectual property you take from somebody else must be appropriately cited. Plagiarism is unacceptable.
		+
		+	===Lab report grading===
		+
		+	Lab reports will be graded on a 25 point scale. An outstanding report:
		+
		+	*Demonstrates mastery of the theory and practical implementation of the key techniques used in the experiment.
		+	*Presents results for each of the required experimental procedures
		+	*Draws appropriate conclusions from the data
		+	*Contains a thorough, correct, and well explained analysis
		+	*Address shortcomings of the experimental procedure and problems that cropped up during experimentation
		+	*Acknowledges everything that is not original work with an appropriate citation
		+	*Is well communicated
		+
		+	Outstanding reports will receive a numerical grade of 23-25 points.
		+
		+	Reports with minor deficits in one or two areas will receive an excellent score in the range of 20-22 points.
		+
		+	Reports with important shortcomings in one area will be awarded 17-19 points.
		+
		+	Manuscripts not meeting the above criteria will be graded accordingly.

	===Homework===		===Homework===

Steven Wasserman: /* Lab hours and scheduling */

Steven Wasserman — Sat, 13 Sep 2008 22:39:48 GMT

Lab hours and scheduling

←Older revision		Revision as of 22:39, 13 September 2008
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	\|+'''Lab Opening Hours'''		\|+'''Lab Opening Hours'''
	\|-		\|-
-	\|Monday\|\|11:00 AM - 7:00 PM	+	\|Monday\|\|10:00-7:00
	\|-		\|-
-	\|Tuesday\|\|1:00 PM - 7:00 PM	+	\|Tuesday\|\|1:00-11:00
	\|-		\|-
-	\|Wednesday\|\|10:00 AM - 8:00 PM	+	\|Wednesday\|\|10:00-9:00
	\|-		\|-
-	\|Thursday\|\|10:00 AM - 7:00 PM	+	\|Thursday\|\|1:00-9:00
	\|-		\|-
-	\|Friday\|\|10:00 AM - 6:00 PM	+	\|Friday\|\|1:00-7:00
	\|}		\|}

Scottm: /* Assignments */

Scottm — Sat, 13 Sep 2008 16:45:35 GMT

Assignments

←Older revision		Revision as of 16:45, 13 September 2008
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	==Assignments==		==Assignments==

-	All assignments will be due by ~~12:05~~ pm on the days designated in the schedule. Late assignments ~~(those that arrive after 12:05)~~ will not be accepted~~. Solutions will be posted in afternoon~~.	+	All assignments will be due by 5 pm on the days designated in the schedule. The homework drop-off box is located on the 4th floor of Bldg 16 located near the junction to Bldg 8. Late assignments will not be accepted.

	You are encouraged to seek advice from the instructors, TAs and other students, however, the work that is turned in must be your own.		You are encouraged to seek advice from the instructors, TAs and other students, however, the work that is turned in must be your own.

Steven Wasserman: /* Computers */

Steven Wasserman — Thu, 04 Sep 2008 02:55:27 GMT

Computers

←Older revision		Revision as of 02:55, 4 September 2008
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	===Computers===		===Computers===

-	Lab stations are equipped with PCs running Windows XP. Each PC has a data acquisition ~~card that is connected by a long cable to a signal breakout box at the lab station~~. MatLab and LabVIEW software are installed on all lab PCs.	+	Lab stations are equipped with PCs running Windows XP. Each PC has a National Instruments [http://sine.ni.com/nips/cds/view/p/lang/en/nid/204054 USB-6212] data acquisition system. MatLab and LabVIEW software are installed on all lab PCs.

	Lab PCs are members of the <code>WIN.MIT.EDU</code> domain. Press ctrl-alt-delete to log on. Make sure the <code>Log On To:</code> dropdown menu is set to <code>ATHENA.MIT.EDU (Kerberos Realm)</code>. Use your Athena username and password.		Lab PCs are members of the <code>WIN.MIT.EDU</code> domain. Press ctrl-alt-delete to log on. Make sure the <code>Log On To:</code> dropdown menu is set to <code>ATHENA.MIT.EDU (Kerberos Realm)</code>. Use your Athena username and password.

Steven Wasserman: /* Lab stations */

Steven Wasserman — Thu, 04 Sep 2008 02:46:19 GMT

Lab stations

←Older revision		Revision as of 02:46, 4 September 2008
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	===Lab stations===		===Lab stations===

-	There are 8 lab stations in room 16-352. Each station is equipped with:	+	There are 12 lab stations in room 16-352. Each station is equipped with:

	#anti-vibration optical table		#anti-vibration optical table
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	#computer workstation with data acquisition card		#computer workstation with data acquisition card

-	~~Station number 3 is~~ reserved for instructor use ~~at all times~~.	+	Stations 10 and 11 are normally reserved for instructor use.
	<!-- TODO: add links to equipment manuals -->		<!-- TODO: add links to equipment manuals -->

Steven Wasserman: /* Assignments */

Steven Wasserman — Thu, 04 Sep 2008 01:05:23 GMT

Assignments

←Older revision		Revision as of 01:05, 4 September 2008
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	You are encouraged to seek advice from the instructors, TAs and other students, however, the work that is turned in must be your own.		You are encouraged to seek advice from the instructors, TAs and other students, however, the work that is turned in must be your own.

-	We will not accept late assignments for any reason (~~accept~~ ones that are excused by the Dean’s office). However, we will omit the one lowest homework grade for the calculation of the term homework grade (20%). Students are encouraged to use this to their benefit and to accommodate special situations such as interview travel.	+	We will not accept late assignments for any reason (except ones that are excused by the Dean’s office). However, we will omit the one lowest homework grade for the calculation of the term homework grade (20%). Students are encouraged to use this to their benefit and to accommodate special situations such as interview travel.

	===Lab assignment===		===Lab assignment===

Steven Wasserman: /* Lab assignment */

Steven Wasserman — Thu, 04 Sep 2008 01:04:21 GMT

Lab assignment

←Older revision		Revision as of 01:04, 4 September 2008
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	===Lab assignment===		===Lab assignment===

-	There are four laboratory ~~sections~~ that require a ~~dedicated assignment~~: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.	+	There are four laboratory modules that require a written report: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.

	It is important that data is presented properly. This includes:		It is important that data is presented properly. This includes:

Steven Wasserman at 01:02, 4 September 2008

Steven Wasserman — Thu, 04 Sep 2008 01:02:35 GMT

←Older revision		Revision as of 01:02, 4 September 2008
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-
	{{Template:20.309}}		{{Template:20.309}}

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	\|+'''Lab Opening Hours'''		\|+'''Lab Opening Hours'''
	\|-		\|-
-	\|Monday\|\|10:00 AM - 6:00 PM	+	\|Monday\|\|11:00 AM - 7:00 PM
	\|-		\|-
-	\|Tuesday\|\|1:00 PM - 9:00 PM	+	\|Tuesday\|\|1:00 PM - 7:00 PM
	\|-		\|-
-	\|Wednesday\|\|1:00 PM - 9:00 PM	+	\|Wednesday\|\|10:00 AM - 8:00 PM
	\|-		\|-
-	\|Thursday\|\|10:00 AM - 6:00 PM	+	\|Thursday\|\|10:00 AM - 7:00 PM
	\|-		\|-
	\|Friday\|\|10:00 AM - 6:00 PM		\|Friday\|\|10:00 AM - 6:00 PM