840:153g - Revision history

Axel: /* Foreword */

Axel — Mon, 20 Aug 2012 16:29:15 GMT

Foreword

←Older revision		Revision as of 16:29, 20 August 2012
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	<blockquote>"If you want truly to understand something, try to change it"		<blockquote>"If you want truly to understand something, try to change it"
	(Kurt Lewin) </blockquote>		(Kurt Lewin) </blockquote>
-	This page is the course homepage for the "Recombinant DNA Techniques" (840:153g) lab at the University of Northern Iowa. '''''Current version: Fall ~~2011~~!''''' This page will be updated each summer.	+	This page is the course homepage for the "Recombinant DNA Techniques" (840:153g) lab at the University of Northern Iowa. '''''Current version: Fall 2012!''''' This page will be updated each summer.

	You may want to watch this really good [http://web.mit.edu/smcs/csbi/2006/q2/mit-csbi-foundation-08apr2006-220k.ram video from Drew Endy] before (or after) you read on. Please also read his groundbreaking article about [http://openwetware.org/images/0/0d/Nature04342.pdf Foundations for Engineering Biology].		You may want to watch this really good [http://web.mit.edu/smcs/csbi/2006/q2/mit-csbi-foundation-08apr2006-220k.ram video from Drew Endy] before (or after) you read on. Please also read his groundbreaking article about [http://openwetware.org/images/0/0d/Nature04342.pdf Foundations for Engineering Biology].

Axel at 19:44, 22 August 2011

Axel — Mon, 22 Aug 2011 19:44:09 GMT

←Older revision		Revision as of 19:44, 22 August 2011
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	==Tutorials==		==Tutorials==
	Check out this nice [http://openwetware.org/wiki/Arking:JCAOligoTutorialHome tutorial by Prof. Arking] to get started in the lab. I am just in the process of "converting" his material to the needs of our course. You can find that updated material on the [http://openwetware.org/wiki/Axel:Schwekendiek_Tutorials Schwekendiek_Lab homepage] here at OWW.		Check out this nice [http://openwetware.org/wiki/Arking:JCAOligoTutorialHome tutorial by Prof. Arking] to get started in the lab. I am just in the process of "converting" his material to the needs of our course. You can find that updated material on the [http://openwetware.org/wiki/Axel:Schwekendiek_Tutorials Schwekendiek_Lab homepage] here at OWW.
-
-	~~==Syllabus==~~
-	~~Please download the syllabus here.~~

	<!-- Replace everything above this line with information about your course. -->		<!-- Replace everything above this line with information about your course. -->

	</div>		</div>

Axel at 19:41, 22 August 2011

Axel — Mon, 22 Aug 2011 19:41:30 GMT

←Older revision		Revision as of 19:41, 22 August 2011
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	==Tutorials==		==Tutorials==
	Check out this nice [http://openwetware.org/wiki/Arking:JCAOligoTutorialHome tutorial by Prof. Arking] to get started in the lab. I am just in the process of "converting" his material to the needs of our course. You can find that updated material on the [http://openwetware.org/wiki/Axel:Schwekendiek_Tutorials Schwekendiek_Lab homepage] here at OWW.		Check out this nice [http://openwetware.org/wiki/Arking:JCAOligoTutorialHome tutorial by Prof. Arking] to get started in the lab. I am just in the process of "converting" his material to the needs of our course. You can find that updated material on the [http://openwetware.org/wiki/Axel:Schwekendiek_Tutorials Schwekendiek_Lab homepage] here at OWW.
		+
		+	==Syllabus==
		+	Please download the syllabus here.

	<!-- Replace everything above this line with information about your course. -->		<!-- Replace everything above this line with information about your course. -->

	</div>		</div>

Axel: /* Foreword */

Axel — Wed, 17 Aug 2011 20:56:17 GMT

Foreword

←Older revision		Revision as of 20:56, 17 August 2011
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	<blockquote>"If you want truly to understand something, try to change it"		<blockquote>"If you want truly to understand something, try to change it"
	(Kurt Lewin) </blockquote>		(Kurt Lewin) </blockquote>
-	This page is the course homepage for the "Recombinant DNA Techniques" (840:153g) lab at the University of Northern Iowa. '''''Current version: Fall ~~2010~~!''''' This page will be updated each summer.	+	This page is the course homepage for the "Recombinant DNA Techniques" (840:153g) lab at the University of Northern Iowa. '''''Current version: Fall 2011!''''' This page will be updated each summer.

	You may want to watch this really good [http://web.mit.edu/smcs/csbi/2006/q2/mit-csbi-foundation-08apr2006-220k.ram video from Drew Endy] before (or after) you read on. Please also read his groundbreaking article about [http://openwetware.org/images/0/0d/Nature04342.pdf Foundations for Engineering Biology].		You may want to watch this really good [http://web.mit.edu/smcs/csbi/2006/q2/mit-csbi-foundation-08apr2006-220k.ram video from Drew Endy] before (or after) you read on. Please also read his groundbreaking article about [http://openwetware.org/images/0/0d/Nature04342.pdf Foundations for Engineering Biology].

Axel: /* Grading */

Axel — Mon, 26 Jul 2010 19:10:11 GMT

Grading

←Older revision		Revision as of 19:10, 26 July 2010
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	<BR>		<BR>
	<BR>		<BR>
-	Last word of wisdom:	+	'''Last word of wisdom:'''
	Don't be scared. If you prepare for each session and contribute well to this class, you will have no problems. In this class you will be honored for what you put in and what you learn. The learning experience itself accounts for 50% of the grade. If you put in a lot of effort you will learn a lot and you will receive a good grade. If you don't, then you don't. It is up to you.		Don't be scared. If you prepare for each session and contribute well to this class, you will have no problems. In this class you will be honored for what you put in and what you learn. The learning experience itself accounts for 50% of the grade. If you put in a lot of effort you will learn a lot and you will receive a good grade. If you don't, then you don't. It is up to you.

Axel: /* Grading */

Axel — Mon, 26 Jul 2010 19:09:41 GMT

Grading

←Older revision		Revision as of 19:09, 26 July 2010
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	==Grading==		==Grading==
-	Your team needs to develop a proposal in which you describe your project in as much detail as possible. The first 10% of the grade will be given for selecting a part, module, device, developing an experimental outline to produce it~~, and~~ completing the project proposal (due by the end of week 3). However, your proposal should be complete by the end of week two to allow for a review and for making improvements. A complete proposal does not mean that you have to have all answers. You probably won't. I just expect that you have your ideas down and know what you need to do to achieve what you proposed. Each team will present its proposal in a 15 minute presentation in the last session of week 3. This presentation is ~~part of the~~ 10% of ~~your proposal~~ grade.	+	Your team needs to develop a proposal in which you describe your project in as much detail as possible. The first 20% of the grade will be given for selecting a part, module, device, developing an experimental outline to produce it. 10% will be given for completing the project proposal on your project homepage and another 10% for presenting it to class (both due by the end of week 3). However, your proposal should be complete by the end of week two to allow for a review and for making improvements. A complete proposal does not mean that you have to have all answers. You probably won't. I just expect that you have your ideas down and know what you need to do to achieve what you proposed. Each team will present its proposal in a 15 minute presentation in the last session of week 3. This presentation is worth 10% of you grade.
	<BR>		<BR>
	<BR>		<BR>
-	A large and very important part of the class grade will be based on writing a detailed lab notebook. This personal lab notebook is required and will be graded based on completeness, accuracy, and content. It should contain all experimental procedures carried out during each lab session (incl. observations, calculations, remarks, etc.), as well as description and discussion of results. Based on the results obtained, it MUST also contain a brief description of the steps you plan and materials you need for the next session. The notebook has to be written at the day of the lab - during the lab! Everyone has to write her/his own notebook. It is necessary that everyone writes a good notebook and keeps it updated. The notebook will be worth 40% of your grade!!! It will be graded 3 times during the semester (after 5, 10, 15 weeks). Notebook keeping is essential for your work and grade and therefore must be done while you work - not after. You cant take the notebooks home to finish your writing after class. There will often be lag times while experiments run. Use them for writing your lab notebook or discuss progress within your team or with me. The notebooks can never leave the lab and have to be available any time for review.	+	A large and very important part of the class grade will be based on writing a detailed lab notebook. This personal lab notebook is required and will be graded based on completeness, accuracy, and content. It should contain all experimental procedures carried out during each lab session (incl. observations, calculations, remarks, etc.), as well as description and discussion of results. Based on the results obtained, it MUST also contain a brief description of the steps you plan and materials you need for the next session. The notebook has to be written at the day of the lab - during the lab! Everyone has to write her/his own notebook. It is necessary that everyone writes a good notebook and keeps it updated. The notebook will be worth 30% of your grade!!! It will be graded 3 times during the semester (after 5, 10, 15 weeks). Notebook keeping is essential for your work and grade and therefore must be done while you work - not after. You cant take the notebooks home to finish your writing after class. There will often be lag times while experiments run. Use them for writing your lab notebook or discuss progress within your team or with me. The notebooks can never leave the lab and have to be available any time for review.
	<BR>		<BR>
	<br>		<br>
-	Finally, I expect each team to develop their part and test it. If a team does not accomplish it, the achievements as well as problems must be explained thoroughly in the lab notebooks and the summary report. Enough evidence must be provided in the lab notebooks that sufficient efforts have been undertaken to achieve the goals mentioned in the proposal. After all, this is real science (none of the parts you attempt to build have ever been generated) and there is no guarantee that any group will succeed (though chances are high that you will). Therefore, keeping a good notebook is essential. The individual notebook will account for 40% of the grade.	+	Finally, I expect each team to develop their part and test it. If a team does not accomplish it, the achievements as well as problems must be explained thoroughly in the lab notebooks and the summary report. Enough evidence must be provided in the lab notebooks that sufficient efforts have been undertaken to achieve the goals mentioned in the proposal. After all, this is real science (none of the parts you attempt to build have ever been generated) and there is no guarantee that any group will succeed (though chances are high that you will). Therefore, keeping a good notebook is essential. The individual notebook will account for 30% of the grade.
	<BR>		<BR>
	<br>		<br>
	I will assign another 30% of the grade based on my individual assessment of everyone's personal contribution.		I will assign another 30% of the grade based on my individual assessment of everyone's personal contribution.
-	Here, I will consider ideas presented during class sessions, ~~including~~ preparation for class, ~~discussion of~~ experiments and results, timeliness, and teamwork capabilities. I will access how well you come prepared to class (do you understand the protocols? do you understand what you are doing and why?), how well you develop your bench skills (do you improve carrying out procedures accurately? do you get clear results?) and how well you plan ahead (do you always have the materials you need or do you come ask?), and how well you contribute to bringing your project forward (do you think ahead? do you look yourself for alternatives, modification, solutions? or do you always ask me or your partner?). These contributions are worth another 30% of your grade. And please believe me: you can only perform well here if you do your homework and your planning. I will never assign homework but nevertheless you will have to do it. And believe me a second time: I will be able to judge if you come prepared or not! So please spend enough time BEFORE each session to review your progress and make sure you know that is next. In addition to my assessment, your team partner(s) will also have some say for this grade. Everyone's personal contribution will be weighed by a peer assessment, which will be done the week before finals. Peer evaluations have to be turned the week BEFORE finals (or they won't count).	+	Here, I will consider ideas presented during class sessions, preparation for class, background knowledge about procedures, bench performance, capability to discuss experiments and results, timeliness, cleanness of workspace, organization and handling of materials, and teamwork capabilities. I will access how well you come prepared to class (do you understand the protocols? do you understand what you are doing and why?), how well you develop your bench skills (do you improve carrying out procedures accurately? do you get clear and consistent results?) and how well you plan ahead (do you always have the materials you need or do you come ask?), and how well you contribute to bringing your project forward (do you think ahead? do you look yourself for alternatives, modification, solutions? or do you always ask me or your partner?). These contributions are worth another 30% of your grade. And please believe me: you can only perform well here if you do your homework and your planning. I will never assign homework but nevertheless you will have to do it. And believe me a second time: I will be able to judge if you come prepared or not! So please spend enough time BEFORE each session to review your progress and make sure you know that is next. In addition to my assessment, your team partner(s) will also have some say for this grade. Everyone's personal contribution will be weighed by a peer assessment, which will be done the week before finals. Peer evaluations have to be turned the week BEFORE finals (or they won't count).
	<br>		<br>
	<br>		<br>
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	<BR>		<BR>
	<BR>		<BR>
-	Please be aware that are no make-ups possible in this class!!! If you miss a class, it will affect your individual contribution and your peer assessment~~. The only chance to make up for a low grade is by giving a superior presentation (really, I expect a perfect one) in our last session before finals~~. There will be no final exams during final week. But we will have a final review meeting (mandatory) during finals.	+	Please be aware that are no make-ups possible in this class!!! If you miss a class, it will affect your individual contribution and your peer assessment. There will be no final exams during final week. But we will have a final review meeting (mandatory) during finals.
	<BR>		<BR>
	<BR>		<BR>
	Last word of wisdom:		Last word of wisdom:
-	Don't be scared. If you prepare for each session and contribute well to this class, you will have no problems. In this class you will be honored for what you put in and what you learn. If you put in a lot of effort~~, if~~ you learn a lot, you will receive a good grade. If you don't, then you don't. It is up to you.	+	Don't be scared. If you prepare for each session and contribute well to this class, you will have no problems. In this class you will be honored for what you put in and what you learn. The learning experience itself accounts for 50% of the grade. If you put in a lot of effort you will learn a lot and you will receive a good grade. If you don't, then you don't. It is up to you.

	==Getting Started with OWW==		==Getting Started with OWW==

Axel: /* 1) Select a part, module, device, or system to build */

Axel — Mon, 26 Jul 2010 19:03:15 GMT

1) Select a part, module, device, or system to build

←Older revision		Revision as of 19:03, 26 July 2010
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	==How to Start==		==How to Start==
	===1) Select a part, module, device, or system to build===		===1) Select a part, module, device, or system to build===
-	Your first team task is to select a project. You may take a look at the [http://parts.mit.edu/igem07/index.php/Presentations iGEM presentations] for some ideas and an overview of what undergraduate teams achieved. However, it is completely up to you what you want to do in this class. Please do not get confused by thinking you don't know enough to design a project. Just think about what kind of FUNCTION you want your part to carry out. For example, do you want to produce a certain smell or color? Do you want to build an oscillating device or something that can be activated under certain external triggers? Do you want to build a biological sensor? Or simply convert a plant gene into a biobrick? These are just a few ideas. Do whatever you like to work on. Please do not consider the assumed complexity of your project. We will brake it down to something that is achievable. At this point, JUST FOCUS ON WHAT YOU WOULD LIKE TO WORK ON. Everything else is irrelevant for the design step. Be curious and select something interesting. Don't be afraid to select a project that looks challenging. We will learn something from each project - regardless of how far you get with it. So please select a project that really interests you; something you really would like to do.	+	Your first team task is to select a project. You may take a look at the [http://parts.mit.edu/igem07/index.php/Presentations iGEM presentations] for some ideas and an overview of what undergraduate teams achieved. However, it is completely up to you what you want to do in this class. Please do not get confused by thinking you don't know enough to design a project. Just think about what kind of FUNCTION you want your part to carry out. For example, do you want to produce a certain smell or color? Do you want to build an oscillating device or something that can be activated under certain external triggers? Do you want to build a biological sensor? Or simply convert a plant gene into a biobrick? These are just a few ideas. Do whatever you like to work on. Please do not consider the assumed complexity of your project. We will brake it down to something that is achievable. At this point, '''JUST FOCUS ON WHAT YOU WOULD LIKE TO WORK ON'''. Come with some creative and challenging ideas. Everything else is irrelevant for the design step. Be curious and select something interesting. Don't be afraid to select a project that looks challenging. We will learn something from each project - regardless of how far you get with it. So please select a project that really interests you; something you really would like to do.

	Once you found something interesting to work on, find a partner who wants to work together with you or join someone in their project. Browse the parts in the [http://partsregistry.org/Main_Page registry] to find out what is available to use and what you can build on to achieve your plans. Then, make a list of what needs to be done. We will discuss all proposals in the third week. I will assist you in the planning as much as you need. But you have to come with ideas for discussion and ask specific questions. I will not give you suggestions on what to do, except for the above. And I will not tell you if something is possible or not. Everything is possible and we should not limit ourselves.		Once you found something interesting to work on, find a partner who wants to work together with you or join someone in their project. Browse the parts in the [http://partsregistry.org/Main_Page registry] to find out what is available to use and what you can build on to achieve your plans. Then, make a list of what needs to be done. We will discuss all proposals in the third week. I will assist you in the planning as much as you need. But you have to come with ideas for discussion and ask specific questions. I will not give you suggestions on what to do, except for the above. And I will not tell you if something is possible or not. Everything is possible and we should not limit ourselves.

Axel: /* Getting Started with OWW */

Axel — Mon, 26 Jul 2010 19:01:41 GMT

Getting Started with OWW

←Older revision		Revision as of 19:01, 26 July 2010
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	==Getting Started with OWW==		==Getting Started with OWW==
-	To get started with your online journal, you need to [http://openwetware.org/wiki/OpenWetWare:How_to_join apply for an account at OWW] (which is free). Please ~~write~~ down your username and password from your confirmation email. After you obtained your account details, please go to the [[840:153g:Projects\|Project Page]] and start developing your proposal. There is help available on how to use this WIKI in the left-handed navigation pane and in the top menu bar.	+	To get started with your online journal, you need to [http://openwetware.org/wiki/OpenWetWare:How_to_join apply for an account at OWW] (which is free). Please use '''membership code 562c90''' when you apply. Write down your username and password from your confirmation email. After you obtained your account details, please go to the [[840:153g:Projects\|Project Page]] and start developing your proposal. There is help available on how to use this WIKI in the left-handed navigation pane and in the top menu bar.

	==Tutorials==		==Tutorials==

Axel: /* Grading */

Axel — Mon, 26 Jul 2010 18:59:11 GMT

Grading

←Older revision		Revision as of 18:59, 26 July 2010
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	* 10% project presentation (THU of week 3 - all teams)		* 10% project presentation (THU of week 3 - all teams)
	* 30% lab notebook		* 30% lab notebook
-	* 30% individual contribution (ideas presented, preparation for class, performance, knowledge)	+	* 30% individual contribution (quality of ideas presented, preparation for class, bench performance, knowledge acquired, cleanness of workspace, timeliness)
	* 10% project summary report (10+ pages, scientific journal style)		* 10% project summary report (10+ pages, scientific journal style)
	* 10% final summary presentation (last day before finals week)		* 10% final summary presentation (last day before finals week)

Axel at 18:57, 26 July 2010

Axel — Mon, 26 Jul 2010 18:57:37 GMT

←Older revision		Revision as of 18:57, 26 July 2010
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	<BR>		<BR>
	Final Grade Composition:		Final Grade Composition:
-	* 10% project proposal ~~and presentation~~ (due by ~~end~~ of week 3)	+	* 10% project proposal (due online at OWW by THU of week 3)
-	* 40% lab notebook	+	* 10% project presentation (THU of week 3 - all teams)
		+	* 30% lab notebook
	* 30% individual contribution (ideas presented, preparation for class, performance, knowledge)		* 30% individual contribution (ideas presented, preparation for class, performance, knowledge)
-	* 20% project summary report (10+ pages, scientific journal style)	+	* 10% project summary report (10+ pages, scientific journal style)
-	~~optional extra credit:~~ 10% final summary presentation (~~15 minutes~~)~~. If you opt for it, you need to confirm this with your teacher BEFORE Thanksgiving!!!~~	+	* 10% final summary presentation (last day before finals week)
	<BR>		<BR>
	<BR>		<BR>