840:153g/2008 - Revision history

Axel: /* 2) Describe your project on the team homepage */

2009-07-31T21:43:12Z

2) Describe your project on the team homepage

←Older revision		Revision as of 21:43, 31 July 2009
Line 40:		Line 40:
	*proof of function		*proof of function

-	Developing your ideas and figuring out what is involved is a complex task that involves all team members - and the instructor. You have to sit together and play around with your ideas. Brainstorm, make plans, assign work pieces to everyone, find information, discuss what you found, revise your concepts, look up protocols and describe your approach on your homepage. Familiarize yourself (everyone) with OpenWetWare, how to edit pages~~, how to link to other information~~, and how to upload pictures. Just use the "help" function on the left or on top of each page. Do not forget to apply for an account (which is free) as soon as possible~~. Do it after~~ the ~~first~~ class session. You need ~~the working~~ account ~~very soon~~. ~~So please don't delay applying~~. Your experimental design, the approach you take, and the results you expect must be explained in form of a research proposal ~~and uploaded to~~ your project website. This proposal needs approval by the instructor before any lab work can commence.	+	Developing your ideas and figuring out what is involved is a complex task that involves all team members - and the instructor. You have to sit together and play around with your ideas. Brainstorm, make plans, assign work pieces to everyone, find information, discuss what you found, revise your concepts, look up protocols and describe your approach on your homepage. Familiarize yourself (everyone) with OpenWetWare, how to edit pages, and how to upload pictures (very important for a good grade). Just use the "help" function on the left or on top of each page. Do not forget to apply for an account (which is free) as soon as possible, but at the latest before the second class session. You will need your account by then. The sooner you start writing (even rough drafts, lists of ideas) the easier it will be for your team to keep track of your progress and find relevant information. And the more you write the better your grade will be. WRITE IN EVERY SESSION! The completeness and clarity of your online journal will be assessed and graded (15%). Your experimental design, the approach you take, and the results you expect must be explained in form of a research proposal on your project website. This proposal needs approval by the instructor before any lab work can commence.
	<BR>		<BR>
	<BR>		<BR>
-	You almost certainly will identify a couple of gaps in your knowledge that have to be addressed in order to complete or even start your project. A good selection of "need to know" questions is very helpful in developing your experimental approach. Ask yourself: "What information (about the part and the experimental procedures) do I need in order to produce and verify ~~my part/device/system~~?" Prepare a list of issues you need to address!	+	You almost certainly will identify a couple of gaps in your knowledge that have to be addressed in order to complete or even start your project. Questions you cannot solve on your own should be listed at the end of your experimental strategy under the "Need to Know" section. This section can be quite large. A good selection of "need to know" questions is very helpful in developing your experimental approach. Ask yourself: "What information (about the part and the experimental procedures) do we need in order to produce and verify it?" Prepare a list of issues you need to address! Keep in mind that the WIKI pages can be easily edited. So start writing as soon as possible. You can revise and modify it later.
	<BR>		<BR>
	<BR>		<BR>
-	Please be aware that the first 2-3 weeks ~~will~~ be spend developing your experimental plan rather than working in the lab. If you wish, you can consider this as the combined lecture part of the course~~. After you started your bench work, we will have no more lectures or formal instruction. From than on, we devote every minute to practical work~~.	+	Please be aware that the first 2-3 weeks may indeed be spend developing your experimental plan rather than working in the lab. If you wish, you can consider this as the combined lecture part of the course.

	==Attendance Policy==		==Attendance Policy==

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

2009-07-31T21:42:21Z

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

←Older revision		Revision as of 21:42, 31 July 2009
Line 31:		Line 31:
	==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. Please 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. Then, select a project your team wants to work on. 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. 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. Then, make a list of what needs to be done. We will discuss all proposals in the third week.
-		+
-	~~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.	+

	===2) Describe your project on the team homepage===		===2) Describe your project on the team homepage===

Axel: /* Your Assignment */

2009-07-31T21:41:00Z

Your Assignment

←Older revision		Revision as of 21:41, 31 July 2009
Line 25:		Line 25:

	==Your Assignment==		==Your Assignment==
-	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. ~~The~~ planning is very important ~~and~~ it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class~~. Based on the quality of your presentation, the understanding you show, and completeness or your experimental design, you now may (or not) start your bench work~~.	+	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. Therefore, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. Since good planning is very important, it will contribute 20% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class.

-	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts from ~~any of~~ the ~~previous parts distribution (~~2007, 2008~~, or 2009~~) and~~/or~~ use some DNA that you can easily amplify from readily available tissue by PCR ~~(plant tissues are generally most easy to come by)~~. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is ~~made~~ biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think ~~about an easy functional assay~~ and discuss it with your ~~teacher~~. After doing all the work, each team will ~~write~~ a ~~10+ page summary report (a summary~~ presentation ~~is optional)~~. This ~~report should be done in form of a journal article. It~~ is worth 20% of ~~your~~ grade ~~and has to be submitted during finals week. The report must be uploaded (as MS-Word or PDF) to your project homepage for consideration. No late submissions can be accepted~~.	+	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts (from the 2007 or 2008 repository) and use some DNA that you can easily amplify from readily available plant tissue by PCR. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think it over and discuss it with your instructor. After doing all the work, each team will present its results in a graded presentation at the end of the semester. This presentation is worth 15% of the grade.

	==How to Start==		==How to Start==

Axel: /* 2) Describe your project on the team homepage */

2009-07-31T21:33:42Z

2) Describe your project on the team homepage

←Older revision		Revision as of 21:33, 31 July 2009
Line 42:		Line 42:
	*proof of function		*proof of function

-	Developing your ideas and figuring out what is involved is a complex task that involves all team members - and the instructor. You have to sit together and play around with your ideas. Brainstorm, make plans, assign work pieces to everyone, find information, discuss what you found, revise your concepts, look up protocols and describe your approach on your homepage. Familiarize yourself (everyone) with OpenWetWare, how to edit pages, and how to upload pictures ~~(very important for a good grade)~~. Just use the "help" function on the left or on top of each page. Do not forget to apply for an account (which is free) as soon as possible~~, but at the latest before~~ the ~~second~~ class session. You ~~will~~ need ~~your~~ account ~~by then~~. The sooner you start writing (even rough drafts, lists of ideas) the easier it will be for your team to keep track of your progress and find relevant information. And the more you write the better your grade will be. WRITE IN EVERY SESSION! The completeness and clarity of your online journal will be assessed and graded (15%). Your experimental design, the approach you take, and the results you expect must be explained in form of a research proposal on your project website. This proposal needs approval by the instructor before any lab work can commence.	+	Developing your ideas and figuring out what is involved is a complex task that involves all team members - and the instructor. You have to sit together and play around with your ideas. Brainstorm, make plans, assign work pieces to everyone, find information, discuss what you found, revise your concepts, look up protocols and describe your approach on your homepage. Familiarize yourself (everyone) with OpenWetWare, how to edit pages, how to link to other information, and how to upload pictures. Just use the "help" function on the left or on top of each page. Do not forget to apply for an account (which is free) as soon as possible. Do it after the first class session. You need the working account very soon. So please don't delay applying. Your experimental design, the approach you take, and the results you expect must be explained in form of a research proposal and uploaded to your project website. This proposal needs approval by the instructor before any lab work can commence.
	<BR>		<BR>
	<BR>		<BR>
-	You almost certainly will identify a couple of gaps in your knowledge that have to be addressed in order to complete or even start your project~~. Questions you cannot solve on your own should be listed at the end of your experimental strategy under the "Need to Know" section. This section can be quite large~~. A good selection of "need to know" questions is very helpful in developing your experimental approach. Ask yourself: "What information (about the part and the experimental procedures) do we need in order to produce and verify it?" Prepare a list of issues you need to address! ~~Keep in mind that the WIKI pages can be easily edited. So start writing as soon as possible. You can revise and modify it later.~~	+	You almost certainly will identify a couple of gaps in your knowledge that have to be addressed in order to complete or even start your project. A good selection of "need to know" questions is very helpful in developing your experimental approach. Ask yourself: "What information (about the part and the experimental procedures) do I need in order to produce and verify my part/device/system?" Prepare a list of issues you need to address!
	<BR>		<BR>
	<BR>		<BR>
-	Please be aware that the first 2-3 weeks ~~may indeed~~ be spend developing your experimental plan rather than working in the lab. If you wish, you can consider this as the combined lecture part of the course.	+	Please be aware that the first 2-3 weeks will be spend developing your experimental plan rather than working in the lab. If you wish, you can consider this as the combined lecture part of the course. After you started your bench work, we will have no more lectures or formal instruction. From than on, we devote every minute to practical work.

	==Attendance Policy==		==Attendance Policy==

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

2009-07-31T21:28:05Z

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

←Older revision		Revision as of 21:28, 31 July 2009
Line 33:		Line 33:
	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. 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 ~~this step~~ as much as you need. But you have to come with ideas for discussion. I will not give you suggestions on what to do, except for the above.	+	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.

	===2) Describe your project on the team homepage===		===2) Describe your project on the team homepage===

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

2009-07-31T21:26:36Z

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

←Older revision		Revision as of 21:26, 31 July 2009
Line 31:		Line 31:
	==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. ~~Please~~ 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. ~~Then~~, ~~select~~ a project your ~~team wants~~ to work on. 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. 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. Then, make a list of what needs to be done. We will discuss all proposals in the third week.	+	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.
		+
		+	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 this step as much as you need. But you have to come with ideas for discussion. I will not give you suggestions on what to do, except for the above.

	===2) Describe your project on the team homepage===		===2) Describe your project on the team homepage===

Axel: /* Your Assignment */

2009-07-31T21:17:22Z

Your Assignment

←Older revision		Revision as of 21:17, 31 July 2009
Line 27:		Line 27:
	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class. Based on the quality of your presentation, the understanding you show, and completeness or your experimental design, you now may (or not) start your bench work.		Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class. Based on the quality of your presentation, the understanding you show, and completeness or your experimental design, you now may (or not) start your bench work.

-	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts from any of the previous parts distribution (2007, 2008, or 2009) and/or use some DNA that you can easily amplify from readily available tissue by PCR (plant tissues are generally most easy to come by). In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is made biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think about an easy functional assay and discuss it with your teacher. After doing all the work, each team will write a 10+ page summary report (a summary presentation is optional). This report should be done in form of a journal article. It is worth 20% of your grade and has to be submitted during finals week. The report must ~~also~~ be uploaded (as MS-Word or PDF) to your project homepage ~~(during finals week)~~. No late submissions can be accepted.	+	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts from any of the previous parts distribution (2007, 2008, or 2009) and/or use some DNA that you can easily amplify from readily available tissue by PCR (plant tissues are generally most easy to come by). In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is made biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think about an easy functional assay and discuss it with your teacher. After doing all the work, each team will write a 10+ page summary report (a summary presentation is optional). This report should be done in form of a journal article. It is worth 20% of your grade and has to be submitted during finals week. The report must be uploaded (as MS-Word or PDF) to your project homepage for consideration. No late submissions can be accepted.

	==How to Start==		==How to Start==

Axel: /* Your Assignment */

2009-07-31T21:16:28Z

Your Assignment

←Older revision		Revision as of 21:16, 31 July 2009
Line 27:		Line 27:
	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class. Based on the quality of your presentation, the understanding you show, and completeness or your experimental design, you now may (or not) start your bench work.		Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class. Based on the quality of your presentation, the understanding you show, and completeness or your experimental design, you now may (or not) start your bench work.

-	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts (from the 2007 or 2008 ~~repository~~) and use some DNA that you can easily amplify from readily available ~~plant~~ tissue by PCR. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think ~~it over~~ and discuss it with your ~~instructor~~. After doing all the work, each team will ~~present its results in~~ a ~~graded~~ presentation ~~at the end of the semester~~. This ~~presentation~~ is worth 15% of ~~the~~ grade.	+	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts from any of the previous parts distribution (2007, 2008, or 2009) and/or use some DNA that you can easily amplify from readily available tissue by PCR (plant tissues are generally most easy to come by). In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is made biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think about an easy functional assay and discuss it with your teacher. After doing all the work, each team will write a 10+ page summary report (a summary presentation is optional). This report should be done in form of a journal article. It is worth 20% of your grade and has to be submitted during finals week. The report must also be uploaded (as MS-Word or PDF) to your project homepage (during finals week). No late submissions can be accepted.

	==How to Start==		==How to Start==

Axel: /* Your Assignment */

2009-07-31T21:10:08Z

Your Assignment

←Older revision		Revision as of 21:10, 31 July 2009
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	==Your Assignment==		==Your Assignment==
-	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class.	+	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class. Based on the quality of your presentation, the understanding you show, and completeness or your experimental design, you now may (or not) start your bench work.

	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts (from the 2007 or 2008 repository) and use some DNA that you can easily amplify from readily available plant tissue by PCR. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think it over and discuss it with your instructor. After doing all the work, each team will present its results in a graded presentation at the end of the semester. This presentation is worth 15% of the grade.		It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts (from the 2007 or 2008 repository) and use some DNA that you can easily amplify from readily available plant tissue by PCR. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think it over and discuss it with your instructor. After doing all the work, each team will present its results in a graded presentation at the end of the semester. This presentation is worth 15% of the grade.

Axel: /* Your Assignment */

2009-07-31T21:08:34Z

Your Assignment

←Older revision		Revision as of 21:08, 31 July 2009
Line 25:		Line 25:

	==Your Assignment==		==Your Assignment==
-	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. ~~Therefore~~, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. ~~Since good~~ planning is very important, it will contribute 20% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class.	+	Like in the "[http://2008.igem.org/Main_Page International Genetically Engineered Machine]" (iGEM) competition, you will work in a small team to develop a new biological part, module, or device. Our teams are small, but I expect each team to develop something new - something that does not yet exist in the repository of biological standard parts. This is a very challenging task for the few sessions we have and not necessarily something all teams will be able to accomplish. But please do not worry about the outcomes. Since they are pretty unpredictable and depend on a large extend on the project you select to work on, the results will not affect your grade. However, in order to most likely succeed, very good planning is required. The better your team plans the entire project from the beginning, the better your chances are being able to complete your project. The planning is very important and it will contribute 10% to your grade. Your team has to carefully describe your project on your [http://openwetware.org/wiki/840:153g:Projects project homepage] and give a presentation during the third week of class.

	It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts (from the 2007 or 2008 repository) and use some DNA that you can easily amplify from readily available plant tissue by PCR. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think it over and discuss it with your instructor. After doing all the work, each team will present its results in a graded presentation at the end of the semester. This presentation is worth 15% of the grade.		It is up to each team to make a decision which new part to make. However, teams should carefully study the parts list to find something that's not already there. New parts can be as simple as a new protein coding device or regulatory region, a combination of existing parts, or something else you would like to do. However, we cannot synthesize DNA because that is too costly. Therefore, you have to work with existing parts (from the 2007 or 2008 repository) and use some DNA that you can easily amplify from readily available plant tissue by PCR. In addition to the particular part, module, or device your team wants to produce, each team needs to make sure that the new part is biobricks compatible. This means your part must eventually be modified by site-directed mutagenesis to substitute for conflicting restriction sites (e.g. those used in the [http://partsregistry.org/Assembly:Standard_assembly biobricks standard assembly]). Finally, you (as a team) have to provide evidence that your part, module, or device is functioning in the way you predicted. Figuring out how to do this can be quite tricky. Therefore, think it over and discuss it with your instructor. After doing all the work, each team will present its results in a graded presentation at the end of the semester. This presentation is worth 15% of the grade.