Aim: a wiki where first class educational material for Synthetic Biology is collected.

It is important that we make this wiki “first class”. Since there is no free SynBio textbook online, this will be the site to go to, and if we write it well it can be the major place where people will learn SynBio.

In addition to this wiki we will need a platform where we can discuss our questions and ideas. We can use existing groups like one from Facebook, or we can build a social platform on the top of facebook, if the existing groups do not work. I strongly believe that, with this project, we see the future of learning. We will study the textbook/wiki at home, class or social will be for discussion and solving problems. At the moment I read the Steve Jobs bio, and it says that one of his last plans was to revolutionize education and the (old-fashion) textbook. His plans go in the direction I have sketched so it will be really interesting to see, what Apple will come up with. However, with our project, we will be on the forefront of this development, and, if we do well, provide a model for other people. We also have to keep in mind the development of webpage design, and the coming revolution of HTML5 and the programmable web. I think it will be easy to integrate WikiGenes in a learning App for SynBio. We will see this growing really big, so once again: We have to do really well. I am convinced we are facing a huge opportunity.

... again: We have to do really well. I am convinced we are facing a huge opportunity.

**** Ideas for content to discuss: ****

• Separation of assembly and function in the definition of a Biological Part
• Questions about ethics, which people ask about synthetic biology
• Where can I go to school to learn more about synthetic biology?
• Work and environmental safety in the practice of synthetic biology
• What is the role of companies in synthetic biology development

• ... synthetic biology
• What is the role of companies in synthetic biology development
• A synthetic biology education portal - consisting of publications, lecture videos, protocols (OpenWetWare links?), ebooks

*** ... consisting of publications, lecture videos, protocols (OpenWetWare links?), ebooks  ***

More general considerations:

• Do we need more coworkers to accomplish the task properly?
• Shall we advertise the wiki before the work is completed to attract more contributors?
• What would be our first major result that we would be willing to advertise as an educational wiki?
• How can we prevent someone else from publishing our (free) content as a book or e-book?
• Can we split the workload into several packages and define deadlines?
• Shall we divide the topics so that a specific content is allocated to one or a few contributors?

• ... the topics so that a specific content is allocated to one or a few contributors?
• Can we agree on the level of writing? Maybe a 1st-2nd year university students level for version 1 that could later be upgraded with advanced topics and a higher level of complexity for (eventual) version 2 (e.g. in 2013)?
• It would be best to set a deadline for an agreement on the contents (table of contents) of version 1 (my suggestion is February 15 2012).

**** ... discuss: ****

• Separation of assembly and function in the definition of a Biological Part

• Questions about ethics, which people ask about synthetic biology
• Where can I go to ...

• ... synthetic biology
• Where can I go to school to learn more about synthetic biology?

• Work and environmental safety in the practice of synthetic biology
• What is the role ...

*** ... general considerations: ***

• Do we need more coworkers to accomplish the task properly?

• Shall we advertise the wiki before the work is completed to attract more contributors?

• ... we advertise the wiki before the work is completed to attract more contributors?

• What would be our first major result that we would be willing to advertise as an ...

• ... we prevent someone else from publishing our (free) content as a book or e-book?

• Can we split the workload into several packages and define deadlines?
• Shall we divide ...

• ... the contents (table of contents) of version 1 (my suggestion is February 15 2012).

• ... can I go to school to learn more about synthetic biology?

• Work and environmental safety in the practice of synthetic biology
• What is the role ...

• ... first major result that we would be willing to advertise as an educational wiki?
• There was some talk of submitting the Mesh as a review article in a research journal (JBE). We should contact the journal editor for suggestions.
• How can we prevent someone else from publishing our (free) content as a book or ...

... throughout the internet, on facebook, google+, twitter and so on. We can do it again.

No need as I think we have a reasonable amount of diversity

• What would be our first major result that we would be willing to advertise as an ...

• ... first major result that we would be willing to advertise as an educational wiki?

• There was some talk of submitting the Mesh as a review article in a research journal ...

• ... in a research journal (JBE). We should contact the journal editor for suggestions.,

• How can we prevent someone else from publishing our (free) content as a book or ...

• ... we prevent someone else from publishing our (free) content as a book or e-book?

• ... the topics so that a specific content is allocated to one or a few contributors?

• Can we agree on the level of writing? Maybe a 1st-2nd year university students level ...

• ... contents (table of contents) of version 1 (my suggestion is February 15 2012).

... with another article/page, like we have done with 7.2 Software Tools for instance.

Table of content

We might wish to discuss the table of content:

1) What do we miss?

2) Do we wish to restructure or is it fine like this?

• 1. Introduction[Link]

• 2. History[Link]

• 3. Basic Concepts[Link]

• 3.1 Bioinformatics and systems biology for synthetic biology[Link]

• 3.1.1 The relationship between systems biology and synthetic biology[Link]

• 3.1.2 The Engineering design cycle and rational design[Link]

• 3.1.3 Bioparts[Link]

• 4. Methods and Fundamental Techniques in Synthetic Biology[Link]

• 4.1 Computational modeling[Link]

• 4.3 DNA sequencing[Link]

• 4.4 DNA Parts Assembly[Link]

• 4.6 DNA arrays[Link]

• 5.Biological networks and circuits[Link]

• 7. Discussion[Link]

• 8. Resources[Link]

• 8.1 DNA synthesis, sequencing[Link]

• 8.2 Software Tools[Link]

• 8.2.1 Useful learning resources and programs:[Link]

• 8.3 Educational materials: videos, reviews, journals, mashups, news, comics[Link]

• 8.3.1 Videos:[Link]

• 8.3.2 Reviews:[Link]

• 8.3.3 Journals:[Link]

• 8.3.4 Mashup:[Link]

• 8.3.5 News:[Link]

• 8.3.6 Comics:[Link]

• 8.3.7 iGEM Foundation and Competition :[Link]

• 8.3.8 Community:[Link]

• 8.5 Influential Articles

• ... Methods and Fundamental Techniques in Synthetic Biology[Link]

• 4.1 Computational modeling[Link]
• [Link].2 DNA synthesis
• 4.3 DNA sequencing[Link]

• 4.4 DNA Parts Assembly[Link]

• 4.6 DNA arrays[Link]

• 5.Biological networks and ...

... content:

1) What do we miss?

2) Do we wish to restructure or is it fine like this?

3) Do we wish to split the article: Introduction on the first page, all other chapters on separate pages as we have done for a few?

• 1. Introduction[Link]

• 2. History[Link]

• 3. Basic Concepts[Link]

• 3.1 Bioinformatics and systems biology ...

• 8.3.5 News:[Link]

• 8.3.6 Comics:[Link]

• 8.3.7 iGEM Foundation and Competition :[Link]

• 8.3.8 Community:[Link]
• 8.4 Graduate programs in Synthetic Biology. [Link]

• 8.5 Influential Articles

• There was some talk of submitting the Mesh as a review article in a reputed research journal (JBE). We researched on a topic and then didn't let the community know about it, it is tantamount to committing a selfish act. We should contact the journal editor for suggestions,

• ... publishing our (free) content as a book or e-book?

... me....Do we need to make a separate TOC or it will be automatically done from the wiki pageYes page Yes, and also I think that we should keep the introduction and history on the main page, ...

**** ... discuss: ****

• Separation of assembly and function in the definition of a Biological Part
• If you think that it is better, it is ok for meQuestions about ethics, which people ask about synthetic biology
• Where can I go to ...

• ... synthetic biology
• Where can I go to school to learn more about synthetic biology?
• There are a few coursesWork and environmental safety in the practice of synthetic biology
• What is the role ...

*** ... general considerations: ***

• Do we need more coworkers to accomplish the task properly?
• Yes, I think that if the person writes relevant things in a good manner, it should be fine.Shall we advertise the wiki before the work is completed to attract more contributors?
...

• ... we advertise the wiki before the work is completed to attract more contributors?
• We have spread our project throughout the internet, on facebook, google+, twitter and so on. We can do it again.No need as I think we have a reasonable amount of diversity
• What would be our first ...

... good suggestion could be actually submitting our final content to CK12 flex books [Link],[Link], We can also think an ipad style book, but it will involve some work on graphics ...

• ... (JBE). We researched on a topic and then didn't let the community know about it here[Link], here (YouTube Education)[Link], it is tantamount to committing a selfish act and also I think that we should keep the introduction and history on the main page, but the rest could be linked with another article/page, like we have done with 7.2 Software Tools for instance.. We should contact the journal editor for suggestions,

This is a good idea as well

... an open source license, so that if somebody uses our content it acknowledge us.

• We can prove that this is our work because there is the date that we edited it on the history (it is below the "Discussion page" in our main page[Link]Can we split the workload into several packages and define deadlines?
• Shall we divide ...

• ... the contents (table of contents) of version 1 (my suggestion is February 15 2012).

Yes fine with me....Do we need to make a separate TOC or it will be automatically done from the wiki page Yes,Table of content

We might wish to discuss the table of content:

1) What do we miss?

... page, all other chapters on separate pages as we have done for a few?

• 1. Introduction[Link][Link]
• 2. History[Link][Link]
• 3. Basic Concepts[Link][Link]
• 3.1 Bioinformatics and systems biology for synthetic biology[Link][Link]
• 3.1.1 The relationship between systems biology and synthetic biology[Link][Link]
• 3.1.2 The Engineering design cycle and rational design[Link][Link]
• 3.1.3 Bioparts[Link][Link]
• 4. Methods and Fundamental Techniques in Synthetic Biology[Link][Link]
• 4.1 Computational modeling[Link][Link].[Link]
• [Link].2 DNA synthesis
• 4.3 DNA sequencing[Link][Link]
• 4.4 DNA Parts Assembly[Link][Link]
• 4.6 DNA arrays[Link][Link]
• 5.Biological networks and circuits[Link][Link]
• 7. Discussion[Link][Link]
• 8. Resources[Link][Link]
• 8.1 DNA synthesis, sequencing[Link][Link]
• 8.2 Software Tools[Link][Link]
• 8.2.1 Useful learning resources and programs:[Link][Link]
• 8.3 Educational materials: videos, reviews, journals, mashups, news, comics[Link][Link]
• 8.3.1 Videos:[Link][Link]
• 8.3.2 Reviews:[Link][Link]
• 8.3.3 Journals:[Link][Link]
• 8.3.4 Mashup:[Link][Link]
• 8.3.5 News:[Link][Link]
• 8.3.6 Comics:[Link][Link]
• 8.3.7 iGEM Foundation and Competition :[Link][Link]
• 8.3.8 Community:[Link][Link]
• 8.4 Graduate programs in Synthetic Biology. [Link][Link]
• 8.5 Influential Articles

Aim: a wiki where first class educational material for Synthetic Biology is collected.It is important that we make this wiki “first class”. Since there is no free SynBio textbook online, this will be the site to go to, and if we write it well it can be the major place where people will learn SynBio.In addition to this wiki we will need a platform where we can discuss our questions and ideas. We can use existing groups like one from Facebook, or we can build a social platform on the top of facebook, if the existing groups do not work. I strongly believe that, with this project, we see the future of learning. We will study the textbook/wiki at home, class or social will be for discussion and solving problems. At the moment I read the Steve Jobs bio, and it says that one of his last plans was to revolutionize education and the (old-fashion) textbook. His plans go in the direction I have sketched so it will be really interesting to see, what Apple will come up with. However, with our project, we will be on the forefront of this development, and, if we do well, provide a model for other people. We also have to keep in mind the development of webpage design, and the coming revolution of HTML5 and the programmable web. I think it will be easy to integrate WikiGenes in a learning App for SynBio. We will see this growing really big, so once again: We have to do really well. I am convinced we are facing a huge opportunity.Ideas for content to discuss:Separation of assembly and function in the definition of a Biological Part.Questions about ethics, which people ask about synthetic biologyWhere can I go to school to learn more about synthetic biology? on a topic and then didn't let the community know about itWork and environmental safety in the practice of synthetic biologyWhat is the role of companies in synthetic biology developmentA synthetic biology education portal - consisting of publications, lecture videos, protocols (OpenWetWare links?), ebooksMore general considerations:Do we need more coworkers to accomplish the task properly?Shall we advertise the wiki before the work is completed to attract more contributors?No need as I think we have a reasonable amount of diversityWhat would be our first major result that we would be willing to advertise as an educational wiki?I think we need to think through clearly what is the purpose of this article. I believe that the purpose is to shorten time it take from scientific frontier to reach text books or introductory texts, A good suggestion could be actually submitting our final content to CK12 flex books[Link], We can also think an ipad style book, but it will involve some work on graphics i presume, some novel design figuresThere was some talk of submitting the Mesh as a review article in a reputed research journal (JBE). We researched We should contact the journal editor for suggestions.,This is a good idea as wellHow can we prevent someone else from publishing our (free) content as a book or e-book?The least we can do is explicitly label it an open source license, so that if somebody uses our content it acknowledge us.Can we split the workload into several packages and define deadlines?Shall we divide the topics so that a specific content is allocated to one or a few contributors?I can volunteer for bioinformatics and systems biology in synthetic biology contentCan we agree on the level of writing? Maybe a 1st-2nd year university students level for version 1 that could later be upgraded with advanced topics and a higher level of complexity for (eventual) version 2 (e.g. in 2013)?It would be best to set a deadline for an agreement on the contents (table of contents) of version 1 (my suggestion is February 15 2012)., it is tantamount to committing a selfish actTable of contentWe might wish to discuss the table of content:1) What do we miss?2) Do we wish to restructure or is it fine like this?3) Do we wish to split the article: Introduction on the first page, all other chapters on separate pages as we have done for a few?1. Introduction[Link]2. History[Link]3. Basic Concepts[Link]3.1 Bioinformatics and systems biology for synthetic biology[Link]3.1.1 The relationship between systems biology and synthetic biology[Link]3.1.2 The Engineering design cycle and rational design[Link]3.1.3 Bioparts[Link]4. Methods and Fundamental Techniques in Synthetic Biology[Link]4.1 Computational modeling[Link]2 DNA synthesis4.3 DNA sequencing[Link]4.4 DNA Parts Assembly[Link]4.6 DNA arrays[Link]5.Biological networks and circuits[Link]7. Discussion[Link]8. Resources[Link]8.1 DNA synthesis, sequencing[Link]8.2 Software Tools[Link]8.2.1 Useful learning resources and programs:[Link]8.3 Educational materials: videos, reviews, journals, mashups, news, comics[Link]8.3.1 Videos:[Link]8.3.2 Reviews:[Link]8.3.3 Journals:[Link]8.3.4 Mashup:[Link]8.3.5 News:[Link]8.3.6 Comics:[Link]8.3.7 iGEM Foundation and Competition :[Link]8.3.8 Community:[Link]8.4 Graduate programs in Synthetic Biology.[Link]8.5 Influential Articles