Team:Groningen/Notebook/20 June 2009

From 2009.igem.org

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{{Team:Groningen/Notebook/Day|<b>Day 1: European workshop in London</b><br> To be written by [http://2009.igem.org/User:Wilfred Wilfred]}}
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{{Team:Groningen/Notebook/Day|<b>Day 1: [http://2009.igem.org/Workshops/Europe European workshop in London]</b><br>  
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<center><b><i>Can Simple Biological Systems be Built from Standard, Interchangeable Parts and Operated in Living Cells?</i></b><BR><i>Or, is Biology so Complex that Each Case is Unique?</i></center>
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[http://2009.igem.org/User:Jaspervdg Jasper] and [http://2009.igem.org/User:Wilfred Wilfred] went to London to be at the "Teach the teachers workshop". After hearing the same intro song three times, it became clear that iGEM needs more musical tunes. Also they really seem to like the idea of team mascottes. And bright shirts! First things first, a 1000 parts of the 3500 available parts were sent to every team and sequenced. The sequences for all of them are available and should be checked before use.
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Next the composition of the different websites were explained, with the partsregistry having a Wiki and a non-wiki part. And this non-wiki giving information to the wiki part of the registry and possibly to the 2009.igem.org wiki's. And it was made clear that Parts should be well documented and more than just [http://partsregistry.org/wiki/index.php/Part:BBa_I769902 test]. Because parts, in contrary to some believes are not only the sequence of the parts but also experiences and everything. So please edit bad parts was the message, the partsregistry does not yet want to [http://partsregistry.org/Part:BBa_I746901 delete parts]. A nice example to add to your parts are measurements of promotor strength as with [http://www.jbioleng.org/content/3/1/4 Jason Kelly's promotor strength kit].
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Also the possibilities of iGEM was discussed, with commercial applications being in the near future and publishers thinking about publishing iGEM Specials.
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So much for an introduction, of to Developing & Refining an iGEM Idea. How do you get idea's? Well ofcourse they mentioned:
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*Talk to people
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*Think about topics and relevant subjects ([http://2008.igem.org/Team:Rice_University/Project Resveratrol in Biobeer])
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*Look at [http://2009.igem.org/Previous_iGEM_Competitions previous wiki's] (especially medals might give an insight to interesting subjects)
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*Look at interesting applications (e.g. [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood])
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*Think about using new organisms (like [http://2008.igem.org/Team:Harvard Harvard] and their <i>Shewanella oneidensis</i>)
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Also it would be nice to look at the general purpose tools (e.g. [http://partsregistry.org/Part:BBa_B0015 terminator],[http://partsregistry.org/Part:BBa_F2620 inducible promotor], [http://partsregistry.org/Part:BBa_B0034 Ribosomal binding sites] or [http://partsregistry.org/Plasmid_backbones plasmid backbones].
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Most importantly, <u>let the students choose...</u><i>but help them make a smart choice</i>. Supervisors can do this by pointing at the following.
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*Local skills, if no one around is experienced.. who to call for help?
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*Assembly stages, how many parts and how long does it take?
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*Independent subgoals, so to make sure that they can finish something
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*Unnecessary to make brand new idea
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**Characterizing is widely appreciated
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**Combining devices will provide enough fun
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<b>Making parts</b><BR>
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First needed for making parts is ofcourse the sequence, which was in the example taken from [http://ecocyc.org/ Ecocyc]. But could also for example been taken from [http://www.ddbj.nig.ac.jp/index-e.html DDBJ], [http://www.ncbi.nlm.nih.gov/Genbank/ Genbank], or [http://www.ebi.ac.uk/embl/ EMBL]. Next the sequence can be [http://partsregistry.org/Add_a_Part_to_the_Registry added to the registry] and giving it a short description (including the parttype) and a long description (wat is the part? What is interesting about it? What's its function?). Mentioning the source where you got the idea, wikicodes are possible to refer. And adding design considerations, use in project, purifying it of restriction sites. And adding features to specify. All parts added are automatically put in your [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Groningen sandbox], which was referred to as 'child's play' and so it is possible to start adding parts soon during the process and should be done. To appear in search tables the part needs to be tagged in categories.
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*More
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**Control page
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***Make new category
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Also add parameters, which were not really clearly defined yet.
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Parts should be supplied in plasmid backbones (about 5 - 15 ng), for plasmid backbones with [http://partsregistry.org/Part:BBa_P1010 P1010] inside [http://partsregistry.org/Part:BBa_V1005 a special strain]. Alternative locations of plasmid backbones are supplied in the distribution kit and can be PCR'ed to be used as backbones.
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Eventually, we had too little time and we went for dinner with the entire group. Very nice, socializing with nice [[Team:SDU-Denmark| Danish]] people and learning how they do it in China from team [[Team:SJTU-BioX-Shanghai| Shanghai]]. Visiting a nice pub, talking with [http://2009.igem.org/Team:TUDelft Delft] before heading back to the [http://www.st-christophers.co.uk/london-hostels/london/shepherds-bush hostel] getting some energy for the next day!

Revision as of 13:57, 26 June 2009

{{Team:Groningen/Notebook/Day|Day 1: European workshop in London

Can Simple Biological Systems be Built from Standard, Interchangeable Parts and Operated in Living Cells?
Or, is Biology so Complex that Each Case is Unique?

Jasper and Wilfred went to London to be at the "Teach the teachers workshop". After hearing the same intro song three times, it became clear that iGEM needs more musical tunes. Also they really seem to like the idea of team mascottes. And bright shirts! First things first, a 1000 parts of the 3500 available parts were sent to every team and sequenced. The sequences for all of them are available and should be checked before use. Next the composition of the different websites were explained, with the partsregistry having a Wiki and a non-wiki part. And this non-wiki giving information to the wiki part of the registry and possibly to the 2009.igem.org wiki's. And it was made clear that Parts should be well documented and more than just test. Because parts, in contrary to some believes are not only the sequence of the parts but also experiences and everything. So please edit bad parts was the message, the partsregistry does not yet want to delete parts. A nice example to add to your parts are measurements of promotor strength as with Jason Kelly's promotor strength kit. Also the possibilities of iGEM was discussed, with commercial applications being in the near future and publishers thinking about publishing iGEM Specials.

So much for an introduction, of to Developing & Refining an iGEM Idea. How do you get idea's? Well ofcourse they mentioned:

  • Talk to people
  • Think about topics and relevant subjects (Resveratrol in Biobeer)
  • Look at previous wiki's (especially medals might give an insight to interesting subjects)
  • Look at interesting applications (e.g. Bactoblood)
  • Think about using new organisms (like Harvard and their Shewanella oneidensis)

Also it would be nice to look at the general purpose tools (e.g. terminator,inducible promotor, Ribosomal binding sites or plasmid backbones.

Most importantly, let the students choose...but help them make a smart choice. Supervisors can do this by pointing at the following.

  • Local skills, if no one around is experienced.. who to call for help?
  • Assembly stages, how many parts and how long does it take?
  • Independent subgoals, so to make sure that they can finish something
  • Unnecessary to make brand new idea
    • Characterizing is widely appreciated
    • Combining devices will provide enough fun

Making parts
First needed for making parts is ofcourse the sequence, which was in the example taken from Ecocyc. But could also for example been taken from DDBJ, Genbank, or EMBL. Next the sequence can be added to the registry and giving it a short description (including the parttype) and a long description (wat is the part? What is interesting about it? What's its function?). Mentioning the source where you got the idea, wikicodes are possible to refer. And adding design considerations, use in project, purifying it of restriction sites. And adding features to specify. All parts added are automatically put in your sandbox, which was referred to as 'child's play' and so it is possible to start adding parts soon during the process and should be done. To appear in search tables the part needs to be tagged in categories.

  • More
    • Control page
      • Make new category

Also add parameters, which were not really clearly defined yet. Parts should be supplied in plasmid backbones (about 5 - 15 ng), for plasmid backbones with P1010 inside a special strain. Alternative locations of plasmid backbones are supplied in the distribution kit and can be PCR'ed to be used as backbones.

Eventually, we had too little time and we went for dinner with the entire group. Very nice, socializing with nice Danish people and learning how they do it in China from team Shanghai. Visiting a nice pub, talking with Delft before heading back to the hostel getting some energy for the next day!