From 2008.igem.org
Newcastle University
GOLD MEDAL WINNER 2008
Home >> Dry Lab >> Dry Lab Journal
| May
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| [http://2008.igem.org/Newcastle_University_Drylab/1_May_2008 1]
| [http://2008.igem.org/Newcastle_University_Drylab/2_May_2008 2]
| [http://2008.igem.org/Newcastle_University_Drylab/3_May_2008 3]
| [http://2008.igem.org/Newcastle_University_Drylab/4_May_2008 4]
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| [http://2008.igem.org/Newcastle_University_Drylab/5_May_2008 5]
| [http://2008.igem.org/Newcastle_University_Drylab/6_May_2008 6]
| [http://2008.igem.org/Newcastle_University_Drylab/7_May_2008 7]
| [http://2008.igem.org/Newcastle_University_Drylab/8_May_2008 8]
| [http://2008.igem.org/Newcastle_University_Drylab/9_May_2008 9]
| [http://2008.igem.org/Newcastle_University_Drylab/10_May_2008 10]
| [http://2008.igem.org/Newcastle_University_Drylab/11_May_2008 11]
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| [http://2008.igem.org/Newcastle_University_Drylab/12_May_2008 12]
| [http://2008.igem.org/Newcastle_University_Drylab/13_May_2008 13]
| [http://2008.igem.org/Newcastle_University_Drylab/14_May_2008 14]
| [http://2008.igem.org/Newcastle_University_Drylab/15_May_2008 15]
| [http://2008.igem.org/Newcastle_University_Drylab/16_May_2008 16]
| [http://2008.igem.org/Newcastle_University_Drylab/17_May_2008 17]
| [http://2008.igem.org/Newcastle_University_Drylab/18_May_2008 18]
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| [http://2008.igem.org/Newcastle_University_Drylab/19_May_2008 19]
| [http://2008.igem.org/Newcastle_University_Drylab/20_May_2008 20]
| [http://2008.igem.org/Newcastle_University_Drylab/21_May_2008 21]
| [http://2008.igem.org/Newcastle_University_Drylab/22_May_2008 22]
| [http://2008.igem.org/Newcastle_University_Drylab/23_May_2008 23]
| [http://2008.igem.org/Newcastle_University_Drylab/24_May_2008 24]
| [http://2008.igem.org/Newcastle_University_Drylab/25_May_2008 25]
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| [http://2008.igem.org/Newcastle_University_Drylab/26_May_2008 26]
| [http://2008.igem.org/Newcastle_University_Drylab/27_May_2008 27]
| [http://2008.igem.org/Newcastle_University_Drylab/28_May_2008 28]
| [http://2008.igem.org/Newcastle_University_Drylab/29_May_2008 29]
| [http://2008.igem.org/Newcastle_University_Drylab/30_May_2008 30]
| [http://2008.igem.org/Newcastle_University_Drylab/31_May_2008 31]
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| June
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| [http://2008.igem.org/Newcastle_University_Drylab/1_June_2008 1]
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| [http://2008.igem.org/Newcastle_University_Drylab/2_June_2008 2]
| [http://2008.igem.org/Newcastle_University_Drylab/3_June_2008 3]
| [http://2008.igem.org/Newcastle_University_Drylab/4_June_2008 4]
| [http://2008.igem.org/Newcastle_University_Drylab/5_June_2008 5]
| [http://2008.igem.org/Newcastle_University_Drylab/6_June_2008 6]
| [http://2008.igem.org/Newcastle_University_Drylab/7_June_2008 7]
| [http://2008.igem.org/Newcastle_University_Drylab/8_June_2008 8]
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| [http://2008.igem.org/Newcastle_University_Drylab/9_June_2008 9]
| [http://2008.igem.org/Newcastle_University_Drylab/10_June_2008 10]
| [http://2008.igem.org/Newcastle_University_Drylab/11_June_2008 11]
| [http://2008.igem.org/Newcastle_University_Drylab/12_June_2008 12]
| [http://2008.igem.org/Newcastle_University_Drylab/13_June_2008 13]
| [http://2008.igem.org/Newcastle_University_Drylab/14_June_2008 14]
| [http://2008.igem.org/Newcastle_University_Drylab/15_June_2008 15]
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| [http://2008.igem.org/Newcastle_University_Drylab/16_June_2008 16]
| [http://2008.igem.org/Newcastle_University_Drylab/17_June_2008 17]
| [http://2008.igem.org/Newcastle_University_Drylab/18_June_2008 18]
| [http://2008.igem.org/Newcastle_University_Drylab/19_June_2008 19]
| [http://2008.igem.org/Newcastle_University_Drylab/20_June_2008 20]
| [http://2008.igem.org/Newcastle_University_Drylab/21_June_2008 21]
| [http://2008.igem.org/Newcastle_University_Drylab/22_June_2008 22]
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| [http://2008.igem.org/Newcastle_University_Drylab/23_June_2008 23]
| [http://2008.igem.org/Newcastle_University_Drylab/24_June_2008 24]
| [http://2008.igem.org/Newcastle_University_Drylab/25_June_2008 25]
| [http://2008.igem.org/Newcastle_University_Drylab/26_June_2008 26]
| [http://2008.igem.org/Newcastle_University_Drylab/27_June_2008 27]
| [http://2008.igem.org/Newcastle_University_Drylab/28_June_2008 28]
| [http://2008.igem.org/Newcastle_University_Drylab/29_June_2008 29]
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| [http://2008.igem.org/Newcastle_University_Drylab/30_June_2008 30]
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| July
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| [http://2008.igem.org/Newcastle_University_Drylab/1_July_2008 1]
| [http://2008.igem.org/Newcastle_University_Drylab/2_July_2008 2]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/3_July_2008&action=edit 3]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/4_July_2008&action=edit 4]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/5_July_2008&action=edit 5]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/6_July_2008&action=edit 6]
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| [http://2008.igem.org/Newcastle_University_Drylab/7_July_2008 7]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/8_July_2008&action=edit 8]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/9_July_2008&action=edit 9]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/10_July_2008&action=edit 10]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/11_July_2008&action=edit 11]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/12_July_2008&action=edit 12]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/13_July_2008&action=edit 13]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/14_July_2008&action=edit 14]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/15_July_2008&action=edit 15]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/16_July_2008&action=edit 16]
| [http://2008.igem.org/Newcastle_University_Drylab/17_July_2008 17]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/18_July_2008&action=edit 18]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/19_July_2008&action=edit 19]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/20_July_2008&action=edit 20]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/21_July_2008&action=edit 21]
| [http://2008.igem.org/Newcastle_University_Drylab/22_July_2008 22]
| [http://2008.igem.org/Newcastle_University_Drylab/23_July_2008 23]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/24_July_2008&action=edit 24]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/25_July_2008&action=edit 25]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/26_July_2008&action=edit 26]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/27_July_2008&action=edit 27]
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| [http://2008.igem.org/Newcastle_University_Drylab/28_July_2008 28]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/29_July_2008&action=edit 29]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/30_July_2008&action=edit 30]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/31_July_2008&action=edit 31]
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| August
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/1_August_2008&action=edit 1]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/2_August_2008&action=edit 2]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/3_August_2008&action=edit 3]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/4_August_2008&action=edit 4]
| [http://2008.igem.org/Newcastle_University_Drylab/5_August_2008 5]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/6_August_2008&action=edit 6]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/7_August_2008&action=edit 7]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/8_August_2008&action=edit 8]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/9_August_2008&action=edit 9]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/10_August_2008&action=edit 10]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/11_August_2008&action=edit 11]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/12_August_2008&action=edit 12]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/13_August_2008&action=edit 13]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/14_August_2008&action=edit 14]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/15_August_2008&action=edit 15]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/16_August_2008&action=edit 16]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/17_August_2008&action=edit 17]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/18_August_2008&action=edit 18]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/19_August_2008&action=edit 19]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/20_August_2008&action=edit 20]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/21_August_2008&action=edit 21]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/22_August_2008&action=edit 22]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/23_August_2008&action=edit 23]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/24_August_2008&action=edit 24]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/25_August_2008&action=edit 25]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/26_August_2008&action=edit 26]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/27_August_2008&action=edit 27]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/28_August_2008&action=edit 28]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/29_August_2008&action=edit 29]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/30_August_2008&action=edit 30]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/31_August_2008&action=edit 31]
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21 May 2008
Mark
Plan for today is basically to get my java program to work. Been working on it all morning and have been trying to access by array of stored double numbers witrh my gaussian method in a forLoop. This has proven a sticking point and is very anoying as for some reason the array cannot be accessed even though both methods are under the same class. Have e-mailed matt about this and we are communicating freely now via MSN messenger.
Have also (under Matt's instructions) e-mailed Dan at support@bsu.ncl.ac.uk to set up and log into the svn repository, which is for code developing and sharing. Have also downloaded the Tortoise development tool. It is worth mentioning the usefulness of this tool in that I now have access to a code repository. As i alter or change my code I can then commit any changes once I have updated the files and they can then be accessed in the repository. The Tortoise development tool simply enables you to carry out this task.
It is just after lunchtime at this point, and I have fixed a big problem with file access on the server, and I am now just waiting for Matt to have a look at my code. In the meantime I am going to look at sourceforge at past API's, to get an idea of how to structure my evolutionary algorithm.
Link to sourceforge
Started looking through sourceforge for relevant programs/
Megan
Try to define the broad parts that I want to make models for. Activator, Repressor, Regulator, Transcription factor, coding region (Output) try to define vairable and units for these however this is quite confusing, CellML appears to model baed on MathsML and numbers however a lot of the information that I would like to store is not numerical?!?
After looking at COR and Physiome CellML environment it looks as though the general structure of cellML is relatively straightforward. However only for names of models and their variables, I am still extremely confused as to how these are going to work as mathematical models. For some variables it may be possible as there are will be certain conditions the parts can work under, but this is probably more constraints. For the actual parts information will be stored on their sequence and length, source orgainsim, encoding gene etc. but I do not see how this can be converted to cellML at all....
This is a problem. When attempting to create a basic model in COR it seems to want unit information, and for this to some how link to an equation, e.g. milisecond = second.10-3 this type of unit is fine for modelling reactions in cells however not really when there are no units :-\
Also COR is not very self explanatory, it is clearly unhappy when a big warning sign appears but so far I have not found any explanation of why the sign appears.
I thought that physiome was quite good initially. The tutorial is useful. I started to attempt to model in physiome, but now it seems to have a problem, it freezes and doesn't respond quite a lot which is very annoying and impractical when trying to use it.
Morgan
I have working tooltips on my canvas! Right now it just reports the basics of what's in the Element, without any human-friendliness, but once I have actual data in there it'll be prettier. I just thought that until I have actual data, I don't need to spend time making it purty.
I also got deletion to also work with edges. It only worked with elements before. It's also more flexible, so you can click within about 2 pixels of the line and still have it respond. Woot. All I did was take the Point p, and drew a line from (p.x-2, p.y-2) and (p.x+2, p.y+2) and checked to see if that little line intersected with any of the connector lines. Seems to work okay.
I cleaned up the Constants class a little, because I had a few ints that were running around doing the same job as some Strings. Simplified it to just Strings.
Pulled out a separate Legend class, in the process of de-hacking the legend (WB todo Build #6).
The legend has been de-hacked! I pulled code from Bluejay to do it. Oops. But mostly I re-wrote it. The background isn't white and there's no label to identify it as the legend, but the whiteness is currently subject to a strange bug that I don't feel like finding.
Nina
The matrix.
To populate the compatibility matrix I used three methods.
Literature searching (google the parts and look through journals for conformation that they can interact/control gene expression of the connecting part)
Look at homologous structures of parts that have been confirmed to interact. If the structure is the same, they may also be compatible.
Use blast of the DNA sequence two parts together to see the sequence exists at all. This would confirm compatibility.
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