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3 June 2008

Mark

Continued coding up EA.

Wrote up slides for presentation in the evening

Megan

Tried to write out the pseudocode for the Java exercise so that I could work out where to start. Didn't really help much. Mark tried to explain how he thought I should tackle it to start with. Still confusing, am annotating the practice exercises that we carried out on friday in detail so that I can completely understand it again and hopefully use it to model my code for this exercise. Completed the first exercise. Went over some of the user stories.

Created slides for mini_talk._1.ppt

Morgan

Started CellML Tutorial. Installed COR on my laptop. Working my way through it now...

Went downstairs to help Mark and Megan with their programming.

Back to CellML Tutorial. This COR thing is very like Pascal, with its def/enddef thing.

Objects like models or components seem to be defined using the as keyword. As in:

def model TestModel as

   def comp TestComp as
   enddef;

enddef;

Units are defined using the from keyword. For the parameter, you can either use //expo//, for exponent, or //pref//, for prefixes like micro- or nano-.

def unit uM from

   unit mole {pref: micro};
   unit liter {expo: -1};

enddef;

The built-in units are: ampere farad katal lux pascal tesla becquerel gram kelvin meter radian volt candela gray kilogram metre second watt celsius henry liter mole siemens weber coulomb hertz litre newton sievert dimensionless joule lumen ohm steradian

The built-in prefixes are: yotta 1024 deci 10-1 zetta 1021 centi 10-2 exa 1018 milli 10-3 peta 1015 micro 10-6 tera 1012 nano 10-9 giga 109 pico 10-12 mega 106 femto 10-15 kilo 103 atto 10-18 hecto 102 zepto 10-21 deka 101 yocto 10-24

Well, just that little tutorial in COR makes the XML spectacularly more easy to read. Awesome. Except for the MathML. Hm... let's see....

<apply>

 <eq/> 
 <ci>J</ci>
 <apply>
   <minus/> 
   <apply>
     <times/>
     <ci>kf</ci> 
     <ci>A</ci>
     <ci>B</ci>
   </apply>
   <apply>
     <times/> 
     <ci>kb</ci>
     <ci>C</ci> 
   </apply>
 </apply>

</apply>

So this says... = J - * kf A B * kb C . Which means... J = kf * A * B - kb * C. Eheh, I guess it's a good thing that I liked this stuff in school. I never saw the need till now. Imagine if I'd hated it and thus forgot it? I guess then I'd be in the same state as when I did all that linear algebra last summer.... Next part: <apply>

 <eq/>
 <apply>
   <diff/>
   <bvar>
     <ci>t</ci>
   </bvar>
   <ci>A</ci>
 </apply>
 <apply>
   <minus/>
   <ci>J</ci>
 </apply>

</apply>

This means... = diff bvar(t) A - J , or A(t)/d(t) = -J. Awzum.

Tutorial 2! This is all exciting.

Took a break to help the interface discussions. Then there was an impromptu iGEM meeting where we mostly talked about what Nina's Constraints Repository really means. Then Matt talked to mostly Megan and Nina more about the interfaces between the parts and explained it better than what I was managing.

Nina

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