Team:Newcastle/Modeling/Population/Pseudo

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== Population modelling Pseudo code==
== Population modelling Pseudo code==
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This page will provide an overview of the code which the Newcastle team has developed for thier population simulation model.
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Due to the complexities of running the model, as it is designed for distributed systems, the full code for our population simulation model is available on request. Please email one of our advisors, <html><a href="mailto: m.taschuk@ncl.ac.uk">Morgan Taschuk</a></html>, for more information.
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Throughout this article some programming knowledge is assumed, but here are some selected definitions of terminology:
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* ''Class'' - In object orientated programming, such as Java, it is a collection of computer code which is dedicated to one idea or entity. For example a student class may contain information about a student such as their name, date of birth, etc.
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* ''A Thread of Execution'' - Inside a computer program or process there may be two or more concurrently running tasks, these tasks, called Threads. These threads each compete for time on the computer processor and can communicate with shared objects.
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* ''Java'' - One of many object orientated programming languages. Java allows the same code to be run on lots of different types of machines (eg. Windows, Mac or Linux).
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=== Bacterial simulation overview ===
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For the actual simulation of the bacterial life cyles, we decided to allow each cell of bacteria to run as a thread. As the life processes of a bacterial cell change depending on what state they are in, we decided to have a number of different classes to represent these states. These classes have some common attributes, which can be represented as a superclass in object orientated computing.
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Superclass:
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* Cell - contains the common attributes, such as levels of cadmium and nutrients, and access to the database.
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Subclasses:
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* Subtilis - represents vegative cells. From here cells can make various life choices and enter other states accordingly.
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* Spore - represents the spore stage of the life cycle. Note that for our project we have made it so that the cells have to choose whether they are going to become a "metal sequestering" spore, and thus cannot germinate.
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* Biofilm - represents the biofilm state in the cells.
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* Motile - represents motility in the cells.
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Revision as of 15:10, 21 October 2009


Population modelling Pseudo code

This page will provide an overview of the code which the Newcastle team has developed for thier population simulation model.

Due to the complexities of running the model, as it is designed for distributed systems, the full code for our population simulation model is available on request. Please email one of our advisors, Morgan Taschuk, for more information.

Throughout this article some programming knowledge is assumed, but here are some selected definitions of terminology:

  • Class - In object orientated programming, such as Java, it is a collection of computer code which is dedicated to one idea or entity. For example a student class may contain information about a student such as their name, date of birth, etc.
  • A Thread of Execution - Inside a computer program or process there may be two or more concurrently running tasks, these tasks, called Threads. These threads each compete for time on the computer processor and can communicate with shared objects.
  • Java - One of many object orientated programming languages. Java allows the same code to be run on lots of different types of machines (eg. Windows, Mac or Linux).

Bacterial simulation overview

For the actual simulation of the bacterial life cyles, we decided to allow each cell of bacteria to run as a thread. As the life processes of a bacterial cell change depending on what state they are in, we decided to have a number of different classes to represent these states. These classes have some common attributes, which can be represented as a superclass in object orientated computing.

Superclass:

  • Cell - contains the common attributes, such as levels of cadmium and nutrients, and access to the database.

Subclasses:

  • Subtilis - represents vegative cells. From here cells can make various life choices and enter other states accordingly.
  • Spore - represents the spore stage of the life cycle. Note that for our project we have made it so that the cells have to choose whether they are going to become a "metal sequestering" spore, and thus cannot germinate.
  • Biofilm - represents the biofilm state in the cells.
  • Motile - represents motility in the cells.



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