====== Random-model of simulated evolution ======
\\ 


|392163 | Marília Braga, Nils Hoffmann, Jens Stoye, Roland Wittler|Summer 2009 |Dates: see below |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=11023037|ekvv]] |**Attendees:** Eyla Willing, Kai Frederic Engelmann, Stefan Marfilius, Christoph Brinkrolf, Madis Rumming, Marvin Meinold, Rolf Hilker, Daniel Dörr, Konstantin Otte  \\ \\ 


|**Date, time, place**|**Topic**|
| 16.04., 9:15, U10-155   |Preliminaries|
| 20.04., 18:15, U10-146  |Journal Club 1: [[http://bioinformatics.oxfordjournals.org/cgi/reprint/14/2/157.pdf|Rose]] (Eyla)|
| 27.04., 18:15, U10-146  |Journal Club 2: [[http://bioinformatics.oxfordjournals.org/cgi/reprint/21/Suppl_3/iii31.pdf|DAWG]] (Kai), [[http://mbe.oxfordjournals.org/cgi/reprint/24/3/640.pdf|Strope et al.]] (Stefan)|
| 04.05., 18:15, U10-146  |Journal Club 3: [[http://genomebiology.com/content/pdf/gb-2008-9-10-r147.pdf|Varadarajan et al.]] (Christoph), [[http://www.pnas.org/content/105/38/14254.full.pdf+html?sid=38965c59-a832-411c-bbf9-e06cbe3cd7bb|Ma et al.]] (Madis)|
| 06.05., 17:30, U10-146 |Discussion on topics|
| 12.05., 10:15, U10-146 |Further discussions |
| 19.05., 17:15, U10-146 |specification & architecture|
| 28.05., 17:15, U10-146 |For now last group meeting, Further meetings in subgroups|
| 04.06., 17:15, U10-146 |SHORT-Meeting|
| 15.06., 17:15, U10-146 |yet another Rose Meeting|
| 01.09., 10:15, U10-155 |status-update meeting|
| 08.09., 13:15, U10-155 |status-update meeting|
| 15.09., 13:15, U10-155 |status-update meeting|
| 24.09., 11:00, U10-155 |status-update meeting|TREFFEN: jeden Donnerstag 16 Uhr 



===== Milestones =====
**MILESTONE**: Funktion **nur** gültig, wenn JUnit Test vorliegt!! 


|**Milestone**|**Date**|**Topic**|
|0  |sofort |Use Cases, Projektprozent |
|I  |2.10.  |Inputs in Rose Data, Mock Object, Use Cases im Wiki|
|II |9.10.  |Probe Durchlauf (Mock), spez. output |
|III|16.10. |Output visualisierung, annotation klopfen |
|IV |23.10. |Feature-stop, Doku konzept |
|V  |30.10. |ALLES FERTIG |
  * [[:Teaching:2009summer:RoseP:AlphaStatus0|Alpha Status 0]]: Use Cases 
  * **[[:Teaching:2009summer:RoseP:ToDo|ToDo's]]** 


===== Project Sections =====

  * [[:Teaching:2009summer:RoseP:CodeQuality|Tutorial on code quality conventions for the project]] (sagt Dany) 
  * [[:Teaching:2009summer:RoseP:Overview|Overview about the program]] 
  * [[:Teaching:2009summer:RoseP:InputOutput|Input-Output]] (Stefan, Marvin, Rolf) 
  * [[:Teaching:2009summer:RoseP:TreeEvolution|Tree based Evolution and Rearrangements]] (Konstantin, Kai) 
  * [[:Teaching:2009summer:RoseP:HMMEvolution|HMM based Evolution]] (Madis, Daniel) 
  * [[:Teaching:2009summer:RoseP:EvOpL|Evolutionary Operations and Edge Evolve Function]] (Eyla, Christoph) 
  * [[:Teaching:2009summer:RoseP:PreliminaryDiscussion|Preliminary Discussion]] 
SVN URL: [[http://svn.cebitec.uni-bielefeld.de/svn/aggiprojects/rose/|http://svn.cebitec.uni-bielefeld.de/svn/aggiprojects/rose/]] 

:!: Build Server URL: [[http://dev.dany2k.de/build|http://dev.dany2k.de/build]] :!: 

===== Official Announcement =====
This project is about the simulation of evolution. 

Based on Darwin's fundamental observations we have the following general scheme: 


  - The individual organisms in a population vary in some random way. 
  - They overproduce (if the available resources allow). 
  - Natural selection favors the reproduction of those individuals that are best adapted to the environment. 
  - Some of the variations are inherited to the offspring. 
Here, an individual may be represented by its DNA or protein sequence, its genome, or any other collection of characteristic data items, even bitmaps showing some type of animals are conceivable. The production of new individuals may happen by random events, through recombination with other individuals (a.k.a. sex), or a combination of both. A fitness function determines which individuals will form the next generation. 

The goal of this project is to write a software that simulates this scheme through the definition of individuals, species, mutational operators, fitness functions, and a control structure working on top of all this. The resulting tool may be used to create data sets for the experimental assessment of multiple sequence alignment, genomic distance, and phylogenetic tree reconstruction algorithms. Technically, the implementation will be done in Java, following a modular, service-oriented software architecture. The user interface shall be graphical, and a visual output is desired. 

An extension of the project may be the implementation of a game where the goal of the players is to define individuals with properties such that they produce a maximum amount of offspring in the course of evolution. Obviously, many particular instances of such a game are possible ... 

**Prerequisites:** Knowledge of Java programming, basic insights in evolutionary processes. 

Back to [[:teaching|Teaching]]