https://gi.cebitec.uni-bielefeld.de/ 2026-05-20T04:10:10+0200 https://gi.cebitec.uni-bielefeld.de/ https://gi.cebitec.uni-bielefeld.de/ttps://gi.cebitec.uni-bielefeld.de/lib/tpl/aggi-theme/images/favicon.ico text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/alphastatus0?rev=1581667636&do=diff Use Cases General Use Cases * Alphabet auswaehlen √ (Rolf) * ~Alphabet eingeben (NewAlphabetPage √ (Rolf) * rootsequence(s)/organisms √ (Rolf) * ~durchschnittliche sequenzlaenge √ (Rolf) * Auftrittswahrscheinlichkeiten der characters eingeben text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/codequality?rev=1581667636&do=diff /* UndefinedMacro: TableOfContents(None) */ Vorwort Mit den jüngsten Umstellungen auf ein einheitliches Build-System gibt es eine Reihe von weiteren Regeln, die beim Coden beachtet werden sollen. Zum einen soll diese Page eine Anleitung für den im Projekt enthaltenen ANT-Build sein, aber auch andere Aspekte wie Code Qualität und Unit-Testing erläutern. text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/evopl?rev=1581667636&do=diff Interface (Schnittstelle) We need/provide the following parameters: * Edge length * String/Sequence (lowest level annotation) * Substitution probabilities Preferred: HashMap<Character, MagicTable> ==> Either complete HashMap, or probability array for each character separately text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/hmmevolution?rev=1581667636&do=diff Next Meeting: Mo, 29.06., 17h, UV10 HMM Based Evolution The idea is to use Transducers, which act like pairHMM for simulating evolutionary events. Those Transducers should be based on grammars, so there also a need for a specific grammar and its parser. Responsibilities text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/inputoutput?rev=1581667636&do=diff Input Parameters * Alphabet /* UndefinedMacro: latex($\Sigma,\ \ |\Sigma|=\ell$) */ * root sequence s * OR average sequence length n character frequencies /* UndefinedMacro: latex($f=(f_1,\ldots,f_\ell)$) */ mutation guide tree //**T**// (edge length, standard: 1) * OR text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/overview?rev=1581667636&do=diff Overview about the program How the program works * Given a phylogenetic tree and a root sequence, the program creates several automatons with specific parameters * The automatons are transducers, which are markov chains that produces a sequence by the series of states text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/preliminarydiscussion?rev=1581667636&do=diff Preliminary Discussion Discussions on the new Rose What type of program do we want ? * Rose 2.0 (+ Rearrangements + parameter estimation) * Game * Educational * Entertaining Rearrangements + parameter estimation Closer look at Rose 2.0 text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/todo?rev=1581667636&do=diff TODOS Done Wer Was K+K Change Rose Main Data etc √ E+C RNG -> seed √ K+K Logs für jede Kante GUI Protein mxm Alphabet -> dass man nicht immer zurück muss GUI (Baum) aus file laden √ K+K Refactor: Tree, Annotation, depth E Billig Tree -> statisch text/html 2020-02-14T09:07:16+0200 Anonymous (anonymous@undisclosed.example.com) https://gi.cebitec.uni-bielefeld.de/teaching/2009summer/rosep/treeevolution?rev=1581667636&do=diff Back to Rose Main Page Back to Preliminary Discussion for all Meetings Date time placeTopic 09. JUN. 09 16 ct U10 Preliminaries 30. JUN. 09 16 U10 Further discussions Meeting 09. JUN 09 * Nix im Verhaeltnis * Baum (non)ultrametric * discrete vs. continuous x in [0,1) *