http://algorithmics.comp.nus.edu.sg/wiki/ 2009-11-23T15:26:26+08:00 http://algorithmics.comp.nus.edu.sg/wiki/ http://algorithmics.comp.nus.edu.sg/wiki/lib/images/favicon.ico text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/experimental_results?rev=1198892253 Simulated data The following two sections shows some of the initial results we have obtained with the MGR-BR (best rearrangements) and MGR-GT (grow tree) algorithm. These two algorithms are extensions of the basic MGR algorithm proposed in Bourque and Pevzner, 2002 to handle genomes with unequal content. text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/experimentation_plan?rev=1198892253 Experiments carried out * Model parameters * number of genes in the root (n) * number of genomes in the leaves (m) * number of rearrangements per edge (k) * percentage of deletions (D) * genomes are circular ? (C) * generate outgroup ? (O) text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/final_report?rev=1198892253 Key components * Latex template from senior * TreeGraph for generating eps/svg output of phylogenetic trees * Excel/gnuplot for generating plots for experimental results * ImageMagick's convert for converting other image formats to eps * Inkscape/Dia for creating diagrams text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0001?rev=1198892253 Project Rearrangements in genomes with unequal content Date 24/05/05 Version 1.0 Purpose of Meeting To discuss project outline Supervisor present Leong Hon Wai, Guillaume Bourque Current Task/Sub-Task * Understand what are the focus and requirements of this project * Read up relevant papers/books in the field to get some background knowledge * Understand and analyse the MGR algorithm developed by Dr Bourque text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0002?rev=1198892253 Project Rearrangements in genomes with unequal content Date 30/05/05 Version 1.0 Purpose of Meeting Short update on progress, prototyping Supervisor present Leong Hon Wai Current Task/Sub-Task * Prototyping * Literature review of phylogenetic reconstruction techniques text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0003?rev=1198892253 Project Rearrangements in genomes with unequal content Date 02/06/05 Version 1.0 Purpose of Meeting To discuss the inital approach to the project Supervisor present Leong Hon Wai, Guillaume Bourque Current Task/Sub-Task * Prototyping * Literature review text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0004?rev=1198892253 Project Rearrangements in genomes with unequal content Date 09/06/05 Version 1.0 Purpose of Meeting To discuss issues in prototyping Supervisor present Leong Hon Wai Current Task/Sub-Task * Perform some exploratory analysis on simulated data * Prepare the project plan * Prepare minutes for each meeting * Prepare for a talk on phylogenetic reconstruction using gene order data text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0005?rev=1198892253 Project Rearrangements in genomes with unequal content Date 23/06/05 Version 1.0 Purpose of Meeting Project update Supervisor present Leong Hon Wai Current Task/Sub-Task * Literature review * Prepare the project plan * Prepare for a talk on genome rearrangement studies text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0006?rev=1198892253 Project Rearrangements in genomes with unequal content Date 30/06/05 Version 1.0 Purpose of Meeting Update on project plan, discussion on talks Supervisor present Leong Hon Wai Current Task/Sub-Task * Complete the first draft of the project plan * Prepare for a short talk on genome rearrangements to the group text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0007?rev=1198892253 Project Rearrangements in genomes with unequal content Date 07/07/05 Version 1.0 Purpose of Meeting Discuss project plan and upcoming talks Supervisor present Leong Hon Wai Current Task/Sub-Task * Finish project plan * Prepare a 15 minute presentation on the project plan * Prepare a short talk on phylogenetic reconstruction text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0008?rev=1198892253 Project Rearrangements in genomes with unequal content Date 14/07/05 Version 1.0 Purpose of Meeting Discuss initial project plan and upcoming talks Supervisor present Leong Hon Wai Current Task/Sub-Task * Prepare system architecture * Prepare project plan presentation * Prepare talk on phylogenetic reconstruction * Come up with an intial solution proposal text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0009?rev=1198892253 Project Rearrangements in genomes with unequal content Date 21/07/05 Version 1.0 Purpose of Meeting Discuss solution proposal Supervisor present Leong Hon Wai Current Task/Sub-Task * Develop prototype * Prepare system architecture * Prepare talk on phylogenetic reconstruction text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0010?rev=1198892253 Project Rearrangements in genomes with unequal content Date 28/07/05 Version 1.0 Purpose of Meeting Discuss prototyping Supervisor present Leong Hon Wai Current Task/Sub-Task * Prototying * Design of software architecture Reported On * Progress in the sysetm review text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0011?rev=1198892253 Project Rearrangements in genomes with unequal content Date 02/09/05 Version 1.0 Purpose of Meeting Progress update Supervisor present Leong Hon Wai Current Task/Sub-Task * Finish implementation of prototype Reported On * Completion of software architecture text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0012?rev=1198892253 Project Rearrangements in genomes with unequal content Date 23/09/05 Version 1.0 Purpose of Meeting Report on results of prototype Supervisor present Leong Hon Wai Current Task/Sub-Task * Implementation of second iteration Reported On * Results of prototype text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0013?rev=1198892253 Project Rearrangements in genomes with unequal content Date 14/11/05 Version 1.0 Purpose of Meeting Progress update Supervisor present Leong Hon Wai, Guillaume Bourque Current Task/Sub-Task * None (preparing for examinations) Reported On * Progress made in the project, see Progress report text/html 2008-01-11T18:06:17+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0014?rev=1200045977 Project Rearrangements in genomes with unequal content Date 06/12/05 Version 1.0 Purpose of Meeting Plans for semester break Supervisor present Leong Hon Wai Current Task/Sub-Task * Write the progress report * Implement “best” rearrangements algorithm text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0015?rev=1198892253 Project Rearrangements in genomes with unequal content Date 16/12/05 Version 1.0 Purpose of Meeting Discuss plans for the rest of the project Supervisor present Guillaume Bourque Current Task/Sub-Task * Implementing the “best” rearrangements algorithms * Writing up the interim report text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0016?rev=1198892253 Project Rearrangements in genomes with unequal content Date 30/12/05 Version 1.0 Purpose of Meeting Discuss experimental results Supervisor present Leong Hon Wai Current Task/Sub-Task * Running experiments to compare the best rearrangements algorithm with the original MGR * Integrating Hoang's tree distance algorithms into the program * Looking at using information about the rearrangement distance in the scoring function for rearrangements * Reformulating the computationa… text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0017?rev=1198892253 Project Rearrangements in genomes with unequal content Date 27/01/05 Version 1.0 Purpose of Meeting Discuss experimental results Supervisor present Leong Hon Wai Current Task/Sub-Task * Fine tuning parameters for experiments * Reformulating the computational problem for the case of unequal content * Writing up the report text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0018?rev=1198892253 Project Rearrangements in genomes with unequal content Date 01/03/06 Version 1.0 Purpose of Meeting Update on progress Supervisor present Leong Hon Wai Current Task/Sub-Task * Complete draft of report * Finish running experiments text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/mtg_0019?rev=1198892253 Project Rearrangements in genomes with unequal content Date 07/03/06 Version 1.0 Purpose of Meeting Finalize experiments Supervisor present Leong Hon Wai, Guillaume Bourque Current Task/Sub-Task * Complete draft of report * Finish running experiments text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/progress_report?rev=1198892253 Project Rearrangements in genomes with unequal content Date 04/11/05 Version 1.0 Major milestones * Literature review * Completed project plan * Completed system review * Completed software architecture * Converted code base to C++ * Completed prototype * Solution proposal * Experiments and analysis * Extensions text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/sidebar?rev=1198892253 * Major documents * Project plan * Progress report * Experimentation plan * Experimental results * Final Report * Meeting minutes * Minutes template * Minutes 24/05/05 * Minutes 30/05/05 * Minutes 02/06/05 * Minutes 09/06/05 * Minutes 23/06/05 * Minutes 30/06/05 * Minutes 07/07/05 * Minutes 14/07/05 * Minutes 21/07/05 * Minutes 28/07/05 * Minutes 02/09/05 * Minutes 23/09/05 * Minutes 14/11/05 * Minutes 06/12/05 * … text/html 2008-01-04T17:21:20+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/start?rev=1199438480 Upcoming events Event Honours Year Poster Presentation Title Rearrangements in genomes with unequal content Presenter Melvin Zhang, Honours year student, SOC. Supervisors: A/P Leong Hon Wai and Guillaume Borque, GIS Date 19th April 2006, 4 - 6pm at SOC1 level 5 TR 8 Event Presentation to SoC Computational Biology Lab Title Rearrangements in genomes with unequal content Speaker Melvin Zhang, Honours year student, SOC. Supervisors: A/P Leong Hon Wai and Guillaume Borque, GIS Dat… text/html 2007-12-29T09:37:33+08:00 http://algorithmics.comp.nus.edu.sg/wiki/mgr/template?rev=1198892253 Project Rearrangements in genomes with unequal content Date DD/MM/YY Version 1.0 Purpose of Meeting TBC Supervisor present TBC Current Task/Sub-Task * Task 1 Reported On * Report 1 Discussed Item 1 Details Item 2 Details