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Evolution@home results overview

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This page provides a quick overview over published evolution@home results, which can currently be divided into three categories:

  • Biological results directly computed with the help of evolution@home.
  • Computer science results about the global computing and modelling aspects of evolution@home
  • Biological background results that help preparing future evolution@home simulation projects, but were obtained without the direct help of evolution@home.

 All direct evolution@home results are currently produced by Simulator005.

 

Simulator005

This simulator was designed for analysing Muller's ratchet. It was also used to explore questions in global computing related to minimalist global computing systems.  Here are some reports that link to research papers produced with the help of this simulator:

  • Muller's ratchet in human mtDNA - see news here and here.
    • Loewe L (2006) "Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA" Genetics Research 87:133-159. PDF | ISI | PubMedDOI | Journal  |  This is the most rigorous study of the topic so far. It is also a comprehensive overview over potential solutions for genomic decay paradoxes, where the solutions for the paradox in mtDNA are explained in more detail than the others.  
  • Muller's ratchet in the fish Amazon molly - see news here.
    • Loewe L & Charlesworth B (2008) "Quantifying the threat from Muller's ratchet in the Amazon molly (Poecilia formosa)", BMC Evolutionary Biology 8:88. (20 pages). Designated as ‘highly accessed’ by BMC.  PDF  |  Journal
  • Muller's ratchet in the worm C. elegans - see news here.
    • Loewe L & Cutter A (2008) "On the potential for extinction by Muller’s Ratchet in Caenorhabditis elegans", BMC Evolutionary Biology 8:125. (13 pages).   PDF | Journal 
  • Developing the theory behind Muller's ratchet (evolution@home results help to test the theory)
    • Waxman D & Loewe L (2010) “A stochastic model for a single click of Muller’s ratchet”.  Journal of theoretical Biology, (in print).    DOI  
  • Minimalist global computing with heterogeneous work units
    • Loewe L (2007) "Evolution@home: observations on participant choice, work unit variation and low-effort global computing". Software Practice & Experience 37:1289-1318.  ( DOI link ).
    • Loewe L (2002) "evolution@home: Experiences with work units that span more than 7 orders of magnitude in computational complexity", 425-431. 2nd International Workshop on Global and Peer-to-Peer Computing on Large Scale Distributed Systems at the 2nd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2002), 21-24 May, Berlin, Germany, IEEE Computer Society.    PDF | DOI | ConferenceProceedings  
  • Some other articles that involve material from Simulator005
    • Loewe L (2008) "Evolution@home: The first global computing system for evolutionary biology", invited chapter in the book "Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities" edited by M. Weber, Rechenkraft.net.
    • Loewe L (2005) "Evolution@home: Global computing quantifies evolution due to Muller's ratchet", BMC Bioinformatics 2005, vol. 6, suppl 3, p.18-18.  Published poster abstract. 

 

Global computing and formal modelling

  • A preliminary exploration of how formal modelling could contribute towards making it easier to implement models. Such approaches could contribute to the evolution@home system.
    • Loewe L (2008) “Designing a Front-End for Bio-PEPA”. In: Gilmore S, editor. Proceedings of the 7th Workshop on Process Algebra and Stochastically Timed Activities, 30-31 July 2008, Edinburgh, UK.      http://pastaworkshop.org/proceedings/loewe-pasta2008.pdf (5 pages).
  • Minimalist global computing with heterogeneous work units
    • Loewe L (2007) "Evolution@home: observations on participant choice, work unit variation and low-effort global computing". Software Practice & Experience 37:1289-1318.  ( DOI link ).
    • Loewe L (2002) "evolution@home: Experiences with work units that span more than 7 orders of magnitude in computational complexity", 425-431. 2nd International Workshop on Global and Peer-to-Peer Computing on Large Scale Distributed Systems at the 2nd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2002), 21-24 May, Berlin, Germany, IEEE Computer Society.    PDF | DOI | ConferenceProceedings  
  • A review of global computing in bioinformatics
    • Loewe L (2002) "Global computing for bioinformatics", Briefings in Bioinformatics 3:377-388.   PDF | PubMed | DOI | Journal   
  • Some other articles about evolution@home
    • Loewe L (2008) "Evolution@home: The first global computing system for evolutionary biology", invited chapter in the book "Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities" edited by M. Weber, Rechenkraft.net.
    • Loewe L (2005) "Evolution@home: Global computing quantifies evolution due to Muller's ratchet", BMC Bioinformatics 2005, vol. 6, suppl 3, p.18-18.  Published poster abstract. 

 

Biological background

The following work was done to help prepare the science behind new simulation projects of evolution@home:

  • An overview over some of the most challenging questions in population genetics that keep inspiring the science behind evolution@home.
    • Loewe L & Hill, WG (2010) “Introduction: The population genetics of mutations: good, bad and indifferentPhilosophical Transactions of the Royal Society B  365:1153-1167.   DOI   |   Journal abstract   |   Journal issue   
    • Loewe L & Hill, WG; editors (2010) “The population genetics of mutations: good, bad and indifferent”, Philosophical Transactions of the Royal Society B volume 365, issue number 1544, pages 1149-1294, ISSN 0962-8436, ISBN: 978-0-85403-813-8.    Table of contents   |   News item from evolution@home perspecive   |   The print issue can be ordered from:   http://rstb.royalsocietypublishing.org/site/2010/mutations.xhtml   (for a discount enter special code TB 1544 when prompted).   |   Preface and Introduction are free.
      This collection of papers by influential scientists highlights many of the challenges that we face when trying to understand the evolution of life with a special view on mutations. This is an excellent collection of papers for understanding the complex scientific questions that inspire the work behind evolution@home. Mostly written for reasonably informed professional biologists or experts, some of it can be challenging to understand for others. This issue is dedicated to Brian Charlesworth on the occasion of his 65th birthday for his many contributions to population genetics.
  • A framework for investigating various questions related to evolution.
    Loewe L (2009) "A framework for evolutionary systems biology", BMC Systems Biology 3:27.   PubMed  |  DOI  |  Journal 
  • Inferring the distribution of mutational effects on fitness
    A new population genetics method: PDF - Comparing distributions: PDF - New approach using systems biology PDF
    • Loewe L & Hillston J (2008) "The distribution of mutational effects on fitness in a simple circadian clock", Proceedings of the 6th Conference on Computational Methods in Systems Biology 11-15 Oct 2008 Rostock, Germany, CMSB08, published in: Lecture Notes in Bioinformatics 5307:156-175.   PDF  |  DOI  
    • Loewe L & Charlesworth B (2006) "Inferring the distribution of mutational effects on fitness in Drosophila", Biology Letters 2:426-430.   PDF | ISI | PubMed | DOI | Journal   
    • Loewe L & Charlesworth B, Bartolomé C & Nöel V (2006) "Estimating selection on non-synonymous mutations", Genetics 172:1079-1092.   PDF | ISI | PubMed | DOI | Journal | Poster 
  • Background selection within genes
    • Loewe L & Charlesworth B (2007) "Background selection in single genes may explain patterns of codon bias", Genetics 175:1381-1393.   PDF | PubMed | DOI | Journal  
  • Here is an experiments that raises questions about how bacteria survive under stress. To understand what this means for antibiotics resistance evolution will require many simulations.
    • Loewe L, Textor V & Scherer S (2003) "High deleterious genomic mutation rate in stationary phase of Escherichia coli", Science 302:1558-1560.   PDF-core | PDF-collect | ISI | PubMed | DOI | Journal   Response to a comment:  Science 304:518-518.   PDF | ISI | DOI | Journal   

 

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