The Lattice Project: Difference between revisions

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[[File:University of Maryland (5354729497).jpg|thumb|The Lattice Project was developed and administered at the [[wikipedia:University of Maryland, College Park|University of Maryland, College Park]].]]

'''The Lattice Project''' was a discontinued grid computing and [[wikipedia:volunteer computing|volunteer computing]] system operated by the Laboratory of Molecular Evolution at the [[wikipedia:University of Maryland, College Park|University of Maryland]], College Park.<ref name="wikipedia">{{Cite web |title=The Lattice Project |url=https://en.wikipedia.org/wiki/The_Lattice_Project |work=Wikipedia |access-date=2026-07-14}}</ref> Rather than being a single program, Lattice combined several distinct computing resources, including dedicated [[wikipedia:HTCondor|Condor]] pools, [[wikipedia:Portable Batch System|PBS]] compute clusters, and a public [[wikipedia:BOINC|BOINC]] volunteer pool, into one production Grid system built on the [[wikipedia:Globus Toolkit|Globus Toolkit]].<ref name="bazinet2009thesis">{{Cite ~~thesis~~ |last=Bazinet |first=Adam L. |title=The Lattice Project: A Multi-model Grid Computing System ~~|type=Master's thesis |publisher=University of Maryland, College Park |year=2009~~ |url=https://drum.lib.umd.edu/bitstreams/82bde2fc-1831-47c1-95ad-00ca88268e46/download |access-date=2026-07-14}}</ref> Its best-known use was distributing maximum-likelihood [[wikipedia:phylogenetics|phylogenetic]] analyses through the Genetic Algorithm for Rapid Likelihood Inference (GARLI) program, letting researchers worldwide reconstruct evolutionary relationships from DNA and protein sequence data.<ref name="wikipedia" />

'''The Lattice Project''' was a discontinued grid computing and [[wikipedia:volunteer computing|volunteer computing]] system operated by the Laboratory of Molecular Evolution at the [[wikipedia:University of Maryland, College Park|University of Maryland]], College Park.<ref name="wikipedia">{{Cite web |title=The Lattice Project |url=https://en.wikipedia.org/wiki/The_Lattice_Project |work=Wikipedia |access-date=2026-07-14}}</ref> Rather than being a single program, Lattice combined several distinct computing resources, including dedicated [[wikipedia:HTCondor|Condor]] pools, [[wikipedia:Portable Batch System|PBS]] compute clusters, and a public [[wikipedia:BOINC|BOINC]] volunteer pool, into one production Grid system built on the [[wikipedia:Globus Toolkit|Globus Toolkit]].<ref name="bazinet2009thesis">{{Cite web |last=Bazinet |first=Adam L. |title=The Lattice Project: A Multi-model Grid Computing System |url=https://drum.lib.umd.edu/bitstreams/82bde2fc-1831-47c1-95ad-00ca88268e46/download |work=Master's thesis, University of Maryland, College Park |year=2009 |access-date=2026-07-14}}</ref> Its best-known use was distributing maximum-likelihood [[wikipedia:phylogenetics|phylogenetic]] analyses through the Genetic Algorithm for Rapid Likelihood Inference (GARLI) program, letting researchers worldwide reconstruct evolutionary relationships from DNA and protein sequence data.<ref name="wikipedia" />

== History ==

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== Software and applications ==

The flagship application run on the Lattice Grid was GARLI, the Genetic Algorithm for Rapid Likelihood Inference, an open-source phylogenetic inference program written and maintained by Derrick J. Zwickl that searches for the evolutionary tree, branch lengths, and substitution model parameters maximizing the likelihood of a sequence dataset.<ref name="sysbio2014" /><ref name="garliwiki">{{Cite web |title=Home |url=https://github.com/zwickl/garli/wiki |work=GARLI wiki, GitHub |access-date=2026-07-14}}</ref> GARLI's underlying approach was first developed in Zwickl's 2006 doctoral dissertation at the University of Texas at Austin.<ref name="zwickl2006">{{Cite ~~thesis~~ |last=Zwickl |first=Derrick J. |title=Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion |~~type~~=PhD dissertation ~~|publisher=~~The University of Texas at Austin |year=2006}}</ref> In general terms, a maximum-likelihood phylogenetic search of this kind seeks the tree topology <math>T</math>, branch lengths <math>\mathbf{v}</math>, and model parameters <math>\boldsymbol{\theta}</math> that maximize

The flagship application run on the Lattice Grid was GARLI, the Genetic Algorithm for Rapid Likelihood Inference, an open-source phylogenetic inference program written and maintained by Derrick J. Zwickl that searches for the evolutionary tree, branch lengths, and substitution model parameters maximizing the likelihood of a sequence dataset.<ref name="sysbio2014" /><ref name="garliwiki">{{Cite web |title=Home |url=https://github.com/zwickl/garli/wiki |work=GARLI wiki, GitHub |access-date=2026-07-14}}</ref> GARLI's underlying approach was first developed in Zwickl's 2006 doctoral dissertation at the University of Texas at Austin.<ref name="zwickl2006">{{Cite web |last=Zwickl |first=Derrick J. |title=Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion |url=https://www.bio.utexas.edu/faculty/antisense/garli/Garli.html |work=PhD dissertation, The University of Texas at Austin |year=2006 |access-date=2026-07-14}}</ref> In general terms, a maximum-likelihood phylogenetic search of this kind seeks the tree topology <math>T</math>, branch lengths <math>\mathbf{v}</math>, and model parameters <math>\boldsymbol{\theta}</math> that maximize

<math>L(T, \mathbf{v}, \boldsymbol{\theta} \mid X) = \prod_{i=1}^{n} P(X_i \mid T, \mathbf{v}, \boldsymbol{\theta})</math>

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 [[File:University of Maryland (5354729497).jpg|thumb|The Lattice Project was developed and administered at the [[wikipedia:University of Maryland, College Park|University of Maryland, College Park]].]]
-'''The Lattice Project''' was a discontinued grid computing and [[wikipedia:volunteer computing|volunteer computing]] system operated by the Laboratory of Molecular Evolution at the [[wikipedia:University of Maryland, College Park|University of Maryland]], College Park.<ref name="wikipedia">{{Cite web |title=The Lattice Project |url=https://en.wikipedia.org/wiki/The_Lattice_Project |work=Wikipedia |access-date=2026-07-14}}</ref> Rather than being a single program, Lattice combined several distinct computing resources, including dedicated [[wikipedia:HTCondor|Condor]] pools, [[wikipedia:Portable Batch System|PBS]] compute clusters, and a public [[wikipedia:BOINC|BOINC]] volunteer pool, into one production Grid system built on the [[wikipedia:Globus Toolkit|Globus Toolkit]].<ref name="bazinet2009thesis">{{Cite thesis |last=Bazinet |first=Adam L. |title=The Lattice Project: A Multi-model Grid Computing System |type=Master's thesis |publisher=University of Maryland, College Park |year=2009 |url=https://drum.lib.umd.edu/bitstreams/82bde2fc-1831-47c1-95ad-00ca88268e46/download |access-date=2026-07-14}}</ref> Its best-known use was distributing maximum-likelihood [[wikipedia:phylogenetics|phylogenetic]] analyses through the Genetic Algorithm for Rapid Likelihood Inference (GARLI) program, letting researchers worldwide reconstruct evolutionary relationships from DNA and protein sequence data.<ref name="wikipedia" />
+'''The Lattice Project''' was a discontinued grid computing and [[wikipedia:volunteer computing|volunteer computing]] system operated by the Laboratory of Molecular Evolution at the [[wikipedia:University of Maryland, College Park|University of Maryland]], College Park.<ref name="wikipedia">{{Cite web |title=The Lattice Project |url=https://en.wikipedia.org/wiki/The_Lattice_Project |work=Wikipedia |access-date=2026-07-14}}</ref> Rather than being a single program, Lattice combined several distinct computing resources, including dedicated [[wikipedia:HTCondor|Condor]] pools, [[wikipedia:Portable Batch System|PBS]] compute clusters, and a public [[wikipedia:BOINC|BOINC]] volunteer pool, into one production Grid system built on the [[wikipedia:Globus Toolkit|Globus Toolkit]].<ref name="bazinet2009thesis">{{Cite web |last=Bazinet |first=Adam L. |title=The Lattice Project: A Multi-model Grid Computing System |url=https://drum.lib.umd.edu/bitstreams/82bde2fc-1831-47c1-95ad-00ca88268e46/download |work=Master's thesis, University of Maryland, College Park |year=2009 |access-date=2026-07-14}}</ref> Its best-known use was distributing maximum-likelihood [[wikipedia:phylogenetics|phylogenetic]] analyses through the Genetic Algorithm for Rapid Likelihood Inference (GARLI) program, letting researchers worldwide reconstruct evolutionary relationships from DNA and protein sequence data.<ref name="wikipedia" />
 == History ==
@@ Line 60: / Line 60: @@
 == Software and applications ==
-The flagship application run on the Lattice Grid was GARLI, the Genetic Algorithm for Rapid Likelihood Inference, an open-source phylogenetic inference program written and maintained by Derrick J. Zwickl that searches for the evolutionary tree, branch lengths, and substitution model parameters maximizing the likelihood of a sequence dataset.<ref name="sysbio2014" /><ref name="garliwiki">{{Cite web |title=Home |url=https://github.com/zwickl/garli/wiki |work=GARLI wiki, GitHub |access-date=2026-07-14}}</ref> GARLI's underlying approach was first developed in Zwickl's 2006 doctoral dissertation at the University of Texas at Austin.<ref name="zwickl2006">{{Cite thesis |last=Zwickl |first=Derrick J. |title=Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion |type=PhD dissertation |publisher=The University of Texas at Austin |year=2006}}</ref> In general terms, a maximum-likelihood phylogenetic search of this kind seeks the tree topology <math>T</math>, branch lengths <math>\mathbf{v}</math>, and model parameters <math>\boldsymbol{\theta}</math> that maximize
+The flagship application run on the Lattice Grid was GARLI, the Genetic Algorithm for Rapid Likelihood Inference, an open-source phylogenetic inference program written and maintained by Derrick J. Zwickl that searches for the evolutionary tree, branch lengths, and substitution model parameters maximizing the likelihood of a sequence dataset.<ref name="sysbio2014" /><ref name="garliwiki">{{Cite web |title=Home |url=https://github.com/zwickl/garli/wiki |work=GARLI wiki, GitHub |access-date=2026-07-14}}</ref> GARLI's underlying approach was first developed in Zwickl's 2006 doctoral dissertation at the University of Texas at Austin.<ref name="zwickl2006">{{Cite web |last=Zwickl |first=Derrick J. |title=Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion |url=https://www.bio.utexas.edu/faculty/antisense/garli/Garli.html |work=PhD dissertation, The University of Texas at Austin |year=2006 |access-date=2026-07-14}}</ref> In general terms, a maximum-likelihood phylogenetic search of this kind seeks the tree topology <math>T</math>, branch lengths <math>\mathbf{v}</math>, and model parameters <math>\boldsymbol{\theta}</math> that maximize
 <math>L(T, \mathbf{v}, \boldsymbol{\theta} \mid X) = \prod_{i=1}^{n} P(X_i \mid T, \mathbf{v}, \boldsymbol{\theta})</math>