The Lattice Project: Difference between revisions

Line 73:

Analyses run through the Lattice Grid and its GARLI web service contributed to a range of published phylogenetic studies, particularly in the University of Maryland's own moth and butterfly research program. Examples include a 2009 study on the phylogeny of advanced moths and butterflies (Lepidoptera: Ditrysia), a 2011 study on gene sampling in gracillariid leaf-mining moths, and a 2013 exploratory RNA-Seq study of rapid radiation within Apoditrysia, all of which drew on GARLI analyses of the kind distributed by Lattice.<ref name="sysbio2014" />

== ~~Discontinuation~~ ==

== Scientific Publications ==

The ~~Lattice Project is not currently listed among active~~ BOINC ~~projects~~, and ~~both~~ of ~~its web addresses~~, ~~''lattice~~.~~umiacs~~.~~umd~~.~~edu''~~ and ~~''boinc~~.~~umiacs~~.~~umd~~.~~edu''~~, ~~are offline as~~ of ~~this writing~~. ~~Because BOINC client software depends on~~ a ~~project's own website to retrieve account~~, ~~application~~, and ~~scheduling information~~, the ~~loss~~ of the ~~Lattice BOINC website meant volunteer computers could no longer attach to or receive work~~ from the ~~project~~, ~~effectively ending that instance regardless of whether any~~ Grid ~~infrastructure remained active elsewhere~~.~~<ref name="wikipedia"~~ />

Puplications using BOINC-based results as listed on [https://boinc.berkeley.edu/pubs.php#The Publications by BOINC Projects]

# Bazinet, Adam L. and Michael P. Cummings. [Subdividing Long-Running, Variable-Length Analyses Into Short, Fixed-Length BOINC Workunits](http://link.springer.com/10.1007/s10723-015-9348-5). Journal of Grid Computing (2016). DOI: 10.1007/s10723-015-9348-5.

# Bazinet, Adam L., Derrick J. Zwickl and Michael P. Cummings. [A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0](https://academic.oup.com/sysbio/article/63/5/812/2847779). Systematic Biology (2014). DOI: 10.1093/sysbio/syu031.

# Bazinet, Adam L., Michael P. Cummings, Kim T. Mitter and Charles W. Mitter. [Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study](https://dx.plos.org/10.1371/journal.pone.0082615). PLoS ONE (2013). DOI: 10.1371/journal.pone.0082615.

# Lloyd, Michael W., Lesley Campbell and Maile C. Neel. [The Power to Detect Recent Fragmentation Events Using Genetic Differentiation Methods](https://dx.plos.org/10.1371/journal.pone.0063981). PLoS ONE (2013). DOI: 10.1371/journal.pone.0063981.

# Regier, Jerome C. and Andreas Zwick. [Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods](https://dx.plos.org/10.1371/journal.pone.0023408). PLoS ONE (2011). DOI: 10.1371/journal.pone.0023408.

# Zwick, Andreas, Jerome C. Regier, Charles Mitter and Michael P. Cummings. [Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera)](https://onlinelibrary.wiley.com/doi/10.1111/j.1365-3113.2010.00543.x). Systematic Entomology (2011). DOI: 10.1111/j.1365-3113.2010.00543.x.

# Cho, Soowon, Andreas Zwick, Jerome C. Regier *et al*. [Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?](https://academic.oup.com/sysbio/article/60/6/782/1678055). Systematic Biology (2011). DOI: 10.1093/sysbio/syr079.

# Kawahara, Akito Y, Issei Ohshima, Atsushi Kawakita *et al*. [Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)](http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-11-182). BMC Evolutionary Biology (2011). DOI: 10.1186/1471-2148-11-182.

# Reyna-Fabián, Miriam E., Juan Pedro Laclette, Michael P. Cummings and Martín García-Varela. [Validating the systematic position of Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase](http://link.springer.com/10.1007/s10750-010-0203-1). Hydrobiologia (2010). DOI: 10.1007/s10750-010-0203-1.

# Regier, Jerome C., Jeffrey W. Shultz, Andreas Zwick, April Hussey, Bernard Ball, Regina Wetzer, Joel W. Martin and Clifford W. Cunningham. [Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences](http://www.nature.com/articles/nature08742). Nature (2010). DOI: 10.1038/nature08742.

# Regier, Jerome C, Andreas Zwick, Michael P Cummings *et al*. [Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study](https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-9-280). BMC Evolutionary Biology (2009). DOI: 10.1186/1471-2148-9-280.

# Pettengill, James B and Maile C Neel. [Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae)](http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-264). BMC Evolutionary Biology (2008). DOI: 10.1186/1471-2148-8-264.

# Bazinet, Adam L., Daniel S. Myers, John Fuetsch and Michael P. Cummings. [Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services](https://linkinghub.elsevier.com/retrieve/pii/S0167739X06001464). Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.009.

# Tishkoff, S. A., M. K. Gonder, B. M. Henn *et al*. [History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation](https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msm155). Molecular Biology and Evolution (2007). DOI: 10.1093/molbev/msm155.

# Myers, Daniel S., Adam L. Bazinet and Michael P. Cummings. [Expanding the Reach of Grid Computing: Combining Globus- and BOINC-Based Systems](https://onlinelibrary.wiley.com/doi/10.1002/9780470191637.ch4). Grid Computing for Bioinformatics and Computational Biology (2007).

# Lee, Sung, Taowei David Wang, Nada Hashmi and Michael P. Cummings. [Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences](https://linkinghub.elsevier.com/retrieve/pii/S0167739X06001439). Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.011.

== See also ==

@@ Line 73: / Line 73: @@
 Analyses run through the Lattice Grid and its GARLI web service contributed to a range of published phylogenetic studies, particularly in the University of Maryland's own moth and butterfly research program. Examples include a 2009 study on the phylogeny of advanced moths and butterflies (Lepidoptera: Ditrysia), a 2011 study on gene sampling in gracillariid leaf-mining moths, and a 2013 exploratory RNA-Seq study of rapid radiation within Apoditrysia, all of which drew on GARLI analyses of the kind distributed by Lattice.<ref name="sysbio2014" />
-== Discontinuation ==
+== Scientific Publications ==
-The Lattice Project is not currently listed among active BOINC projects, and both of its web addresses, ''lattice.umiacs.umd.edu'' and ''boinc.umiacs.umd.edu'', are offline as of this writing. Because BOINC client software depends on a project's own website to retrieve account, application, and scheduling information, the loss of the Lattice BOINC website meant volunteer computers could no longer attach to or receive work from the project, effectively ending that instance regardless of whether any Grid infrastructure remained active elsewhere.<ref name="wikipedia" />
+Puplications using BOINC-based results as listed on [https://boinc.berkeley.edu/pubs.php#The Publications by BOINC Projects]
+# Bazinet, Adam L. and Michael P. Cummings. [Subdividing Long-Running, Variable-Length Analyses Into Short, Fixed-Length BOINC Workunits](http://link.springer.com/10.1007/s10723-015-9348-5). Journal of Grid Computing (2016). DOI: 10.1007/s10723-015-9348-5.
+# Bazinet, Adam L., Derrick J. Zwickl and Michael P. Cummings. [A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0](https://academic.oup.com/sysbio/article/63/5/812/2847779). Systematic Biology (2014). DOI: 10.1093/sysbio/syu031.
+# Bazinet, Adam L., Michael P. Cummings, Kim T. Mitter and Charles W. Mitter. [Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study](https://dx.plos.org/10.1371/journal.pone.0082615). PLoS ONE (2013). DOI: 10.1371/journal.pone.0082615.
+# Lloyd, Michael W., Lesley Campbell and Maile C. Neel. [The Power to Detect Recent Fragmentation Events Using Genetic Differentiation Methods](https://dx.plos.org/10.1371/journal.pone.0063981). PLoS ONE (2013). DOI: 10.1371/journal.pone.0063981.
+# Regier, Jerome C. and Andreas Zwick. [Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods](https://dx.plos.org/10.1371/journal.pone.0023408). PLoS ONE (2011). DOI: 10.1371/journal.pone.0023408.
+# Zwick, Andreas, Jerome C. Regier, Charles Mitter and Michael P. Cummings. [Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera)](https://onlinelibrary.wiley.com/doi/10.1111/j.1365-3113.2010.00543.x). Systematic Entomology (2011). DOI: 10.1111/j.1365-3113.2010.00543.x.
+# Cho, Soowon, Andreas Zwick, Jerome C. Regier *et al*. [Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?](https://academic.oup.com/sysbio/article/60/6/782/1678055). Systematic Biology (2011). DOI: 10.1093/sysbio/syr079.
+# Kawahara, Akito Y, Issei Ohshima, Atsushi Kawakita *et al*. [Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)](http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-11-182). BMC Evolutionary Biology (2011). DOI: 10.1186/1471-2148-11-182.
+# Reyna-Fabián, Miriam E., Juan Pedro Laclette, Michael P. Cummings and Martín García-Varela. [Validating the systematic position of Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase](http://link.springer.com/10.1007/s10750-010-0203-1). Hydrobiologia (2010). DOI: 10.1007/s10750-010-0203-1.
+# Regier, Jerome C., Jeffrey W. Shultz, Andreas Zwick, April Hussey, Bernard Ball, Regina Wetzer, Joel W. Martin and Clifford W. Cunningham. [Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences](http://www.nature.com/articles/nature08742). Nature (2010). DOI: 10.1038/nature08742.
+# Regier, Jerome C, Andreas Zwick, Michael P Cummings *et al*. [Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study](https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-9-280). BMC Evolutionary Biology (2009). DOI: 10.1186/1471-2148-9-280.
+# Pettengill, James B and Maile C Neel. [Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae)](http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-264). BMC Evolutionary Biology (2008). DOI: 10.1186/1471-2148-8-264.
+# Bazinet, Adam L., Daniel S. Myers, John Fuetsch and Michael P. Cummings. [Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services](https://linkinghub.elsevier.com/retrieve/pii/S0167739X06001464). Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.009.
+# Tishkoff, S. A., M. K. Gonder, B. M. Henn *et al*. [History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation](https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msm155). Molecular Biology and Evolution (2007). DOI: 10.1093/molbev/msm155.
+# Myers, Daniel S., Adam L. Bazinet and Michael P. Cummings. [Expanding the Reach of Grid Computing: Combining Globus- and BOINC-Based Systems](https://onlinelibrary.wiley.com/doi/10.1002/9780470191637.ch4). Grid Computing for Bioinformatics and Computational Biology (2007).
+# Lee, Sung, Taowei David Wang, Nada Hashmi and Michael P. Cummings. [Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences](https://linkinghub.elsevier.com/retrieve/pii/S0167739X06001439). Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.011.
 == See also ==