25,176 research outputs found
Land Grant Application- Barker, Daniel (Bethel)
No full textLand grant application submitted to the Maine Land Office on behalf of Daniel Barker for service in the Revolutionary War, by their widow Rachel.https://digitalmaine.com/revolutionary_war_me_land_office/1061/thumbnail.jp
Gene trees for orthologous groups from "The evolution of nitrogen fixation in cyanobacteria"
No full textPhylogenetic trees for the orthologous groups predicted across 49 taxa of Cyanobacteria and 16 Proteobacteria by Latysheva et al. (2012, Bioinformatics 28:603-606; doi:10.1093/bioinformatics/bts008) are provided here. For the 13854 groups containing at least three protein sequences, phylogenies were reconstructed as follows. Multiple alignment of protein sequences was performed using MAFFT (Katoh and Toh 2008, doi:10.1093/bib/bbn013), in "E-INS-I" mode with 1000 iterations. A phylogenetic model was selected for each protein multiple alignment by the Bayesian Information Criterion in MODELGENERATOR (Keane et al. 2006, doi:10.1186/1471-2148-6-29), with four Gamma-distributed rate categories for "+G" models. 200 bootstrap replicates of the multiple alignment were generated using seqboot in the PHYLIP package (Felsenstein, J. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle). Using the selected model, phylogeny was reconstructed by maximum likelihood with PhyML (Guindon et al. 2010, doi:10.1093/sysbio/syq010), both for the original alignment and for the bootstrap replicates.mltrees.zip: 13584 unrooted ML trees in PHYLIP format. The start of each filename gives the orthologous group number. Tip labels in trees consist of the protein accession, followed by an underscore, then the three-letter abbreviation for the taxon. Orthologous group numbers and taxon abbreviations are as in Latysheva et al. (2012, 10.1093/bioinformatics/bts008).
bstrees.zip: 13584 bootstrap samples, each of 200 trees, in PHYLIP format. The start of each filename gives the orthologous group number. Tips are labelled as in mltrees.zip
bms_runner: script using BayesTraits to implement methods from 'Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes'
No full textThis is version 1.4 of bms_runner, released in March 2011 (with an update to the manual in August 2012). bms_runner is a script written by Daniel Barker and Mark Pagel. bms_runner uses the separate program BayesTraits (http://www.evolution.reading.ac.uk) to predict functional links among genes, on the basis of correlated gain and loss of genes from species' genomes. bms_runner accompanies Barker, Meade and Pagel (2007, Bioinformatics 23:14-20, doi:10.1093/bioinformatics/btl558).See 'README.pdf' within the zipfile
Author Meets Reader: Not the Marrying Kind: A Feminist Critique of Same-Sex Marriage
No full textThis is an audio recording of an author meets reader session held at the SLSA Annual Conference, University of York, 27 March 2013. Nicola Barker's book, Not the Marrying Kind: A Feminist Critique of Same-Sex Marriage, was the winner of the 2013 Hart SLSA Book Prize. In the session she introduces the book and then engages in discussion about it with Daniel Monk
Additional files for 'Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena'
No full textGenome-wide protein sets input to OrthoMCL, OrthoMCL output, Perl script to count cross-species occurence of OrthoMCL groups, and output of Perl script, as used by McGill and Barker (2017, BMC Research Notes 10:296, doi:10.1186/s13104-017-2598-5).* fasta_files.zip: Genome-wide protein sets, in FASTA format, for "Candidatus Ruthia magnifica" strain Cm (magnificapep.fa), "Candidatus Vesicomyosocius okutanii" HA (okutaniipep.fa) and Thiomicrospira crunogena XCL-2 (crunogenapep.fa). These files were downloaded from the Ensembl Genomes database (http://ensemblgenomes.org).
* group_count.zip:
- groups_1.4.txt is a text file containing output of OrthoMCL for the three protein sets in fasta_files.zip, with an OrthoMCL inflation parameter of 1.4. Taxon abbreviations are MAG ("Candidatus Ruthia magnifica"), CRU ("Candidatus Ruthia magnifica") and OKU ("Candidatus Vesicomyosocius okutanii").
- group_count_script.pl is the Perl script used to post-process OrthoMCL output, counting groups across the three taxa.
- groups1.4_output.txt is a text file, containing the final output of group_count_script.pl
Barker, Daniel W.
No full textCarte de Visite of Daniel W. Barker, 2nd Maine Cavalry, Company D; From the MacDonald Collectionhttps://digitalmaine.com/arc_civilwarportraits/1855/thumbnail.jp
Barker, Daniel W.
No full textCarte de Visite of Daniel W. Barker, 2nd Maine Cavalry, Company D; From the MacDonald Collectionhttps://digitalmaine.com/arc_civilwarportraits/1855/thumbnail.jp
simpops.mac: population time series simulation script from "The effects of environmental perturbation and measurement error on estimates of the shape parameter in the theta-logistic model of population regulation"
No full textThe simpops.mac script simulates population time series for investigation of the effects of underlying parameters, environmental perturbation, measurement error and time series length on the estimation of theta in the theta-logistic model of density dependence. simpops.mac accompanies Barker and Sibly (2008, Ecological Modeling 219:170-177, doi:10.1016/j.ecolmodel.2008.08.008).simpops.zip: contains simpops.mac, version 1.0. This text file is a macro for Minitab, originally distributed on a Web site at the University of St Andrews. For further details on how to use simpops.mac, please see the comment at the start of the file
genlogistic.ssc: script to estimate theta in the theta-logistic (or generalized logistic) population model from 'On the regulation of populations of mammals, birds, fish, and insects'
No full textThis is version 1.1 of genlogistic.ssc, released in January 2006. genlogistic.ssc is a script written by Daniel Barker and Michael Denham, for estimating theta in the theta-logistic (or generalized logistic) population model. The generalized logistic equation is: pgr = r0[1-(N/K)^theta], where pgr is the population growth rate, N is the population size, K is the carrying capacity, r0 represents pgr at N = 0, and theta describes the curvature of the relationship. The script will estimate theta for one or more population time series provided by the user. genlogistic.ssc accompanies Sibly et al. (2005, Science 309:607-610, doi:10.1126/science.1110760).genlogistic_1_1.zip contains the script itself (genlogistic.ssc; plain text) and an example input file containing hypothetical data, to demonstrate the correct format (genlogistic_in.xls; Microsoft Excel spreadsheet). Instructions are given in a long comment at the start of the genlogistic.ssc script. genlogistic.ssc is an S-Plus script, developed using Insightful S-Plus for Microsoft Windows. However, with slight adaptation it should be possible to make it work under the R software environment instead
Personal Papers (MS 80-0002)
No full textLetter from Harris L. Kempner to Daniel D. Barker discussing a change in plans and schools for Harris L. Kempner, Jr
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