<!-- Begin

//  The following arrays detail which items appear on the front page, the numbers refering to 
//  their positions in their container arrays, detailed below. To add a newer item on the 
//  front page in replacement of an older one, update the container array with the newer 
//  item, then change the position number of the older item to that of the newer item. 
//  The order in which these items appear on the front page can be changed at will by 
//  changing the order in which they appear in these Showcase arrays.

PapersToShowcase = [19,21,17,16,1]; // count starts at 1, not 0
ProjectsToShowcase = [1,2,3]; // count starts at 1, not 0
SoftwareItemsToShowcase = [9,8,7,3]; // count starts at 1, not 0
DataItemsToShowcase = [7]; // count starts at 1, not 0

//---------------------------------------------------------------------------------------------
// Publications
//  format for new entries:
//
//  new aPaper(number, "authors", "title", "journal", year, volume, "pages", issue, "Abstract", [SoftwareArray], [DataArray], inProject, "manuscriptURL"),
//
//  number: non-zero integer - will be used as referencing number for projects, software & 
//  data & not for sorting
//  "authors", "title", "journal", "pages", "Abstract", "manuscriptURL": all strings
//  pages: string; for submitted papers, use "submitted"
//  year: non-zero integer - for submitted papers, use year of submission
//  volume, issue: integer - 0 if none
//  SoftwareArray, DataArray: arrays of comma-separated integer references to software/data
//  numbers within square brackets; use empty square brackets ("[]") if none
//  arrays are used in case a paper has more than one data set or more than one program 
//  associated with it
//  inProject: integer reference to project number - 0 if none
//  "manuscriptURL": optional link to PDF on server or publisher's link; must include 
//  "http://" if off-site - if no link, end the argument list with 'inProject'
//
//  each aPaper entry within the Papers array is followed by a comma, except the last
//  pre-sorting by year (most recent first) is best; only the first few will appear on the
//  front (home) page, as determined by the value of NumberOfPapersOnFrontPage in the <head> 
//  portion of the home.htm file
//  don't use quotation marks (") within string entries; use &quot; or single quote (')
//  no line breaks within string entries or within argument list
//  when viewed with "no wrap", each entry should be all on one line
//---------------------------------------------------------------------------------------------

Papers = new Array(

new aPaper(16,"Tillier, E. R. M and R. L Charlebois", "The Human Protein Coevolution Network", "Genome research", 2009, 0,"", 0, "", [8],  [], 1 , "http://www.genome.org/cgi/doi/10.1101/gr.092452.109"),

new aPaper(17,"Xu, YongBai and Tillier, E. R. M", "Regional covariation and its application for predicting protein contact patches", "PROTEINS: Structure, Function and Bioinformatics", 2010, 78, "548-58", 0, "", [9],  [], 1 , "http://www3.interscience.wiley.com/journal/122540783/abstract"),

new aPaper(18,"Clark, Greg W. and Tillier E. R. M","Loss and gain of GroEL in the Mollicutes","Biochemistry and Cell Biology", 2010, 88 , "185-194", 0, "",[], [], 3, "http://www.nrcresearchpress.com/doi/abs/10.1139/O09-157"),

new aPaper(19,"Clark, Greg W. Dar, V., Bezginov, A, Yang, J.M. and Tillier E. R. M","Using Coevolution to predict protein-protein interactions","Methods in Molecular Biology", 2011, 781, "237-56", 0, "", [8], [7], 1, "http://www.springerlink.com/content/l0hm46t600p1m536/#section=953411@page=1"),

new aPaper(20,"Rodionov, A., Bezginov, A, Rose, J. and Tillier E. R. M","Faster Coevolution Detection of Proteins using Maximum Similar Cliques","Proceedings of the first ACM International Conference on Bioinformatics and Computational Biology", 2010, 0, "484-486", 0, "", [8], [7], 1, "http://portal.acm.org/citation.cfm?id=1854865"),

new aPaper(21,"Rodionov, A., Bezginov, A, Rose, J. and Tillier E. R. M","A new, fast algorithm for detecting protein coevolution using Maximum Similar Cliques","Algorithms Mol Biol", 2011, 6, "17", 0, "", [8], [7], 1, "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130660/"),

new aPaper(22,"Laura A. Hug, Maryam Salehi, Paulo Nuin, Elisabeth R. Tillier, and Elizabeth A. Edwards","Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp.","Applied and Environmental Microbiology",2011, 77,"5361-5369", 15, "",[7], [], 3 ,"http://aem.asm.org/cgi/content/full/77/15/5361?view=long&pmid=21666017"),

new aPaper(1, "Feng, S. and E.R.M. Tillier", "A Fast and Flexible Approach to Oligonucleotide Probe Design for Genomes and Gene Families.", "Bioinformatics", 2007, 23, "1188-1194",0,"",[7],[],3,"http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm114?ijkey=5uzgqmUzBac6SJX&keytype=ref"),

new aPaper(2, "Tillier, E. R. M., L. Biro, G. Li and D. Tillo", "Maximizing Co-Evolutionary dependencies to discover interacting proteins.", "PROTEINS: Structure, Function and Bioinformatics", 2006, 63, "822-31", 0, "",[5],[], 1, "http://www3.interscience.wiley.com/cgi-bin/abstract/112596985/"),

new aPaper(3, "Nuin PAS., Wang Z., and E.R.M. Tillier","The accuracy of several multiple sequence alignments for proteins"," BMC Bioinformatics", 2006, 7, "471", 0, "", [],[],1,"http://www.biomedcentral.com/1471-2105/7/471"),

new aPaper(4, "Burgetz. I.J, , Shariff S., Pang A. and E.R.M Tillier", "Positional Homology in Bacterial Genomes.", "Evolutionary Bioinformatics Online", 2006, 2, "42-65", 0, "", [], [6], 3, "http://www.la-press.com/EBO-2-Burgetz(Pr).pdf"),

new aPaper(5, "Wang, Z. and E.R.M. Tillier", "Aligning Two RNA Secondary Structures with l-Block.", "Biomolecular Engineering", 2007, 24, "321-326 ", 0, "", [], [], 2, "http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRM-4N5TNHB-3-7&_cdi=6238&_user=994540&_orig=search&_coverDate=09%2F30%2F2007&_sk=999759996&view=c&wchp=dGLzVtb-zSkWA&md5=819853b81dae945f9d1eb2b9f73c7c69&ie=/sdarticle.pdf"),

new aPaper(6, "Wang, Z. and E.R.M. Tillier", "A Bayesian approach to pairwise RNA Secondary Structure Alignment", "CICB ", 2006, 0,"accepted",0,"",[],[],2,"http://www.uhnresearch.ca/labs/tillier/papers/CICB.pdf"),

new aPaper(7, "Pang, A., Smith A., Nuin P., and Tillier, E. R. M.", "SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution", "BMC Bioinformatics", 2005, 6 , "236", 0, "", [3], [], 1, "http://www.biomedcentral.com/1471-2105/6/236"),

new aPaper(8, "Elisabeth R. M. Tillier and Thomas W. H. Lui", "Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments", "Bioinformatics", 2003, 19, "750-755", 0, "", [2], [4], 1, "http://bioinformatics.oupjournals.org/cgi/content/abstract/19/6/750?etoc"),

new aPaper(9, "Thomas W. H. Lui and Elisabeth R. M. Tillier", "Finding the functional amino acid associations with and without assuming the protein sequence phylogeny", "Joint Conference on Information Science", 2003, 0, "855-856", 0, "", [], [], 1, "http://www.uhnresearch.ca/labs/tillier/papers/ET_JCIS2003.pdf"),

new aPaper(10, "Shalini Veerassamy, Andrew Smith and Elisabeth R. M. Tillier", "A transition probability model for amino acid substitutions from BLOCKS", "J. Computational Biology", 2003, 10, "997-1010", 6, "", [6], [1], 2, "http://www.uhnresearch.ca/labs/tillier/pmb/pmb.pdf"),

new aPaper(11, "Andrew Smith, Thomas W. H. Lui and Elisabeth R. M. Tillier", "Empirical substitution models for Ribosomal RNA", "Mol Biol Evol", 2004, 21, "419-427", 0, "", [1], [5], 2, "http://mbe.oupjournals.org/cgi/content/full/msh029?ijkey=57GtzbqaGDNt6&keytype=ref"),

new aPaper(12, "Tillier, E. R. M. and R. A. Collins", "Replication orientation affects the rate and direction of bacterial gene evolution", "Journal of Molecular Evolution", 2000, 51, "459-463", 0, "", [], [], 3, "http://link.springer.de/link/service/journals/00239/papers/0051005/00510459.pdf"),

new aPaper(13, "Tillier, E. R. M. and R. A. Collins", "Genome Rearrangement by Replication-Directed Translocation", "Nature Genetics", 2000, 26, "195-197", 0, "", [], [3], 3, "http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v26/n2/full/ng1000_195.html"),

new aPaper(14, "Tillier, E. R. M. and R. A. Collins", "The Contributions of Replication Orientation, Transcription Orientation and Signal Sequences to Base-Composition Asymmetries in Prokaryotic Genomes", "Journal of Molecular Evolution", 2000, 50, "249-257", 0, "", [], [2], 3, "http://link.springer.de/link/service/journals/00239/papers/0050003/00500249.pdf"),

new aPaper(15, "Tillier, E. R. M. and R. A. Collins", "High apparent rate of simultaneous compensatory base-pair  substitutions  in ribosomal RNA", "Genetics", 1998, 148, "1993-2002", 0, "", [1], [], 2,"")

);


//  new aPaper(number, "authors", "title", "journal", year, volume, "pages", issue, "Abstract", [SoftwareArray],  [DataArray], inProject, "manuscriptURL"),

//---------------------------------------------------------------------------------------------
// Projects
//  format for new entries:
//
//  new aProject(number, "long title", "short title", "description", [PapersArray]),
//
//  number: non-zero integer - will be used as referencing number for papers, software & data
//   & not for sorting
//  "long title", "short title", "description": all strings
//  "short title" is optional - should be in Initial Capitals; leave empty (""), if desired, 
//  or use the long title
//  PapersArray: array of comma-separated integer references to aPaper numbers within square 
//  brackets; use empty square brackets ("[]") if none
//  arrays are used in case a project has more than one paper associated with it
//
//  each aProject entry within the Projects array is followed by a comma, except the last
//  pre-sorting may be done (e.g. most interesting/important first); by default, all project 
//  titles appear on the front (home) page, but may be limited by changing the value of 
//  NumberOfProjectsOnFrontPage, in the <head> portion of the home.htm file, to a number less 
//  than the total number of aProject entries
//  don't use quotation marks (") within string entries; use &quot; or single quote (')
//  no line breaks within string entries or within argument list
//  when viewed with "no wrap", each entry should be all on one line
//---------------------------------------------------------------------------------------------

Projects = new Array(
new aProject(1, "Protein sequence analysis and Protein-Protein Interactions", "Protein sequence analysis", "We develop tools for protein sequence analysis that allow us to infer functional relationships between the amino acids in a sequence and to predict protein-protein interactions. ", [2,3,7,8,9,16,17,18]),
new aProject(2, "Modeling and simulation of sequence evolution", "Evolutionary Models", "The analysis tools we and others develop for sequence analysis often require accurate models of sequence evolution.", [5,6,7,10,11,15]),
new aProject(3, "Bacterial genomes and Metagenomes", "Bacterial Genomes and Metagenomes", "After having analyzed patterns of sequence and genomic evolution in bacterial genomes, we are embarking on the study of the gene distribution and expression patterns in environmental communities. Stay tuned ...", [1,4,12,13,14,18])

);

//---------------------------------------------------------------------------------------------
// Software Programs
//  format for new entries:
//
//  new aProgram(number, "title", "description", "instructions", "WindowsURL", "UnixURL", "MacURL",[PapersArray]),
//
//  number: non-zero integer - will be used as referencing number for papers, projects & 
//  data, & not for sorting
//  "title", "description", "instructions", "WindowsURL", UnixURL": all strings
//  "title" refers to something like "ProgramName version2"
//  "description" is brief; "instructions" may be long; leave empty (""), if desired
//  URL strings must include "http://" if off-site; these are the filenames for downloading; 
//  leave blank ("") if not available in one platform version or another
//  PapersArray: array of comma-separated integer references to aPaper numbers within square 
//  brackets; use empty square brackets ("[]") if none
//  an array is used in case a program has more than one paper associated with it
//
//  each aProgram entry within the Programs array is followed by a comma, except the last
//  pre-sorting may be done (e.g. most interesting/important first); only the first few will 
//  appear on the front (home) page, as determined by the value of 
//  NumberOfSoftwareItemsOnFrontPage in the <head> portion of the home.htm file
//  don't use quotation marks (") within string entries; use &quot; or single quote (')
//  no line breaks within string entries or within argument list
//  when viewed with "no wrap", each entry should be all on one line
//---------------------------------------------------------------------------------------------

Programs = new Array(


new aProgram(1, "rRNA phylogeny", "A program package to phylogenetic analyses (using Phylip) of rRNA using a matrix of empirical substitution rates and the OTRNA model.", "<h5>Description of Programs</h5><ul><li><b>4to20</b> translates DNA/RNA sequences to <i>rRNA</i>-coded sequences in 20-letter code<br><u>Input</u>: <ul><li>rRNA structure in .bpseq format (see <a href='http://www.rna.icmb.utexas.edu/'>Comparative RNA Web Site</a> for details)<li>rRNA</i> alignment in <i>fasta</i> format<br>the first sequence should be that of the corresponding <i>.bpseq</i> structure file</ul><u>Output</u>: <ul>  <li>Coded <i>rRNA</i> alignment in both <i>fasta</i> and <i>phylip</i> formats.</ul> <li><b>20to4</b> translates <i>rRNA</i>-coded sequences to 4-letter code<br> <u>Input</u>: <ul> <li>rRNA-coded sequences in <i>fasta</i> or <i>phylip</i> format</ul> <u>Output</u>:   <ul> <li>dna sequences in <i>phylip</i> format</ul><li><b>rnadist</b> performs Distance analysis using the OTRNA model and gamma-distributed rates. <br> <u>Input</u>: <ul> <li>coded rRNA sequences file in <i>fasta</i> format <li>Gamma parameters for single-stranded sites and for double-stranded sites (enter 0 for equal rates)</ul> <u>Output</u>: <ul> <li>Distance matrices (opper triangular) include: <ul> <li>Ks.txt for single stranded sites only - Kimura (1981) model <li>Kd.txt for double stranded sites only - OTRNA model <li>KsKd.txt for both - weighted average</ul> </ul> <li><b>rRNAdist</b>, <b>rRNAml</b>, <b>rnaml</b>: modified versions of <i>protdist</i>, <i>protml</i>, <i>protmlk</i> from <a href='http://evolution.genetics.washington.edu/phylip.html'>PHYLIP</a> to use the rRNA matrices. <li><b>etseqgen</b>: modification of  <a href='http://evolve.zoo.ox.ac.uk/software.html?id=pseqgen'>PSeq-gen</a> to use the PMB model or the Bacterial SSU rRNA model. <br> <u>Input</u>: <ul> <li>tree file <li>choose PMB or RNA for substitution model (default is PMB)</ul> <u>Output</u>: <ul> <li>protein sequences or coded rRNA sequences in <i>fasta</i> format</ul> </ul>", "dependent_files/RNA/rRNA_dos.zip", "dependent_files/RNA/rRNA_unix.tar.Z", "", [11,15]),

new aProgram(2, "Dependency <i>v2.1</i>", "A program using <i>Multiple Interdependency</i> to detect functional interactions between amino acids in proteins.", "Update 2009- see <a href='http://www.uhnresearch.ca/labs/tillier/PatchDWEB/PatchDWEP.php'>PatchD Web Server</a> <br><br>This version of the dependency program allows for variable statistical parameters. <br> The input file does not have to be in the same location as the dependency program. <br>When output switch = 0, only gamma outliers will be produced. If the switch = 1, then a separate file that contains R for all pairs in S1 will be created. <br> <Phylogenetic method> In this release we allow either the sum Mutual Information or the sum Self Information (Original method) to be used for calculating the phylogenetic signal <p> <b>USAGE:</b> at the command line, type: <br> dependency &lt;input_file&gt; &lt;denominator significance&gt; &lt;min pairs for denominator significance&gt; &lt;mutual info significance (nominator)&gt; &lt;min pairs for mutual info&gt; &lt;output_dir&gt; &lt;output switch&gt &lt;phylogenetic signal method (denominator) &gt ; <br>e.g. dependency example_seq.txt 2.58 5 2.58 5 . 1  2 <br> <p><u>Note</u>: if only <i>input file</i> is provided in the command line, the default statistical parameters would be 2.58, 5, 2.58, 5, 2, respectively, the output file will be placed in the current directory and the S1 file will also be produced. <br> Windows GUI now available <br> <a rowspan=2 align='right'><img width='200' src='depend2/depend.png'></a> <br>", "dependent_files/depend2/dependencyGUI.v2.1.zip", "dependent_files/depend2/dependency.v.2.1.tar.gz", "", [8]),

new aProgram(3, "Simprot <i>v1.03</i>", "A program to simulate protein evolution by substitution, insertion and deletion","<a href='http://www.uhnresearch.ca/labs/tillier/simprotWEB/simprotWEB.php'>Simprot Web Server</a><p>Simprot Introduction<br>--------------------<br>Protein evolution has been largely modelled by considering the amino acid substitution<br>process; however they have been few studies of the process of insertion and deletion. <br>Simprot allows for several models of amino acid substitution (PAM, JTT <br>and PMB), allows for gamma distributed sites rates according to Yang's model, and implements a <br>parameterised Qian and Goldstein distribution model for insertion and deletion. <br> <br> Version 1.01 New features and improvements:<br> <br>- root sequence input - from a sequence file or directly on the interface <br>- ability to simulate multiple protein segments with distinct evolutionary histories, either different parameters or different phyloegenetic trees or both <br>- automatic detection of taxa when different trees are used to simulate multiple segments <br> <br> Version 1.02 improves memory management allowing for bigger trees and faster execution <br> <p> <br> Version 1.03 adds the ability to input a user-defined indel distribution, output the length of indels as they are generated, and have unequal frequencies of insertion and deletion<br> <p> <br> <a rowspan=2 align='right'><img width='200' src='simprot/simprot.png'></a> <br> ", "simprot/simprot1.01.zip", "simprot/simprot1.03_linux.tar.gz","",[7]),

new aProgram(4, "PMB matrix", "Implementation of PMB in Pseq-gen and Data file to use with Ziheng Yang's PAML for protein sequence analysis. PMB now available in Phylip. ", "This version uses the <a href='ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blocksplus-01Aug01/minus.dat.Z'>Aug '01 version of Blocks+</a>. <br> This <i>pmb.dat</i> file can be used with <i>codeml</i> from Ziheng Yang's <a href='http://abacus.gene.ucl.ac.uk/software/paml.html'>PAML package</a>. Otherwise, the PMB model is now available in Joe Felsenstein's <a href='http://evolution.genetics.washington.edu/phylip.html'>Phylip package</a>. <br> Also see <li><b>etseqgen</b>: modification of  <a href='http://evolve.zoo.ox.ac.uk/software.html?id=pseqgen'>PSeq-gen</a> to use the PMB model or the Bacterial SSU rRNA model. <br> <u>Input</u>: <ul> <li>tree file <li>choose PMB or RNA for substitution model (default is PMB)</ul> <u>Output</u>: <ul> <li>protein sequences or coded rRNA sequences in <i>fasta</i> format</ul> </ul>", "", "dependent_files/pmb/etseqgen.tar.Z" ,"",[10]),

new aProgram(5, "Codep", "Maximizing co-evolutionary interdependencies to discover interacting proteins", "Update 2009. See  MatrixMatchMaker <a href='http://www.uhnresearch.ca/labs/tillier/FMMMWEB/FMMMWEB.php'>MMM Web Server</a> <br><br>Codep V.1.0 Written by Laurence Biro, Ginny Li and Elisabeth Tillier. Copyright University Health Network. Codep is protected by copyright and trade-mark and may not be copied or rewritten without prior written permission. However, you may download and use Codep. only for non-commercial, personal or educational use and University Health Network must be acknowledged as the source of Codep. Permission to use Codep. for commercial purposes must be obtained from University Health Network at www.uhnres.utoronto.ca/rbdo . By downloading and/or using Codep. you are agreeing to these terms. <br>&nbsp; <p> A compiled version for Linux is included in this distribution. Executables for other platforms can be requested from the authors by contacting e.tillier@utoronto.ca. <br>All questions comments and bug reports are welcome. <br>&nbsp; <p>The compiled C++ program is run from a Perl script which handles all the input switches and will convert alignments to the required format for analysis. The help is provided by the following perldoc which&nbsp; can be obtained by typing <p>perldoc Codep.pl <p>", "", "codep/Codep_linux.tar.gz", "",[2]),

new aProgram(6, "AutoMatrix", "AutoMatrix is a Matlab script that will calculate an instantaneous rate matrix (and its eigen value decompostion for use in phylip programs) from a series of substitution count matrices calculated for different levels of sequence identity/similarity."," The code assumes 20x20 matrices. <br>Note that a solution can not always be found. <br>Please read Veerassamy et al J. Comp Biol (2003) for details and before emailing me with questions. <br> <br> AutoMatrix takes a single parameter: the directory where the count matrices .fij files are stored (see example directory provided for file format)<br> The output files are:<br> pmb_deriv: for each matrix the observed distance and its derivative<br> pmb_fit: the polynomial that fits the curve<br> pmb_exp.txt: the solution equation for the expected distance <br> pmb_dist.txt: the observed and expected distance for each matrix<br> rate_matrix: the universal rate matrix<br> freqs.txt: the aa frequencies calculated over the sum of all matrices<br> matrix.txt: for phylip <br> eigen.txt: for phylip", "", "dependent_files/pmb/AutoMatrix.tar.gz" , "", [10]),

new aProgram(7, "ProDesign", "Prodesign is used to generate oligonucleotide probes for genes and gene families", " <br> ProDesign is still under development.  <br> <a rowspan=2 align='right'><img width='200' src='ProDesign/prodesign.png'></a> <br> A Web server with limited functionality is available. <br> <br> <a href='http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html'>ProDesign Web Server</a> <br>","", "ProDesign/Downloads/ProDesign1.0.tar.gz","",[1,22]),

new aProgram(8, "MatrixMatchMaker","MMM predicts interacting proteins using coevolution ","New Web Server<br><a href='http://www.uhnresearch.ca/labs/tillier/MMMWEBvII/MMMWEBvII.php'>New MMM Web Server</a> <br>","","MMMWEBvII/mmmWithL_linux.gz","",[16,19,20,21]),

new aProgram(9, "PatchD","Regional covariation for predicting protein contact patches", "Web Server now running<br><a href='http://www.uhnresearch.ca/labs/tillier/PatchDWEB/PatchDWEP.php'>PatchD Web Server</a> <br>","","","",[17])



);

//---------------------------------------------------------------------------------------------
// Data & Plots
//  format for new entries:
//
//  new aDataItem(number, "title", "description", "update date", "instructions", "URL", [PapersArray]),
//  number: non-zero integer - will be used as referencing number for papers, projects & 
//  programs, & not for sorting
//  "title", "description", "update date", "instructions", "URL": all strings
//  "title" refers to something like "ProgramName version2"
//  "description" is meant to be brief, "instructions" long; leave empty (""), if desired
//  "update date" is optional; leave empty is desired ("")
//  URL strings must include "http://" if off-site; these are the filenames for downloading; 
//  PapersArray: array of comma-separated integer references to aPaper numbers within square 
//  brackets; use empty square brackets ("[]") if none
//  an array is used in case a data item has more than one paper associated with it
//
//  each aDataItem entry within the DataItems array is followed by a comma, except the last
//  pre-sorting may be done (e.g. most interesting/important first); only the first few will 
//  appear on the front (home) page, as determined by the value of 
//  NumberOfDataItemsOnFrontPage in the <head> portion of the home.htm file
//  don't use quotation marks (") within string entries; use &quot; or single quote (')
//  no line breaks within string entries or within argument list
//  when viewed with "no wrap", each entry should be all on one line
//---------------------------------------------------------------------------------------------

DataItems = new Array(
new aDataItem(1, "PMB matrix", "Data file to use with Ziheng Yang's PAML for protein sequence analysis.", "This version uses the <a href='ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blocksplus-01Aug01/minus.dat.Z'>Aug '01 version of Blocks+</a>.", "This <i>pmb.dat</i> file can be used with <i>codeml</i> from Ziheng Yang's <a href='http://abacus.gene.ucl.ac.uk/software/paml.html'>PAML package</a>. Otherwise, the PMB model is now available in Joe Felsenstein's <a href='http://evolution.genetics.washington.edu/phylip.html'>Phylip package</a>.", "dependent_files/pmb/pmb.dat", [10]),

new aDataItem(2, "Skew Plots (Supplementary Information)", "Base composition asymmetries in prokaryotic genomes.", "July 2004", "", "http://www.uhnresearch.ca/labs/tillier/Skew.html", [14]),

new aDataItem(3, "X Plots (Supplementary Information)", "Replication-directed gene translocation in prokaryotic genomes.", "July 2004", "", "http://www.uhnresearch.ca/labs/tillier/Xplots.html", [13]),

new aDataItem(4, "Dependency", "Postscript (.ps) file of Supplementary Figures and Tables", "", "Refer to the paper for details.", "dependent_files/depend2/supplementary.ps", [8]),

new aDataItem(5, "rRNA matrices", "", "", "Download file matrices.tar.Z","dependent_files/RNA/matrices.tar.Z", [11]),

new aDataItem(6, "Analysis of COG database positional homologs that are not BBH ", "Supplementary Data for 66 genomes", "","Refer to the paper for details.","dependent_files/orthologs/Sup_Table.html", [4]),

new aDataItem(7, "MMM-D ", "", "MMM-D is used for querying HUMAN and YEAST proteins with high MMM scores and all their known protein-protein interactions","","http://tillier.uhnres.utoronto.ca/MMMD.php", [16])

);
//  new aDataItem(number, "title", "description", "update date", "instructions", "URL", [PapersArray]),

//---------------------------------------------------------------------------------------------
// People
//  format for new entries:
//
//  new aPerson(number, "name", "optional description", "picture URL", [PapersArray]),
//  number: non-zero integer - will be used as referencing number for papers, projects & 
//  programs, & not for sorting
//  "name", "optional description", "picture URL": all strings
//  URL strings must include "http://" if off-site; these are the filenames for downloading; 
//  PapersArray: array of comma-separated integer references to aPaper numbers within square 
//  brackets; use empty square brackets ("[]") if none
//  an array is used in case a person has more than one paper associated with him/her
//
//  each aPerson entry within the People array is followed by a comma, except the last
//  pre-sorting may be done (e.g. most recent first)
//  don't use quotation marks (") within string entries; use &quot; or single quote (')
//  no line breaks within string entries or within argument list
//  when viewed with "no wrap", each entry should be all on one line
//---------------------------------------------------------------------------------------------

People = new Array(

new aPerson(29, "Ewa Wywial", " Post-doctoral fellow", "", []),
new aPerson(25, "Alexandr Bezginov", " Graduate Student", "", [19,20,21]),
new aPerson(24, "Greg Clark", " Graduate Student", "http://www.uhnresearch.ca/labs/tillier/pictures/greg.jpg", [18,19]),
new aPerson(28, "Nisa Dar", " Research associate", "", [19]),
new aPerson(6, "", "cluster 2", "http://www.uhnresearch.ca/labs/tillier/pictures/crw_0595.jpg", []),
new aPerson(8, "Previous lab members", "", "", []),
new aPerson(26, "Maryam Salehi", " Graduate Student", "", [22]),
new aPerson(1, "YongBai Xu", " Graduate Student", "http://www.uhnresearch.ca/labs/tillier/pictures/YongBai.jpg", [17]),
new aPerson(27, "Mary Yang", "NSERC Summer student","",[19]),
new aPerson(19, "Paulo Nuin", " Post-Doc <br>  <a href='http://genedrift.org'>Paulo's own site </a> ","pictures/paulo&joy.JPG",[3,7]),
new aPerson(23, "Shengzhong Feng" , "Visiting Professor", "pictures/feng.JPG",[1]),
new aPerson(20, "Joy Abramson", " Graduate Student", "pictures/paulo&joy.JPG", []),
new aPerson(2, "Zhuozhi Wang", " Research Associate ", "pictures/zhuozhi.JPG", [3,5,6]),
new aPerson(21, "Daniel Lei", " 4th year Medical Genetics and Microbiology student", "",[]),
new aPerson(3, "Bin Tang", " Post-Doc  ", "pictures/BinTang.JPG", []),
new aPerson(4, "Desiree Tillo", " 4th year Medical Genetics and Microbiology student", "pictures/Desiree.jpg",[2]),
new aPerson(9, "Ingrid Burgetz", "research associate", "http://www.uhnresearch.ca/labs/tillier/pictures/ingrid.jpg", [4]),
new aPerson(10, "Andrew D. Smith", "research assistant (at left) <br> <a href='http://www.cmb.usc.edu/people/andrewds/'> Now at USC </a> ", "http://www.uhnresearch.ca/labs/tillier/pictures/Thomas_Andrew.jpg", [7,10,11]),
new aPerson(11, "Thomas Lui", "research assistant (at right)", "http://www.uhnresearch.ca/labs/tillier/pictures/Thomas_Andrew.jpg", [8,9,11]),
new aPerson(12, "Shalini Veerassamy ", "research assistant", "http://www.uhnresearch.ca/labs/tillier/pictures/shalini.jpg", [10]),
new aPerson(13, "Salimah Shariff", "Waterloo Coop student", "http://www.uhnresearch.ca/labs/tillier/pictures/salimah.jpg", [4]),
new aPerson(14, "Andy Pang", "Waterloo Coop student", "http://www.uhnresearch.ca/labs/tillier/pictures/Andy.jpg", [4,7]),
new aPerson(15, "Ginny Li", "Waterloo Coop Student", "http://www.uhnresearch.ca/labs/tillier/pictures/image002.jpg", [2]),
new aPerson(16, "Wendy Kwong", "summer student", "http://www.uhnresearch.ca/labs/tillier/pictures/wendy_small.JPG", []),
new aPerson(17, "Laurence Biro", "MBP summer student", "pictures/lbiro.jpg", [2]),
new aPerson(18, "Madelene Earp", "MBP summer student", "", []),
new aPerson(22, "Dan Le", "MBP summer student", "", []),
new aPerson(5, "", "cluster 1", "http://www.uhnresearch.ca/labs/tillier/pictures/cluster.jpg", [])

);

//---------------------------------------------------------------------------------------------
// do not edit the following, unless you understand what's going on
//---------------------------------------------------------------------------------------------
function aPaper(Z,A,B,C,D,E,F,G,L,H,I,J,K) {
    this.number = Z; //integer
    this.authors = A; //string
    this.title = B; //string
    this.journal = C; //string
    this.year = D; //integer
    this.volume = E; //integer
    this.pages = F; //string
    this.issue = G; //integer
    this.hasSoftware = 0;
    this.hasData = 0;
    this.SoftwareArray = H; //array
    this.DataArray = I; //array
    if (H.length) this.hasSoftware = 1;
    if (I.length) this.hasData = 1;
    this.inProject = J; //integer
    this.Abstract = L; //string
    if (arguments.length > 11) this.URL = K; //string
}
function aProject(Z,A,B,C,D) {
    this.number = Z; //integer
    this.longTitle = A; //string
    this.shortTitle = B; //string
    this.description = C; //string
    this.hasPapers = 0;
    this.PaperArray = D; //array
    if (D.length) this.hasPapers = 1;
}
function aProgram(Z,A,B,C,D,E,G,F) {
    this.number = Z; //integer
    this.title = A; //string
    this.description = B; //string
    this.instructions = C; //string
    this.forDOS = 0;
    this.forUNIX = 0;
    this.forMAC = 0;
    this.DOSURL = D; //string
    this.UNIXURL = E; //string
    this.MACURL = G; //string
    if (D.length) this.forDOS = 1;
    if (E.length) this.forUNIX = 1;
    if (G.length) this.forMAC = 1;
    this.hasPapers = 0;
    this.PaperArray = F; //array
    if (F.length) this.hasPapers = 1;
}
function aDataItem(Z,A,B,C,D,E,F) {
    this.number = Z; //integer
    this.title = A; //string
    this.description = B; //string
    this.hasUpdate = 0;
    this.updated = C; //string
    if (C.length) this.hasUpdate = 1;
    this.instructions = D; //string
    this.hasURL = 0;
    this.URL = E; //string
    if (E.length) this.hasURL = 1;
    this.hasPapers = 0;
    this.PaperArray = F; //array
    if (F.length) this.hasPapers = 1;
}
function aPerson(Z,A,B,E,F) {
    this.number = Z; //integer
    this.name = A; //string
    this.description = B; //string
    this.hasURL = 0;
    this.URL = E; //string
    if (E.length) this.hasURL = 1;
    this.hasPapers = 0;
    this.PaperArray = F; //array
    if (F.length) this.hasPapers = 1;
}

//  End -->

