changelog.html

<h2>The Triticeae Toolbox (T3) Change History</h2>
<br>
Jan 28, 2018
<ul>
<li>upgraded Pear Spreadsheet_Excel_Writer 0.9.4 and OLE 1.0.0.RC3 to fix compatibility with PHP 7
<li>upgraded File_Archive to fix compatibility with PHP 7
<li>Curate - Phenotype Results - check for required xls file 
</ul>
Jan 21, 2018
<ul>
<li>BrAPI updates
<li>Curator - plot level import - add link to source script
<li>Home page - add not that Federal government is not funded
</ul>
Jan 14, 2018
<ul>
<li>Select - Lines by Properties - add select highlighted lines
<li>Select - Markers - optimize speed for small number of markers
</ul>
Jan 7, 2018
<ul>
<li>website footer - align logo
<li>website menus - rename item to Marker Alignment to Reference
<li>Quick Search - qtl_annotations, display all columns in search results
<li>Reports - Variant Effects - fix bug that caused wrong marker name to display
<li>Login - add captcha refresh
<li>Select - subset by poly - change coding of indels
</ul>
Dec 31, 2017
<ul>
<li>JBrowse - add WheatCAP tracks from Dubcovsky Lab
<li>Apache web server - add mod_expires to enable browser cache
</ul>
Dec 17, 2017
<ul>
<li>Add ARS logo and update links from logos
<li>Select - subset markers by poly - change coding for indels to work with Flapjack
</ul>
Dec 10, 2017
<ul>
<li>Select - subset markers by poly - format output for Flapjack
</ul>
Dec 4, 2017
<ul>
<li>Analysis - Selection index - allow selection of any common line (even if not measured for all trials) then set index to null if baseline not measured
</ul>
Nov 27, 2017
<ul>
<li>Analysis - Selection index - add error checking
</ul>
Nov 20, 2017
<ul>
<li>Reports - content status - if tmp directory does not exists then create it
<li>Trial page - change row label to Breeding or Data program depending on experiment type
<li>Select breeding programs - do not depend on the breeding program of lines
</ul>
Nov 13, 2017
<ul>
<li>BrAPI - fix germplasm and maps
<li>Analysis - GWAS Results - fix selection of analysis method
</ul>
Nov 6, 2017
<ul>
<li>Download - permit negative position in genetic maps
<li>Reports - marker annotation by experiment - fix formatting
</ul>
Oct 30, 2017
<ul>
<li>Curate - remove requirement for filial generation since this value can change each year
<li>Resources - add page with tutorials
<li>Lines by Phenotype - do not show genetic characters
<li>Traits and trials - do not show genetic characters
</ul>
Oct 23, 2017
<ul>
<li>GWAS Results - add genome assembly radio selection
<li>BLAST - added links to view BLAST hits in JBrowse
</ul>
Oct 16, 2017
<ul>
<li>Breeders Datafarm Barley - fix access to website
<li>T3 Barley - fixed search by Breeding Program on home page
</ul>
Oct 9, 2017
<ul>
<li>BrAPI - fixed bugs using BrAPI validator
<li>Report - GWAS Results - chromosome location now match assembly
</ul>
Oct 2, 2017
<ul>
<li>JBrowse Wheat - added Pangenome tracks
<li>Report, Marker Annotation by Experiment - added Pangenome
<li>Physical Map Wheat Pangenome - fixed map to correct problems with unordered chromosomes
</ul>
Sept 25, 2017
<ul>
<li>QuickSearch - added qtl_annotations table
<li>Variant Effect - added RefSeq_v1 (login required)
<li>Download Genotype Phenotype Data - added notes on how to read in file with R-Scripts
</ul>
Sept 18, 2017
<ul>
<li>Use precomputed marker counts to improve performance
</ul>
Sept 11, 2017
<ul>
<li>reload 2017_WheatCAP to use 200 base pairs of flanking sequence on each side of SNP
<li>Report - Variant effects, provide download button if over 1000 entries
<li>Report - Variant effects, now works with consensus genotypes
</ul>
Sept 4, 2017
<ul>
<li>Select - add tool to subset by markers polymorphism
<li>quick search line - show if marker present in genotype experiment
<li>quick search marker - show if line present in genotype experiment
</ul>
Aug 28, 2017
<ul>
<li>modify database schema to use assembly_name in report tables
<li>recoded 2017_WheatCAP so that indels in HapMap format works with TASSEL
</ul>
Aug 21, 2017
<ul>
<li>vacation
</ul>
Aug 14, 2017
<ul>
<li>add unique page titles
</ul>
Aug 7, 2017
<ul>
<li>Report - add page with links to SIFT scores
<li>update Spreadsheet_Excel_Writer to work with PHP 7
</ul>
Jul 31, 2017
<ul>
<li>Select - Markers, order chromosome when selecting map
<li>Report - add page to assist running variant effect predictor
<li>Select - Markers, add sub menu when selecting from map
</ul>
Jul 24, 2017
<ul>
<li>make menu page generic for all species
<li>make tutorial page generic for all species
<li>update INSTALL.html page
<li>Report - Marker Report, set species specific info in config.php page
<li>Report - add menu item for reports
<li>Report - update Marker Report to show results for latest assembly
</ul>
Jul 17, 2017
<ul>
<li>Download - update VCF format to use position from genotype experiment file if no map selected
<li>update INSTALL.html page
<li>manual scripts for loading GBS files use load data infile for better performance 
</ul>
Jul 10, 2017
<ul>
<li>move visualization tools to subdirectory
</ul>
Jul 3, 2017
<ul>
<li>use settings table to store species specific info
<li>BrAPI - fix germplasm details and add commonCropName
</ul>
Jun 26, 2017
<ul>
<li>Download - fix bug in download of genetic map
</ul>
Jun 19, 2017
<ul>
<li>Select - fix bug in calculating markers in genetic maps
<li>BrAPI - add allelematrices list, fix date format
<li>BrAPI - add optional fields and fix pagination
<li>add website specific css to github
</ul>
Jun 12, 2017
<ul>
<li>Analyze - add "rank in trial" to selection index
<li>add link in footer to software availability
</ul>
Jun 5, 2017
<ul>
<li>BrAPI - fix POST call in markerprofiles to handle multiple items
</ul>
May 29, 2017
<ul>
<li>Select - fix asynchronous error in wizard
<li>Analyze - fix "Reselect" button in selection index
</ul>
May 22, 2017
<ul>
<li>Update install instructions for PHP7
<li>Add Ubuntu example in install instructions
</ul>
May 15, 2017
<ul>
<li>Remove PHPIDS requirement, recommend use of Apache ModSecurity
<li>Do not show phenotype categories if no phenotypes
<li>Revert change that broke genetic characters
</ul>
May 8, 2017
<ul>
<li>BrAPI - update pagination, calls, date format
</ul>
May 1, 2017
<ul>
<li>BrAPI - add asynchronous processing to allelematrix-search
<li>Analyze JBrowse (Wheat) - added Wheat Pangenome 2017
<li>Analyze GWAS Results - added links to UniProtKB
<li>Marker page - added links to UniProtKB
</ul>
Apr 24, 2017
<ul>
<li>links to Plant Reactome
</ul>
Apr 17, 2017
<ul>
<li>Analyze JBrowse (Oat) - added OatSeedRef100
<li>Analyze Blast (Oat) - fixed path to BLAST database files and added OatSeedRef100
</ul>
Apr 10, 2017
<ul>
<li>fixed timeout on display_phenotype.php page when there are more than 100 phenotypes measured
<li>updated BrAPI <b>calls</b> page to list current implementation
<li>add BrAPI call <b>germplasm-search</b>
<li>Analyze GWAS Results Expression (wheat and barley) - fixed bug in expVIP (wheat), added EMBL-EBI
</ul>
Apr 3, 2017
<ul>
<li>Analyze GWAS Results - added activity indicator for radio buttons
<li>Analyze GWAS Results (Wheat) - loaded new analysis from breeders data farm
</ul>
Mar 27, 2017
<ul>
<li>fix bad header in template for Pedigree import file
<li>added IBSC_v2 assembly from Ensembl
</ul>
Mar 20, 2017
<ul>
<li>update BrAPI <b>traits</b> page to match standard
<li>transfer Breeders Database phenotype data, experiments, experiment_sets to T3wheat (production)
</ul>
Mar 13, 2017
<ul>
<li>add link in side menu to clear selection
<li>add curator page to delete units
</ul>
Mar 6, 2017
<ul>
<li>fix bug in curator page for importing line properties
<li>change title on home page to indicate species and if site is sandbox
</ul>
Feb 27, 2017
<ul>
<li>security improvements to login page and PHPIDS
</ul>
Feb 20, 2017
<ul>
<li>change login page to remove restriction against special characters
<li>Update to Securimage 3.6.4 used on login page
</ul>
Feb 13, 2017
<ul>
<li>add curator page to edit units
<li>add wheat physical map (restricted use)
</ul>
Feb 6, 2017
<ul>
<li>add bin column to map locations
<li>fixed bug in curator page for importing pedigree
<li>update BLAST databases to include latest public releases
<li>update GWAS results to include WheatExpression Browser: expVIP
<li>convert to HTML5
</ul>
Jan 30, 2017
<ul>
<li>JBrowse new reference track
<li>now using wheat assembly TGACv1 - updated GWAS results, WheatIS search
<li>Traits and Trial Statistics - changed default to only display selected lines
<li>fixed bug in SQL query that prevented download of trait data
<li>add link to crop ontology
</ul>
Jan 23, 2017
<ul>
<li>Download Genotype and Phenotype Data - added file listing genotype experiments when downloading consensus genotypes
<li>Update jquery.smartmenus.js to release 1.0.1
</ul>
Jan 16, 2017
<ul>
<li>Security improvement in Phenotype trial page
<li>Fix bug in curator delete trial page
<li>Use ACTG coding in select lines by haplotype page
</ul>
Jan 9, 2017
<ul>
<li>Modify analyze, traits and trials table to include summary table
<li>Change menu item from "QTL Report" to "GWAS Results"
<li>Change About T3, Overview from Unix to Linux
<li>Change link for GitHub from Dave-Matthews to ClayBirkett
</ul>
Jan 2, 2017
<ul>
<li>Fix coding errors is display of pedigree
</ul>
Dec 19, 2016
<ul>
<li>Refactor curate, phenotype trial to permit xlsx input files
<li>Fix login page to assign account permissions on sandbox
</ul>
Dec 5, 2016
<ul>
<li>Fix login page to assign new account correct permissions
<li>Fix Traits and Trials Table page to show correct Trial Means
</ul>
Nov 21,2016
<ul>
<li>Fix bug that caused failure in building genotype allele_bymarker and allele_byline tables
<li>Fix bug that caused incorrect filter statistics for selected set of markers (as opposed to selecting all markers)
<li>Fix bug that prevented downloading genotype information when only one marker was selected
</ul>
Nov 14, 2016
<ul>
<li>Upgrade fail2ban 0.9.4 software on triticeaetoolbox.org machine to fix connections from mirror machine at Cornell
<li>the calculate trial means from plot level data page in the curators menu will not update the traits listed in experiments table (previously this was only working when uploading trial means)
</ul>
Nov 7, 2016
<ul>
<li>fixed out of memory error when analyzing or downloading large data set
<li>Genetic Maps - added Physical Map for Barley HapMap, private until release of 2016 Barley Assembly
<li>JBrowse - updated to JBrowse 1.12.1
<li>JBrowse - added "Genome" menu item for selecting dataset
<li>JBrowse - added Barley "Variations in HapMap" track
<li>JBrowse - fixed Wheat "Variations in T3" track for markers mapped only to scaffold
</ul>
Oct 31, 2016
<ul>
<li>Curate / Phenotype Results - fix problem loading duplicate plot level data
<li>Download / Weather Data - added option for viewing only airport stations, these have more complete data
</ul>
Oct 24, 2016
<ul>
<li>Analyze / QTL Report - only display entry if there is at least one GWAS that has a q-value < 0.05
<li>remove "close button" from data usage popup
<li>Analyze / Traits and Trials Table - move legend to top of page
<li>Analyze / Traits and Trials Table - fix problem where means row does not match column data
<li>Select /Wizard - fixed problem with query while selecting breeding and data programs
<li>Genetic Maps - added Physical map for Barley, private until release of 2016 Barley assembly
<li>Genetic Maps - change schema to allow for private maps
</ul>
Oct 17, 2016
<ul>
<li>Data Submission - added new tutorials
</ul>
Oct 10, 2016
<ul>
<li>updated jquery.smartmenus.js to release 1.0.0
</ul>
Oct 3, 2016
<ul>
<li>Barley: add QTL Report page
</ul>
Sept 16, 2016
<ul>
<li>Download / Weather Data - added tool for downloading weather data
</ul>
Aug 29, 2016
<ul>
<li>Login - upgrade to Secureimage PHP Captcha
<li>Select / Wizard - add select by experiment to step 1
</ul>
Aug 15, 2016
<ul>
<li>Analyze / Optimized Training Set - added tool for selecting training set 
</ul>

July 29, 2016
<ul>
<li>Analyze / Filter Outlier - added tool for finding outlier data
</ul>
July 11, 2016
<ul>
<li>upgrade to Pear Mail v1.3.0
<li>updated PHPExcel to v1.8.1
</ul>

Jun 17, 2016
<ul>
<li>added option to download genotype data in VCF format
</ul>

Mar 18, 2016
<ul>
<li>change ontology link from gramene to planteome
</ul>

Feb 9, 2016
Wheat: add QTL Report page

Sept 15, 1015
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