-
Notifications
You must be signed in to change notification settings - Fork 3
/
about.php
executable file
·144 lines (136 loc) · 6.72 KB
/
about.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
<?php
require 'config.php';
$pageTitle = "About";
require $config['root_dir'].'includes/bootstrap.inc';
require $config['root_dir'].'theme/normal_header.php';
?>
<h1>About T3</h1>
<div class="section">
<h3>Project Description</h3>
<p>The Triticeae Toolbox (T3) is the web portal for data generated by
the <a href="http://triticeaecap.org/" title="">Triticeae Coordinated
Agricultural Project</a> (T-CAP), funded by
the <a href="http://usda.gov/wps/portal/usda.usdahome">National
Institute for Food and Agriculture (NIFA)</a> of the United States
Department of Agriculture (USDA). It also contains data from US Uniform Regional Nurseries,
supported by the <a href="http://scabusa.org/">US Wheat and Barley Scab Initiative</a>.
The database was initially developed
as <b>The Hordeum Toolbox</b> (THT) to hold barley data generated by
the Barley CAP project (2006-2010).
<b>T3 Barley</b> hods data generated for <i>Hordeum vulgare L</i>. <b>T3
Wheat</b> holds data generated for <i>Triticum</i> spp. <b>T3 Oat</b> holds data generated for <i>Avena</i>. All are
being enhanced in database performance, community curation and user
tools. T3 contains germplasm line information, pedigree, genotype and
phenotypic data from breeding programs participating in the CAP and
core germplasm collections maintained by
the <a href="http://www.ars.usda.gov/Main/docs.htm?docid=21891">USDA
National Small Grains Collection.</a>
<h3>Dataset Acknowledgments</h3>
<b>9K wheat iSelect assay</b>
<p>The 9,000 SNP wheat iSelect assay was designed by research groups
funded by the USDA National Institute of Food and Agriculture (grant
CRIS0219050; PI: E. Akhunov; co-PIs: S. Chao, G. Brown-Guedira,
D. See, M. Sorrells) and the Grains Research and Development
Corporation (GRDC), Australia (PI: Matthew Hayden). The details of
assay design can be obtained from
the <a href="http://wheatgenomics.plantpath.ksu.edu/snp/">USDA wheat
SNP development project</a>
and <a href="http://wheatgenomics.plantpath.ksu.edu/IWSWG/">International
Wheat SNP Working Group</a> websites.
<h3>T3 Team</h3>
<p>
<style type="text/css">
#thtteamtbl td{text-align:left} .strong{font-weight:bold}
</style>
<table id="thtteamtbl" border="0" cellpadding="0" cellspacing="0">
<thead>
<tr>
<th>Name</th><th>Affiliation</th><th>Role</th>
</tr>
</thead>
<tr><td class="strong">Jean-Luc Jannink</td><td>USDA-ARS, NAA, RWHCAH,
Ithaca, NY</td><td>Project coordinator</td></tr>
<tr><td class="strong">Mark Sorrells</td><td>Cornell University, Ithaca,
NY</td><td>Project coordinator</td></tr>
<tr><td class="strong">Clay Birkett</td><td>USDA-ARS, NAA, RWHCAH,
Ithaca, NY</td><td>Database programming and development</td></tr>
<tr><td class="strong">Clare Saied</td><td>Cornell University,
Ithaca, NY</td><td>Data curator</td></tr>
<tr><td class="strong">Dave Matthews</td><td>Cornell University, Ithaca,
NY</td><td>Database development, GrainGenes collaborator</td></tr>
<tr><td class="strong">Shiaoman Chao</td><td>USDA-ARS Biosciences
Research Lab, Fargo, ND</td><td>SNP data production and
curation</td></tr>
<tr><td class="strong">Peter Bradbury</td><td>USDA-ARS, NAA, RWHCAH,
Ithaca, NY</td><td>Pedigree information and links
to <a href="http://www.maizegenetics.net/tassel"
title="">TASSEL</a></td></tr>
<tr><td class="strong">Mike Bonman</td><td>USDA-ARS, Aberdeen,
ID</td><td>GRIN collaboration</td></tr>
<tr><td class="strong">Harold Bockelman</td><td>USDA-ARS, Aberdeen,
ID</td><td>GRIN collaboration</td></tr>
<tr><td class="strong">Tim Close</td><td>Botany and Plant
Sciences<br/>University of California<br/>Riverside, CA</td><td>Assembly
and SNP context information from <a href="http://harvest.ucr.edu/"
title="">HarvEST: Barley</a></td></tr>
<tr><td class="strong"><a href="http://triticeaecap.org/about/t-cap-directory/">T-CAP
Participants</a></td><td>Throughout the U.S.A.</td><td>Data collection
and contribution</td></tr>
</table>
</p>
<h3>THT Alumni</h3>
<style type="text/css">
#thtteamtbl td{text-align:left} .strong{font-weight:bold}
</style>
<table id="thtteamtbl" border="0" cellpadding="0" cellspacing="0">
<thead>
<tr>
<th>Name</th><th>Affiliation</th><th>Role</th>
</tr>
</thead>
<tr><td class="strong">Julie A. Dickerson</td><td>Electrical and
Computer Engineering, Iowa State University</td><td>Principal
Investigator<td></tr>
<tr><td class="strong">Roger P. Wise</td><td>USDA-ARS<br/>Department of
Plant Pathology<br/>Iowa State University</td><td>Principal
Investigator</td></tr>
<tr><td class="strong">Jennifer Kling</td><td>Dept. of Crop and Soil
Science Oregon State University</td><td>Phenotype and pedigree data
curation </td></tr>
<tr><td class="strong">Shreyartha Mukherjee</td><td>Bioinformatics and
Computational Biology, Iowa State
University</td><td>Developer/Bioinformatics</td></tr>
<tr><td class="strong">Kartic Ramesh</td><td>Computer Science, Iowa
State University</td><td>Developer</td></tr>
<tr><td class="strong">Gavin Monroe</td><td>Software Engineering, Iowa
State University</td><td>Developer</td></tr>
<tr><td class="strong">Ethan Wilder</td><td>Computer Engineering, Iowa
State University</td><td>Developer</td></tr>
<tr><td class="strong">Yong Huang</td><td>Bioinformatics and
Computational Biology, Iowa State University</td><td>
Developer/Bioinformatics</td></tr>
</table>
<p>
<h3>Collaborators</h3>
<a href="http://bioinf.scri.ac.uk/germinate" title="">The James Hutton Institute</a>
Development Team (David Marshall, Paul Shaw)<br/>
<a href="http://www.plexdb.org/" title="">PLEXdb</a> Development Team at
Iowa State University (Ethy Cannon and Sudhansu Dash)<br/>
<a href="http://www.gramene.org/" title="">Gramene</a> Database (Doreen
Ware)<br/>
<a href="http://wheat.pw.usda.gov/" title="">GrainGenes</a> Database
(David Matthews) USDA/ARS, Cornell University<br/>
<p>
<h3>Software availability</h3>
The T3 software is available under the GNU General Public License
(<a href="docs/LICENSE">LICENSE</a>) and may be downloaded from
<a href="https://github.com/TriticeaeToolbox/T3">GitHub</a>.<br>
It requires Linux, Apache, MySQL, and PHP. Details are in the <a href="docs/INSTALL.html">INSTALL</a> document.<br>
A list of recent changes to the T3 software are in the <a href="changelog.html">Change Log</a> document.<br>
The database schema in .sql format
is <a href="docs/T3wheat_schema.sql">here</a>. Graphical diagrams are
available in MySQL Workbench (<a href="docs/T3wheat_schema_May2012.mwb">.mwb</a>)
format and <a href="docs/T3wheat_schema_May2012.png">.png</a> format.
</div>
</div>
<?php require $config['root_dir'].'theme/footer.php';