cgi-bin/solanaceae-project/sol-bioinformatics/index.pl

   1
   2 use strict;
   3 use Tie::Function;
   4 use CXGN::Page;
   5 use CXGN::Page::FormattingHelpers qw/ page_title_html info_section_html blue_section_html/;
   6
   7 my $page=CXGN::Page->new('SOL Bioinformatics','Lukas');
   8 $page->header('SOL Bioinformatics Page');
   9
  10 print page_title_html("SOL Bioinformatics Resources");
  11
  12 print info_section_html(title => 'Documents',
  13                         contents => <<EOHTML,
  14 <ul>
  15 <li><a href="http://docs.google.com/View?docid=dggs4r6k_1dd5p56">[Google doc]</a> SOL Bioinformatics Standards and Guidelines</li>
  16 <li><a href="http://www.ab.wur.nl/TomatoWiki">[Wiki]</a> ITAG Wiki</li>
  17 <li><a href="/static_content/solanaceae-project/docs/BAC_mapping_validation_1.ppt">[ppt]</a> Detailed IL-BAC mapping protocol. </li>
  18 </ul>
  19 EOHTML
  20                        );
  21
  22 print info_section_html(title => 'Meeting Records',
  23                         contents => <<EOHTML
  24 <a href="index.pl">[odt]/[odp]</a> &ndash; indicates
  25  OpenDocument format, see <a href="http://www.openoffice.org">http://www.openoffice.org</a><br />
  26 <a href="index.pl">[sxi]</a> &ndash; indicates OpenOffice 1.x format, see <a href="http://www.openoffice.org">http://www.openoffice.org</a><br />
  27 <a href="index.pl">[ppt]</a> &ndash; indicates Microsoft Powerpoint format<br />
  28 <a href="index.pl">[txt]</a> &ndash; indicates plain text format<br />
  29 <a href="index.pl">[pdf]</a> &ndash; indicates PDF format<br /><br />
  30 EOHTML
  31
  32
  33                         .info_section_html(title => 'SOL 2010 Sequencing Meeting',
  34                                            subtitle => 'Tuesday, Sep 7, 2010',
  35                                            is_subsection => 1,
  36                                            contents => <<EOHTML)
  37 <dl>
  38 <dt>Location</dt>
  39 <dd>Apex Hotel, Dundee, UK</dd>
  40 <dt>Notes</dt>
  41 <dd>
  42   meeting minutes by Joyce van Eck <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2010_docs/vanEck_notes.txt">[txt]</a><br />
  43 </dd>
  44 </dl>
  45 EOHTML
  46                         .info_section_html(title => 'PAG 2010 Sequencing Meeting',
  47                                            subtitle => 'Tuesday, Jan 12, 2010',
  48                                            is_subsection => 1,
  49                                            contents => <<EOHTML)
  50 <dl>
  51 <dt>Location</dt>
  52 <dd>Town and Country Hotel, San Diego, CA, USA</dd>
  53 <dt>Progress Reports</dt>
  54 <dd>Assembly Progress: Sandra Smit <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2010_docs/pag2010_assembly_progress.pdf">[pdf]</a></dd>
  55 <dt>Notes</dt>
  56 <dd>Meeting Summary <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2010_docs/pag2010_meeting_notes.docx">[doc]</a></dd>
  57 </dl>
  58
  59 EOHTML
  60
  61                         .info_section_html(title => 'EU-SOL Next Gen Assembly Workshop',
  62                                            subtitle => 'Wednesday, July 15, 2009 12am-5pm',
  63                                            is_subsection => 1,
  64                                            contents => <<EOHTML)
  65 <dl>
  66 <dt>Location</dt>
  67 <dd>Schiphol Airport, The Netherlands</dd>
  68 <dt>Progress Reports</dt>
  69 <dd>
  70 USA: Lukas Mueller <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/mueller.ppt">[ppt]</a><br />
  71 UK: Gerard Bishop <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/bishop.ppt">[ppt]</a><br />
  72 France: Mondher Bouzayen <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/bouzayen.ppt">[ppt]</a><br />
  73 Italy: Giorgio Valle <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/valle.ppt">[ppt]</a>
  74 </dd>
  75 <dt>Other Presentations</dt>
  76 <dd>
  77 Roeland van Ham &ndash; General Outline of the Proposed Assembly Strategy <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/vanham.ppt">[ppt]</a><br />
  78 Antoine Janssen &ndash; The Tomato Whole Genome Profiling Map <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/janssen.ppt">[ppt]</a>
  79 </dd>
  80 <dt>Notes</dt>
  81 <dd>
  82 Meeting Agenda <a href="/static_content/solanaceae-project/sol-bioinformatics/nextgen_docs/agenda.pdf">[pdf]</a>
  83 </dd>
  84 </dl>
  85 EOHTML
  86
  87                         .info_section_html(title => 'PAG 2009 Sequencing Meeting',
  88                                            subtitle => 'Sunday, Jan 11, 2009 10am-3:30pm',
  89                                            is_subsection => 1,
  90                                            contents => <<EOHTML)
  91 <dl>
  92 <dt>Location</dt>
  93 <dd>Town and Country Hotel, San Diego, CA, USA</dd>
  94 <dt>Progress Reports</dt>
  95 <dd>
  96 Chr 1 (USA): Joyce Van Eck <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/chr1.ppt">[ppt]</a><br />
  97 Chr 2 (Korea): Doil Choi <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/chr2.ppt ">[ppt]</a><br />
  98 Chr 3 (China): Ying Wang <span class="ghosted"">[ppt]</span><br />
  99 Chr 4 (UK): Gerard Bishop <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/chr4.ppt">[ppt]</a><br />
 100 Chr 7 (France): Mondher Bouzayen <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/chr7.ppt">[ppt]</a><br />
 101 Chr 12 (Italy): Giovanni Giuliano <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/chr12.ppt">[ppt]</a>
 102 </dd>
 103 <dt>Other Presentations</dt>
 104 <dd>
 105 Todd Vision &ndash; <i>Mimulus guttatus</i> sequencing progress <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/Vision_mimulus.ppt">[ppt]</a><br />
 106 Steven Stack &ndash; Role of FISH in tomato sequencing <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/stack_fish.ppt">[ppt]</a><br />
 107 Roeland van Hamm &ndash; Whole-genome shotgun sequencing for tomato<a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/rvh_wgs.ppt">[ppt]</a><br />
 108 </dd>
 109 <dt>Notes</dt>
 110 <dd>
 111 Meeting Agenda (Joyce Van Eck) <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/Agenda.pdf">[pdf]</a><br />
 112 meeting notes by Robert Buels <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2009_docs/Buels_notes.txt">[txt]</a><br />
 113 </dd>
 114 </dl>
 115 EOHTML
 116                         .info_section_html(title => 'SOL 2008 Sequencing Meeting',
 117                                            subtitle => 'Wednesday, Oct 15, 2008 7pm-11pm',
 118                                            is_subsection => 1,
 119                                            contents => <<EOHTML)
 120 <dl>
 121 <dt>Location</dt>
 122 <dd>Holiday Inn Cologne am Stadtwald, Cologne, NRW, Germany</dd>
 123 <dt>Progress Reports</dt>
 124 <dd>
 125 Chr 1 (USA): Jim Giovannoni <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr1.ppt">[ppt]</a><br />
 126 Chr 2 (Korea): Doil Choi <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr2.ppt ">[ppt]</a><br />
 127 Chr 3 (China): Chuanyou Li <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr3.ppt ">[ppt]</a><br />
 128 Chr 4 (UK): Gerard Bishop <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr4.ppt">[ppt]</a><br />
 129 Chr 5 (India): Akhilesh Tyagi <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr5.ppt">[ppt]</a><br />
 130 Chr 6 (Netherlands): Sander Peters <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr6.ppt">[ppt]</a><br />
 131 Chr 7 (France): Mondher Bouzayen <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr7.ppt">[ppt]</a><br />
 132 Chr 8 (Japan): Shusei Sato <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr8.ppt">[ppt]</a><br />
 133 Chr 9 (Spain): Joyce Van Eck for A. Granell <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr9.ppt">[ppt]</a><br />
 134 Chr 11 (China): not present<br />
 135 Chr 12 (Italy): Giovanni Giuliano <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/chr12.ppt">[ppt]</a>
 136 </dd>
 137 <dt>Other Presentations</dt>
 138 <dd>
 139 Roeland van Hamm &ndash; Whole-genome shotgun sequencing proposal<a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/rvh_wgs.ppt">[ppt]</a><br />
 140 </dd>
 141 <dt>Notes</dt>
 142 <dd>
 143 meeting notes by Robert Buels <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/Buels_notes.txt">[txt]</a><br />
 144 </dd>
 145 <dt>Supplementary Material</dt>
 146 <dd>Titanium-series 454 sequencing overview (from Roche) <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2008_docs/454.pdf">[pdf]</a>
 147 </dd>
 148 </dl>
 149 EOHTML
 150                         .info_section_html(title => 'Wageningen Finishing meeting 2008',
 151                                            subtitle => 'Thu, Apr 24 - Fri Apr 25, 2008, 9:00am-5pm',
 152                                            is_subsection => 1,
 153                                            contents => <<EOHTML)
 154
 155
 156
 157 <dl>
 158 <dt>Location</dt>
 159 <dd>Wageningen Conference Center (WICC), Netherlands</dd>
 160 <dt>Presentions</dt>
 161 <dd>
 162
 163 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr2_Jo.ppt">Chromosome 2 update</a> H. Jo<br />
 164 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr3_Wang.ppt">Chromosome 3 update</a> Y. Wang<br />
 165 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr4_Beasley.ppt">Chromosome 4 update</a> H. Beasley<br />
 166 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr5_Sharma.ppt">Chromosome 5 update</a> T.R. Sharma<br />
 167 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr6_Peters.ppt">Chromosome 6 update</a> S. Peters<br />
 168 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr7_philippot.ppt">Chromosome 7 update</a> M. Philippot<br />
 169 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr8_Sato.ppt">Chromosome 8 update</a> S. Sato<br />
 170 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr9_Zuniga.ppt">Chromosome 9 updat</a> S. Zuniga<br />
 171 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr11_Zhang.ppt">Chromosome 11 update</a> Z. Zhang<br />
 172 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/chr12_Falcone.ppt">Chromosome 12 update</a> J. Falcone<br />
 173
 174 </dd>
 175 <dt>Presentations about discussion topics</dt>
 176 <dd>
 177 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/Sanger_finishing_tools.ppt">Sanger Finishing Tools</a><br />
 178 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/Solexa_Truco.ppt">Solexa Issues</a> <br />
 179 <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_wageningen_2008_docs/Discussion_McLaren.ppt">Discussion slides</a> (K. McLaren)<br />
 180 </dd>
 181 </dl>
 182
 183 <table><tr><td><br />This meeting was organized by the EU-SOL project.</td><td width="30">&nbsp;</td><td> <a href="http://www.eu-sol.net" class="footer"><img src="/documents/img/eusol_logo_small.jpg" /></a></td></tr></table>
 184 EOHTML
 185
 186
 187
 188
 189                         .info_section_html(title => 'PAG 2008 meeting',
 190                                            subtitle => 'Sun, Jan 13, 2008, 9:00am-4pm',
 191                                            is_subsection => 1,
 192                                            contents => <<EOHTML)
 193 <dl>
 194 <dt>Location</dt>
 195 <dd>The Boardroom, Town and Country Hotel, San Diego, California, USA</dd>
 196 <dt>Progress Reports</dt>
 197 <dd>
 198 Chr 1 (USA): Joyce Van Eck <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/VanEck.ppt">[ppt]</a><br />
 199 Chr 2 (Korea): Doil Choi <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Choi.ppt ">[ppt]</a><br />
 200 Chr 3 (China): Mingsheng Chen <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Chen.ppt ">[ppt]</a><br />
 201 Chr 4 (UK): Clare Riddle <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Riddle.ppt">[ppt]</a><br />
 202 Chr 5 (India): Nagendra Singh <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Singh.ppt">[ppt]</a><br />
 203 Chr 6 (Netherlands): Rene Klein-Lankhorst <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/RKL.ppt">[ppt]</a><br />
 204 Chr 7 (France): Mondher Bouzayen <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Bouzayen.ppt">[ppt]</a><br />
 205 Chr 9 (Spain): not present<br />
 206 Chr 11 (China): Sanwen Huang <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Huang.ppt">[ppt]</a><br />
 207 Chr 12 (Italy): Alessandro Vezzi <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Vezzi.ppt">[ppt]</a>
 208 </dd>
 209 <dt>Other Presentations</dt>
 210 <dd>
 211 Hans de Jong &ndash; BAC FISH and repeat bar-coding technology for tomato and potato <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/DeJong.ppt">[ppt]</a><br />
 212 Giovanni Giuliano &ndash; Finishing Criteria <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Giuliano_finishing.ppt">[ppt]</a><br />
 213 Mingsheng Chen &ndash; Towards an Integrated Physical Map of the Tomato Genome <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Chen_physical.ppt">[ppt]</a><br />
 214 Steven Stack &ndash; Role of FISH in Tomato Genome Sequencing <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Stack.ppt">[ppt]</a><br />
 215 </dd>
 216 <dt>Notes</dt>
 217 <dd>
 218 Meeting Agenda (Joyce Van Eck) <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Agenda.doc">[doc]</a><br />
 219 a few notes by Robert Buels <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2008_docs/Buels_notes.txt">[txt]</a><br />
 220 </dd>
 221 </dl>
 222 EOHTML
 223
 224                         .info_section_html(title => 'SOL 2007 meeting',
 225                                            subtitle => 'Fri, Sept 14, 2007, 8:30am-4pm',
 226                                            is_subsection => 1,
 227                                            contents => <<EOHTML)
 228 <dl>
 229 <dt>Location</dt>
 230 <dd>Ramada Plaza Jeju, Jeju City, Korea</dd>
 231 <dt>Progress Reports</dt>
 232 <dd>
 233 Chr 1 (USA): Jim Giovannoni <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Giovannoni.ppt">[ppt]</a><br />
 234 Chr 2 (Korea): Sunghwan Jo <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Jo.ppt ">[ppt]</a><br />
 235 Chr 3 (China): not present<br />
 236 Chr 4 (UK): Gerard Bishop <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Bishop_chr4update.ppt">[ppt]</a><br />
 237 Chr 5 (India): J.P. Khurana <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Khurana.ppt">[ppt]</a><br />
 238 Chr 6 (Netherlands): Sander Peters <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Peters.ppt">[ppt]</a><br />
 239 Chr 7 (France): Mondher Bouzayen <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Bouzayen.ppt">[ppt]</a><br />
 240 Chr 8 (Japan): Erika Asamizu (presented earlier in main conference session)<a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Asamizu.ppt">[ppt]</a><br />
 241 Chr 9 (Spain): Antonio Granell<br />
 242 Chr 12 (Italy): Mara Ercolano <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Ercolano.ppt">[ppt]</a>
 243 </dd>
 244 <dt>Other Presentations</dt>
 245 <dd>
 246 Rene Klein-Lankhorst &ndash; Using FISH to determine euchromatin/heterochromatin boundaries <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/KleinLankhorst.ppt">[ppt]</a><br />
 247 Mondher Bouzayen &ndash; Alternative methods for BAC anchoring <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Bouzayen.ppt">[ppt]</a><br />
 248 Gerard Bishop &ndash; Sequencing standards update <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Bishop_standards.ppt">[ppt]</a><br />
 249 Stephane Rombauts &ndash; ITAG Pipeline <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Rombauts.pdf">[pdf]</a><br />
 250 </dd>
 251 <dt>Notes</dt>
 252 <dd>
 253 Meeting Summary (Giovannoni, Mueller, Van Eck) <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Summary_Giovannoni_Mueller_VanEck.doc">[doc]</a><br />
 254 a few notes by Daniel Buchan <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Buchan_notes.doc">[doc]</a><br />
 255 a few notes by Robert Buels <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2007_docs/Buels_notes.txt">[txt]</a><br />
 256 </dd>
 257 </dl>
 258 EOHTML
 259
 260 .info_section_html(title => '1st International Tomato Finishing Meeting',
 261                                            subtitle => 'Mon, Apr 16 - Tues, Apr 17, 2007',
 262                                            is_subsection => 1,
 263                                            contents => <<EOHTML)
 264 <dl>
 265 <dt>Location</dt>
 266 <dd>Sanger Centre, Hinxton, UK</dd>
 267 <dt>Talk Slides</dt>
 268 <dd>
 269 Mapping presentation by Christine Nicholson <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_sanger_2007_docs/WORKSHOP_MAPPING_TALK.ppt">[ppt]</a><br />
 270 Finishing presentation by Helen Beasley <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_sanger_2007_docs/hr1_tomato_finishing_workshop_april_2007_final_monday.ppt">[ppt]</a> <br />
 271
 272 Meeting Report [Karen McLaren] <a href="/static_content/solanaceae-project/sol-bioinformatics/finishing_sanger_2007_docs/meeting_report_karen.pdf">[pdf]</a>
 273
 274 EOHTML
 275
 276
 277                         .info_section_html(title => 'PAG 2007 meeting',
 278                                            subtitle => 'Sun, Jan 14, 2007',
 279                                            is_subsection => 1,
 280                                            contents => <<EOHTML)
 281 <dl>
 282 <dt>Location</dt>
 283 <dd>Terrace Salon 3, Town and Country Hotel, San Diego, California, USA</dd>
 284 <dt>Progress Reports</dt>
 285 <dd>
 286 Chr 1 (USA): Jim Giovannoni <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up1_jg.ppt">[ppt]</a><br />
 287 Chr 2 (Korea): Doil Choi <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up2_dc.ppt">[ppt]</a><br />
 288 Chr 3 (China): not present<br />
 289 Chr 4 (UK): Christine Nicholson <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up4_cn.ppt">[ppt]</a><br />
 290 Chr 5 (India): Paramjit Khurana <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up5_pk.ppt">[ppt]</a><br />
 291 Chr 6 (Netherlands): Rene Klein-Lankhorst <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up6_rkl.ppt">[ppt]</a><br />
 292 Chr 7 (France): not present<br />
 293 Chr 8 (Japan): not present<br />
 294 Chr 9 (Spain): Antonio Granell <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up9_ag.ppt">[ppt]</a><br />
 295 Chr 12 (Italy): Mara Ercolano <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_up12_gg.ppt">[ppt]</a>
 296 </dd>
 297 <dt>Other Presentations</dt>
 298 <dd>
 299 Rene Klein-Lankhorst &ndash; Using FISH to determine euchromatin/heterochromatin boundaries <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_rkl_eusol.ppt">[ppt]</a><br />
 300 Jim Giovannoni &ndash; Discussion on BAC extension protocols <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_jg_bacext.ppt">[ppt]</a><br />
 301 Jim Giovannoni &ndash; US Contribution to Sequencing <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_jg_us_seq.ppt">[ppt]</a><br />
 302 Robert Buels &ndash; BAC submission and annotation protocols and tools <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_rb.odp">[odp]</a> <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_rb.ppt">[ppt]</a><br />
 303 Giovanni Giuliano &ndash; Tomato Affy chip <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_gg_affy.ppt">[ppt]</a><br />
 304 Nevin Young &ndash; <i>Medicago truncatula</i> sequencing update<a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_ny.ppt">[ppt]</a><br />
 305 Matthew Lorence &ndash; Tomato Affy chip <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_ml_affy.ppt">[ppt]</a><br />
 306 Christian Bachem &ndash; Potato Genome Initiative <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_cb.ppt">[ppt]</a><br />
 307 Syngenta &ndash; Contribution of BAC mapping to sequencing effort <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_syngenta_fpc.ppt">[ppt]</a><br />
 308
 309 <dt>Agenda</dt>
 310 <dd>by Joyce Van Eck <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_agenda.doc">[doc]</a></dd>
 311 </dd>
 312 <dt>Minutes</dt>
 313 <dd>
 314 Notes by Joyce van Eck <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_notes_jve.pdf">[pdf]</a>.<br/>
 315 A few notes by Robert Buels <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2007_docs/pag2007_notes_rb.txt">[txt]</a>.
 316 </dd>
 317 </dl>
 318 EOHTML
 319                         .info_section_html(title => 'Ghent 2006 Tomato Annotation meeting',
 320                                            subtitle => 'Mon, Oct 23-25, 2006',
 321                                            is_subsection => 1,
 322                                            contents => <<EOHTML)
 323 <dl>
 324 <dt>Location</dt>
 325 <dd>LEAF Conference Room, Flanders Interuniversity Institute for Biotechnology, Ghent, Belgium</dd>
 326 <dt>Meeting Summary</dt>
 327 <dd>by Lukas Mueller and Robert Buels <a href="/solanaceae-project/sol-bioinformatics/ghent2006_report.pl">[html]</a> <a href="/static_content/solanaceae-project/sol-bioinformatics/ghent2006_docs/report.odt">[odt]</a></dd>
 328 <dt>Presentations</dt>
 329 <dd>
 330 New Developments at SGN: Lukas Mueller <a href="/static_content/solanaceae-project/sol-bioinformatics/ghent2006_docs/mueller.odp">[odp]</a><br />
 331 Cyrille2 Tomato Annotation: Mark Fiers and Erwin Datema <a href="/static_content/solanaceae-project/sol-bioinformatics/ghent2006_docs/datema.ppt">[ppt]</a><br />
 332 Training GeneID: Francisco Camara <a href="/static_content/solanaceae-project/sol-bioinformatics/ghent2006_docs/camara.ppt">[ppt]</a><br />
 333 India Sequencing Progress: Saloni Mathur <a href="/static_content/solanaceae-project/sol-bioinformatics/ghent2006_docs/mathur.ppt">[ppt]</a><br />
 334 </dd>
 335 </dl>
 336 EOHTML
 337                         .info_section_html(title => 'SOL 2006 meeting',
 338                                            subtitle => 'Wed, Aug 26, 2006, 8:30am-11:45am',
 339                                            is_subsection => 1,
 340                                            contents => <<EOHTML)
 341 <dl>
 342 <dt>Location</dt>
 343 <dd>Hall of Ideas Room E, Monona Terrace Convention Center, Madison, Wisconsin, USA</dd>
 344 <dt>Progress Reports</dt>
 345 <dd>
 346 Chr 1 (USA): Jim Giovannoni <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Giovannoni.ppt">[ppt]</a><br />
 347 Chr 2 (Korea): Sung-Hwan Cho <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Cho.ppt ">[ppt]</a><br />
 348 Chr 3 (China): Eileen Wang <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Wang.ppt">[ppt]</a><br />
 349 Chr 4 (UK): Christine Nicholson and Karen McLaren <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Nicholson.ppt">[ppt]</a><br />
 350 Chr 5 (India): Jitendra Khurana <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Khurana.ppt">[ppt]</a><br />
 351 Chr 6 (Netherlands): Roeland van Hamm <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/vanHamm.ppt">[ppt]</a><br />
 352 Chr 7 (France): Farid Regad <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Regad.ppt">[ppt]</a><br />
 353 Chr 8 (Japan): Erika Asamizu <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Asamizu.ppt">[ppt]</a><br />
 354 Chr 9 (Spain): Antonio Granell <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Granell.ppt">[ppt]</a><br />
 355 Chr 12 (Italy): Silvana Grandillo <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/Grandillo.ppt">[ppt]</a>
 356 </dd>
 357 <dt>Minutes</dt>
 358 <dd>
 359 notes by Robert Buels and Marty Kreuter <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/buels_notes.txt">[txt]</a><br />
 360 notes by Lukas Mueller (includes potato session and afternoon bioinformatics session) <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2006_docs/mueller_notes.txt">[txt]</a>
 361 </dd>
 362 </dl>
 363 EOHTML
 364                         .info_section_html(title => 'PAG 2006 meeting',
 365                                            subtitle => 'Sun, Jan 16, 2006, 1pm-6pm',
 366                                            is_subsection => 1,
 367                                            contents => <<EOHTML)
 368 <dl>
 369 <dt>Location</dt>
 370 <dd>Dover Room, Town and Country Hotel, San Diego, California, USA</dd>
 371 <dt>Progress Reports</dt>
 372 <dd>
 373 Chr 1 (USA): Lukas Mueller<br />
 374 Chr 2 (Korea): not present<br />
 375 Chr 3 (China): Eileen Wang <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/2006PAG_Chromosome_3_update.ppt">[ppt]</a><br />
 376 Chr 4 (UK): Christine Nicholson <!-- <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/2006PAG_Chromosome4_UK.ppt">[ppt]</a> --><br />
 377 Chr 5 (India): not present<br />
 378 Chr 6 (Netherlands): Rene Klein-Lankhorst <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/chr6_SOL_lezing_San_Diego__2006.ppt">[ppt]</a><br />
 379 Chr 7 (France): not present<br />
 380 Chr 8 (Japan): not present<br />
 381 Chr 9 (Spain): not present<br />
 382 Chr 12 (Italy): Giovanni Giuliano  <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/Giuliano_PAG.ppt">[ppt]</a> and Giorgio Valle <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/Valle_PAG.ppt">[ppt]</a>
 383 </dd>
 384 <dt>Other Presentations</dt>
 385 <dd>
 386 Remy Bruggman &ndash; Training Gene Finders for Tomato <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/Bruggmann_SanDiego_January_2006.ppt">[ppt]</a><br />
 387 Robert Buels &ndash; Submitting BACs to SGN <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/submission_system_PAG_2006.sxi">[sxi]</a> <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/submission_system_PAG_2006.ppt">[ppt]</a><br />
 388 Stephen Stack &ndash; Tomato FISH <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/stack_FISH_talk.ppt">[ppt]</a><br />
 389 Naama Menda &ndash; Ontologies for Describing Solanaceae Phenotypes <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/menda_SOL_PAG06.sxi">ppt</a><br />
 390 </dd>
 391 <dt>Minutes</dt>
 392 <dd>
 393 a few notes by Robert Buels <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/buels_notes_pag2006.txt">[txt]</a>.
 394 </dd>
 395 <dt>Dutch BAC extension protocol</dt>
 396 <dd>The complete protocol as presented by Rene Klein Lankhorst, kindly provided by Sander Peters [<a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/STC_protocol.doc">doc</a> | <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2006_docs/STC_protocol.doc">pdf</a>]</dd>
 397 </dl>
 398 EOHTML
 399                         .info_section_html(title => 'SOL 2005 meeting',
 400                                            subtitle => 'Wed, Sep 28, 2005',
 401                                            is_subsection => 1,
 402                                            contents => <<EOHTML)
 403 <dl>
 404 <dt>Location</dt>
 405 <dd>Ischia, Italy</dd>
 406 <dt>Agenda</dt>
 407 <dd><a href="http://www.solanaceae2005.org/">Link</a></dd>
 408 <dt>Progress Reports</dt>
 409 <dd>
 410 Intro: Lukas Mueller <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/SOL2005_Italy_intro.sxi">[sxi]</a><br />
 411 Chromosome 1: Lukas Mueller
 412  <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/SOL2005_Sequencing.sxi">[sxi]</a>
 413 <br />
 414
 415 Chromosome 2:
 416 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/SOL-Cheol-Goo-Hur-0928-annotation-final.ppt">[ppt]</a><br />
 417
 418 Chromosome 3: Eileen Wang
 419 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/chromosome_3_update.ppt">[ppt]</a><br />
 420
 421 Chromosome 4: Christine Nicholson
 422 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/Chrom_4_Ischia_Sep2005.ppt">[ppt]</a><br />
 423
 424 Chromosome 5: Jiten Khurana
 425 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/Khurana-SOL_Ischia05.ppt">[ppt]</a><br />
 426
 427 Chromosome 6: Rene Klein-Lankhorst
 428 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/SOL_lezing_italie_september_2005_part1.ppt">[ppt-part1]</a> |
 429 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/SOL_lezing_italie_september_2005_part2.ppt">[ppt-part2]</a><br />
 430
 431 Chromosome 7: Farid Regad
 432 <br />
 433
 434 Chromosome 8: Satoshi Tabata
 435 <br />
 436
 437 Chromosome 9: No presentation (only recently funded)
 438 <br />
 439
 440 Chromosome 12: Mara Ercolano
 441 <a href="/static_content/solanaceae-project/sol-bioinformatics/sol2005_docs/Mara_Ercolano_Italy.ppt">[ppt]</a><br />
 442
 443 </dd>
 444 <dt>Key conclusions</dt>
 445 <dd>
 446         <ul style="padding: 0">
 447                 <li>Evidence presented indicates that a number of gene prediction programs tested with different matrices don\'t work reliably on tomato genomic sequence. It is therefore necessary to calibrate them for use with tomato. A training/test set will be developed for this purpose by MIPS/Ghent/U Naples.<br /><br /></li>
 448                 <li>Extension BACs were found for all seed BACs on chromosome 6 and for more than half the seed BACs on chromosome 2. This shows that the approach is sound, but the lower success rate on chromosome 2 needs to be investigated.</li>
 449         </ul>
 450 </dd>
 451 </dl>
 452 EOHTML
 453
 454                         .info_section_html(title => 'PAG meeting 2005',
 455                                            subtitle => 'Sat, January 15, 2005, 1pm-6pm',
 456                                            is_subsection => 1,
 457                                            contents => <<EOHTML)
 458 <dl>
 459 <dt>Location</dt><dd>Dover Room, Town and Country Hotel, San Diego, California, USA</dd>
 460 <dt>Agenda</dt>  <dd><a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/agenda.pdf">pdf</a></dd>
 461 <dt>Progress Reports</dt>
 462 <dd>
 463 Chr 1 (USA): Lukas Mueller
 464   <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/PAG_SOL_meeting.ppt">[ppt]</a><br />
 465 Chr 2 (Korea): Doil Choi
 466   <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/chr2_korea.ppt">[ppt]</a><br />
 467 Chr 3 (China): not able to attend<br />
 468 Chr 4 (UK): Christine Nicholson presentation [without slides]<br />
 469 Chr 5 (India): Arun Sharma
 470   <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/chr5_india.ppt">[ppt]</a><br />
 471 Chr 6 (Netherlands): Rene Lank Kleinhorst<br />
 472 Chr 7 (France): Farid Regad presentation [without slides]<br />
 473 Chr 8 (Japan): Satoshi Tabata
 474   <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/chr8_japan.ppt">[ppt]</a><br />
 475 Chr 9 (Spain): (Funding in progress)<br />
 476 Chr 12 (Italy): Maria Luisa Chiusano
 477   <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/ItalyJanuary2005.ppt">[ppt]</a><br />
 478 </dd>
 479 <dt>Other presentations</dt>
 480 <dd>
 481 Lukas' Solanaceae workshop presentation
 482 <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/PAG2005_Lukas.ppt">[ppt]</a><br />
 483 Eileen's Overgo and BAC selection presentation
 484   <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/2005PAG_overgo.ppt">[ppt]</a><br />
 485 </dd>
 486 <dt>Minutes</dt>
 487 <dd>Kindly provided by Robert Buels
 488 <a href="/static_content/solanaceae-project/sol-bioinformatics/pag2005_docs/meeting_notes_Rob.txt">[txt]</a>
 489 </dd>
 490 </dl>
 491 EOHTML
 492
 493                         .info_section_html(title => 'SOL 2004 meeting, Wageningen, The Netherlands',
 494                                            subtitle => 'Sat, Sept 18, 2004, 9am-6pm',
 495                                            is_subsection => 1,
 496                                            contents => <<EOHTML)
 497 <dl>
 498 <dt>Location</dt><dd>Wageningen, The Netherlands</dd>
 499 <dt>Presentations</dt>
 500 <dd>
 501 Sarah Butcher, GB <a href=
 502 "/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/tomato_wageningen.ppt">[ppt]</a><br />Stephane
 503 Rombauts, Belgium <a href=
 504 "/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/Annotation_of_Tomato.ppt">[ppt]</a><br />David de
 505 Koeyer, Canada <a href=
 506 "/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/SOL_Bioinfo_de_Koeyer_final.ppt">[ppt]</a><br />
 507 Silvana Grandillo, Italy <a href=
 508 "/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/Wageningen.g.ppt">[ppt]</a><br /> Lukas Mueller, USA
 509 <a href="/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/Wageningen_Lukas.ppt">[ppt]</a><br />Farid
 510 Regad, France<br />Ralph van Berloo, NL<br />
 511 </dd>
 512 <dt>Key Conclusions</dt>
 513 <dd>
 514   <dl>
 515   <dt>Data archiving, formats and access</dt>
 516   <dd><ul style="padding: 0">
 517       <li>Primary data needs to be archived and available to anyone</li>
 518       <li>Procedure/method/parameters used to generate a dataset need to
 519       be documented</li>
 520       <li>All working on a common datatype should agree on a common
 521       exchange format</li>
 522       </ul>
 523   </dd>
 524   <dt>Data Access</dt>
 525   <dd><ul style="padding: 0">
 526       <li>Central archive at SGN</li>
 527       <li>Method, how data arrives at SGN (upload, download, SMTP) agreed
 528       between SGN and other data source</li>
 529       <li>Data providers should implement the services required to
 530       integrate into the SOL platform/workgroup</li>
 531       </ul>
 532   </dd>
 533   <dt>Credit and Traceability</dt>
 534   <dd><ul style="padding: 0">
 535       <li>Keep original source information even if data travels through
 536       many hands</li>
 537       </ul>
 538   </dd>
 539   <dt>Annotation</dt>
 540   <dd>
 541      <ul style="padding: 0">
 542      <li>Sequences--&gt; a one-stop-shop</li>
 543      <li>Latest BAC, transcripts available</li>
 544      <li>FTP, maintain version and history of sequences \@ SGN</li>
 545      </ul>
 546   </dd>
 547   </dl>
 548 </dd>
 549 <dt>Minutes</dt>
 550 <dd>
 551   <a href="/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/wageningen_minutes_sarah.txt">[from Sarah]</a><br />
 552   <a href="/static_content/solanaceae-project/sol-bioinformatics/wageningen_docs/wageningen_minutes_heiko.txt">[from Heiko]</a><br />
 553 </dd>
 554 </dl>
 555 EOHTML
 556                        );
 557
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