cgi-bin/about/us_tomato_sequencing.pl

   1 use strict;
   2 use CXGN::Page;
   3 use CXGN::Page::FormattingHelpers qw/info_section_html info_table_html columnar_table_html/;
   4 my $page=CXGN::Page->new('us_tomato_sequencing.html','html2pl converter');
   5 $page->header(('About the US Tomato Sequencing Project') x 2);
   6
   7 print <<EOH;
   8 <p>The US Tomato Sequencing project is part of the larger <a href="/about/tomato_sequencing.pl">International Tomato Sequencing Project</a>, which is in turn part of the broad <a href="/solanaceae-project/index.pl">International Solanaceae Genome (SOL) Project</a>.</p>
   9 <!-- <p class="boxbgcolor5"><b>Note:</b> Summer 2010 Internship Positions are available!
  10 Please see <a href="#internships">below</a>!<br /></p> -->
  11
  12 EOH
  13
  14 print info_section_html( title => 'Principal Investigators',
  15                          contents =>
  16                          info_table_html(__border => 0,
  17                                          'Project PIs' =>
  18                                          columnar_table_html( headings => ['PI','Contact','Organization'],
  19                                                               data =>
  20                                                               [
  21                                                                 ['Jim Giovannoni','jjg33@cornell.edu','Boyce Thompson Institute for Plant Research (BTI)'],
  22                                                                 ['Bruce Roe', 'broe@ou.edu', 'University of Oklahoma'],
  23                                                                 ['Lukas Mueller','lam87@cornell.edu','Boyce Thompson Institute for Plant Research (BTI)'],
  24                                                                 ['Stephen Stack','sstack@lamar.colostate.edu','Colorado State University'],
  25                                                                 ['Joyce Van Eck','jv27@cornell.edu','Boyce Thompson Institute for Plant Research (BTI)'],
  26                                                               ],
  27                                                             ),
  28                                          'Project Manager and Educational Outreach Coordinator' => <<EOH,
  29           <p>Joyce Van Eck<br />
  30           The Boyce Thompson Institute for Plant Research<br />
  31           Tower Rd.<br />
  32           Ithaca, NY 14853-1801<br />
  33           USA<br />
  34           e-mail: <a href="mailto:jv27\@cornell.edu">jv27\@cornell.edu</a><br />
  35           Phone: 607-254-1284<br />
  36           Fax: 607-254-1284</p>
  37 EOH
  38                                          'Funding' => <<EOH,
  39           The US Project is funded by the <a href="http://www.nsf.gov">National Science Foundation</a>,
  40           Plant Genome Research Program, Grant <a href="http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0421634">#0421634</a>.
  41 EOH
  42                                         ),
  43                        );
  44
  45 print info_section_html( title => 'Project Summary',
  46                          contents => <<EOH,
  47
  48        <h4>Scientific objectives and approaches</h4>
  49
  50           <p>The tomato genome is comprised of approximately 950 Mb of
  51           DNA -- more than 75\% of which is heterochromatin and
  52           largely devoid of genes. The majority of genes are found
  53           in long contiguous stretches of gene-dense euchromatin
  54           located on the distal portions of each chromosome arm. As
  55           part of an international consortium, these gene rich
  56           regions of the tomato genome will be sequenced using a
  57           minimal tiling path approach. The US project is geared
  58           towards establishing the foundations for sequencing by
  59           establishing 2 additional BAC libraries, obtaining BAC
  60           end sequence (400,000 reads) and sequencing a sheared
  61           library. The Sol Genomics Network (<a href="/">SGN</a>),
  62           an organism database devoted to the genomics of solanaceous species,
  63           will be expanded to accommodate and incorporate all of
  64           the sequencing, annotation and mapping information for
  65           all 12 tomato chromosomes and begin integrating SGN with
  66           other databases through a series of shared, common
  67           software and algorithms so as to create a network of
  68           plant genomic information. Currently, the US has been
  69           assigned chromsomes 1, 10 and 11 for full sequencing in a
  70           follow-up project.</p>
  71
  72         <h4>Broader impact of the project</h4>
  73
  74           <p>Sequencing the tomato genome is the cornerstone of a
  75           larger international effort: "The International
  76           Solanaceae Genome Project". The goal is to establish a
  77           network of information, resources and scientists to
  78           tackle two of the most significant questions in plant
  79           biology/agriculture:</p>
  80           <ol>
  81           <li>How can a common set of
  82           genes/proteins give rise to a wide range of
  83           morphologically and ecologically distinct organisms that
  84           occupy our planet?</li>
  85           <li>How can a deeper understanding of
  86           the genetic basis of plant diversity be harnessed to
  87           better meet the needs of society in an
  88           environmentally-friendly and sustainable manner?</li>
  89           </ol>
  90           <p>The family Solanaceae is ideally suited to answer both of
  91           these questions for reasons that will be enumerated in
  92           this proposal. Immediate application of the tomato genome
  93           sequence to other solanaceous species is possible since
  94           the tomato genome is connected to these other species by
  95           comparative genetic maps and the level of microsynteny
  96           appears to be well conserved with respect to gene content
  97           and order. Finally, because the Solanaceae represents a
  98           distinct and divergent sector of flowering plants,
  99           distant from Arabidopsis, Medicago and rice, the tomato
 100           genome sequence will provide a rich resource for
 101           investigating the forces of gene and genome evolution
 102           over long periods of evolutionary time.</p>
 103 EOH
 104                        );
 105
 106 print info_section_html(title => 'Educational Outreach',
 107                         contents => <<EOH
 108           <p>The mission of our
 109           educational outreach program is to provide
 110           research-training opportunities in computational genomics
 111           to undergraduates and high school students. By offering
 112           hands-on training in computational genomics to these
 113           students, we hope to expose them to the nature of
 114           genomics information/datasets and the myriad of
 115           fascinating biological questions that can be addressed
 116           through the application of computational tools to
 117           genomics information.</p>
 118
 119           <p>The introduction of high capacity DNA sequencing has
 120           changed forever the nature of life sciences research. No
 121           longer are biologists limited by the ability to collect
 122           genetic information, but rather they are limited by the
 123           ability to turn this information into discovery.
 124           Organizing, storing, curating and extracting biological
 125           insights from these data is the central challenge facing
 126           biology today. To meet this challenge, we must attract
 127           and train students who are mathematically and
 128           computationally savvy and yet have attained a level
 129           of biological intuition that can lead them to tackling
 130           important biological questions. These students will have
 131           as part of their undergraduate training hands-on
 132           experience in computational genomics. Their research
 133           experience will also be supplemented through a number of
 134           new course offerings in computational biology now being
 135           offered at Cornell (or to be offered soon) as well as a
 136           genomics minor that is now being developed at
 137           Cornell.</p>
 138
 139     <h4>Student Research Opportunities</h4>
 140     <a name="internships"></a>
 141           <p>Undergraduate positions are available at the <a href="/">SOL
 142           Genomics Network</a>, a database for
 143           genomic information of the nightshade plant family, which
 144           includes important crop species such as tomato, potato
 145           and eggplant.</p>
 146
 147           <p>We are seeking highly motivated individuals with strong
 148           interests in computers and biology to work on different
 149           bioinformatics problems, including web-programming of new
 150           tools for plant scientists and designing and implementing
 151           relational databases for genomics applications.</p>
 152
 153           <p>Knowledge of Perl, SQL, and Linux, BSD or other UNIX-like
 154           operating systems are desirable, but not required.</p>
 155
 156           <p>Hourly paid positions and honor student positions are
 157           available. Work-study students are encouraged to apply.
 158           To apply, please send a summary of prior
 159           experience/interests, list of relevant course work and
 160           names/e-mail addresses of at least 2 references by e-mail
 161           to: Joyce Van Eck, <a href="mailto:jv27\@cornell.edu">jv27\@cornell.edu</a>.</p>
 162
 163 <!--    <h4>Summer 2010 Internships</h4>
 164
 165 <p>Summer internships will be available at the <a href="/">Sol Genomics Network</a> for college undergraduates.</p>
 166
 167 <p>Additional information regarding the internship is available in the flyer. <a href="/documents/help/about/internships_2010/internship_poster_2010.pdf">[pdf]</a></li></p>
 168
 169    <ul>
 170     <li>Application form <a href="/documents/help/about/internships_2010/undergrad_app_internship_2010.pdf">[pdf]</a> </li>
 171     <li>Recommendation form <a href="/documents/help/about/internships_2010/2010_recommendation_form.pdf">[pdf]</a></li>
 172
 173 </ul>
 174 <p>Application materials are due by March 08, 2010.</p> -->
 175
 176 EOH
 177                        );
 178
 179 $page->footer();