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about.html
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---
layout: page
title: About us
---
<p>
Between 2013 and 2014, Biodalliance development was support by the <a href="http://www.bbsrc.ac.uk/pa/grants/AwardDetails.aspx?FundingReference=BB%2fK015427%2f1">BBSRC Tools and Resources
Development Fund.</a></p>
<h3>Developers</h3>
<h4><a href="http://www.biodalliance.org/people/thomas">Thomas Down</a></h4>
<p>
Creator and lead developer of Biodalliance. Developed <a
href="http://www.biojava.org/wiki/Dazzle">Dazzle</a>, one of the
first implementation of a DAS server built on the BioJava library,
which he co-founded in 2000 <a href="#pubmed_18689808">(Holland et al,
2008)</a>. He has also worked on sequence analysis and epigenetics,
and believes that we need more scientific software that is a pleasure to
use.
</p>
<h4><a href="http://uk.linkedin.com/in/matiaspiipari">Matias Piipari</a></h4>
<p>
Has expertise in designing and writing usable software, both academic
research tools (<a href="#pubmed_20106815">Piipari et al, 2010</a>) and
<a href="http://pearcomp.com/">commercial applications</a>.
</p>
<h4><a href="http://www.sanger.ac.uk/research/faculty/thubbard/">Tim Hubbard</a></h4>
<p>Bugfinder General and feature proposer for Dalliance. Has been an advocate
of DAS since its beginning, encouraging its adoption by Ensembl <a
href="#pubmed_11752248">(Hubbard et al, 2002)</a> and the efamily and
biosapiens projects, under which Andreas Prlic developed the SPICE DAS
client <a href="#pubmed_16204122">(Prlic et al, 2005)</a> and the
DAS registry <a href="#pubmed_17850653">(Prlic et al, 2007)</a>. He
has had an interest in methods for layering annotation onto protein
structures in a distributed way since the early days of the SCOP
database <a href="#pubmed_9016544">(Hubbard, et al, 1995)</a></p>
<h3>Thanks to...</h3>
<p>
Special thanks to all our users, especially those who've provided feedback about early versions of Dalliance:
</p>
<p style="margin-left: 30px">
Guillermo Carbajosa, Nicole Cheung, Claire Chewapreecha, Alex Down, Mike Gilchrist, Jing Su, Vardhman Rakyan, Jonathan Warren
</p>
<h3>References:</h3>
<p><a id="pubmed_21252075"></a><b>Dalliance: interactive genome viewing on the web.</b><br>
Down TA, Piipari M, Hubbard TJ<br>
Bioinformatics (2011) 27:889-890<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/21252075" rel="external">21252075</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC3051325" rel="external">3051325</a><br>
</p>
<p><a id="pubmed_20106815" name="pubmed_20106815"></a><b>iMotifs: an integrated sequence motif visualization and
analysis environment.</b><br>
Piipari M, Down TA, Saini H, Enright A and Hubbard TJP<br>
Bioinformatics (2010) vol. 26 (6) pp. 843-4<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/20106815" rel="external">20106815</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC2832821" rel="external">2832821</a><br>
</p>
<p><a id="pubmed_20106815" name="pubmed_20106815"></a><b>iMotifs: an integrated sequence motif visualization and
analysis environment.</b><br>
Piipari M, Down TA, Saini H, Enright A and Hubbard TJP<br>
Bioinformatics (2010) vol. 26 (6) pp. 843-4<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/20106815" rel="external">20106815</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC2832821" rel="external">2832821</a><br>
</p>
<p><a id="pubmed_18673527" name="pubmed_18673527"></a><b>Integrating biological data - the Distributed Annotation System.</b><br>
Jenkinson A, Albrecht M, Birney E, Blankenburg H, Down T, Finn R, Hermjakob H, Hubbard TJP, Jimenez R, Jones P, Kahari A, Kulesha E, Macias J, Reeves G and Prlic A<br>
BMC Bioinformatics (2008) vol. 9 Suppl 8 pp. S3<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/18673527" rel="external">18673527</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC2500094" rel="external">2500094</a><br>
</p>
<p><a id="pubmed_18689808" name="pubmed_18689808"></a><b>BioJava: an open-source framework for bioinformatics.</b><br>
Holland RCG, Down TA, Pocock M, Prlic A, Huen D, James K, Foisy S, Drager A, Yates A, Heuer M, Schreiber MJ<br>
Bioinformatics (2008) vol. 24 (18) pp. 2096-7<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/18689808" rel="external">18689808</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC2530884" rel="external">2530884</a><br>
</p>
<p><a id="pubmed_17850653" name="pubmed_17850653"></a><b>Integrating sequence and structural biology with DAS.</b><br>
Prlic A, Down TA, Kulesha E, Finn RD, Kahari A, Hubbard TJP<br>
Bioinformatics (2007) vol. 8 pp. 333<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/17850653" rel="external">17850653</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC2031907" rel="external">2031907</a><br>
</p>
<p><a id="pubmed_16204122" name="pubmed_16204122"></a><b>Adding some SPICE to DAS.</b><br>
Prlic A, Down TA, Hubbard TJP<br>
Bioinformatics (2005) vol. 21 Suppl 2 pp. ii40-1<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/16204122" rel="external">16204122</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC2656757" rel="external">2656757</a><br>
</p>
<p><a id="pubmed_11752248" name="pubmed_11752248"></a><b>The Ensembl genome database project.</b><br>
Hubbard TJP, Barker D, Birney E, Cameron G, Chen Y, Clark L,
Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J,
Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P,
Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E,
Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E,
Ureta-Vidal A, Vastrik I, Clamp M.<br>
Nucleic Acids Res (2002) vol. 30 (1) pp. 38-41<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/11752248" rel="external">11752248</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC99161" rel="external">99161</a><br>
</p>
<p><a id="pubmed_9016544" name="pubmed_9016544"></a><b>SCOP: a structural classification of proteins database.</b><br>
Hubbard TJP, Murzin AG, Brenner SE, Chothia C<br>
Nucleic Acids Res (1997) vol. 25 (1) pp. 236-9<br>
PUBMED: <a href="http://ukpmc.ac.uk/abstract/MED/9016544" rel="external">9016544</a>;
ukPMC: <a href="http://ukpmc.ac.uk/articles/PMC146380" rel="external">146380</a><br>
</p>