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SyntenyVista

Ela Hunt, Neil Hanlon
2004 Proceedings of the third Nordic conference on Human-computer interaction - NordiCHI '04  
doi:10.1145/1028014.1028094 dblp:conf/nordichi/HuntH04 fatcat:km4nffsfdze5rl2l4cmtvvzkja

The Visual Language of Synteny

Ela Hunt, Neil Hanlon, David P. Leader, Hunter Bryce, Anna F. Dominiczak
2004 Omics  
We believe that SyntenyVista is a significant step towards an improved representation of comparative genomics data.  ...  Acknowledgements SyntenyVista prototype was delivered by Hunter Bryce, as his final BSc project at Glasgow. Run-time connection to Ensembl was implemented by Magnus Ferrier, working for BRIDGES.  ...  SyntenyVista We introduce SyntenyVista, see Figure 7 and Figure 8 , by outlining the interaction required to select a syntenic region.  ... 
doi:10.1089/omi.2004.8.289 pmid:15703477 fatcat:ct6gsssna5d2pldv67anrhqx5i

System level visualization of eQTLs and pQTLs

Joanna Jakubowska, Ela Hunt, Matthew Chalmers, David Leader, Martin McBride, Anna F Dominiczak
2005 BMC Bioinformatics  
Genomics visualization programs such as SyntenyVista, Apollohttp://www.fruitfly.org/annot/apollo/, Artemishttp://www.sanger.ac.uk/Software/Artemis/, BugViewhttp://www.gla.ac.uk/~dpl1n/BugView/, Der Browserhttp  ...  At the moment the information is more clearly presented in SyntenyVista, but we still do not have all the relevant information that the biologists wish to see, and do not have a solution for database connectivity  ... 
doi:10.1186/1471-2105-6-s3-p15 fatcat:yimv7csc4rbwblfsfyftm4h6fy

Development of a Grid Infrastructure for Functional Genomics [chapter]

Richard Sinnott, Micha Bayer, Derek Houghton, David Berry, Magnus Ferrier
2005 Lecture Notes in Computer Science  
Drs Hanlon and Hunt are also acknowledged for their contribution to the original SyntenyVista software.  ...  SyntenyVista was developed for this purpose as shown in Fig. 5 .  ...  To achieve this SyntenyVista has been augmented with OGSA-DAI capabilities. Specifically, SyntenyVista is now able to access remote syntenic data sources and pull down (cache) them as needed.  ... 
doi:10.1007/978-3-540-32251-1_12 fatcat:nfib7xbrhzhglhq465dvjlsyiq

CartoonPlus: A New Scaling Algorithm for Genomics Data [chapter]

Joanna Jakubowska, Ela Hunt, Matthew Chalmers
2008 Lecture Notes in Computer Science  
SyntenyVista shows all genes in the same size and this makes it clear which genes share a homology link.  ...  Exceptions include SyntenyVista [7] and Cinteny [15] which show a comparative view of two genomes but are limited with regard to other data, such as micro array probes.  ... 
doi:10.1007/978-3-540-69389-5_19 fatcat:x2wroo7kljet7bohxvnc6ucwke

CONTROLLING THE CHAOS: DEVELOPING POST-GENOMIC GRID INFRASTRUCTURES

RICHARD SINNOTT, MICHA BAYER
2006 Grid Computing in Life Sciences  
Drs Hanlon and Hunt are also acknowledged for their contribution to the original SyntenyVista software. Magnus Ferrier is acknowledged  ...  Users of SyntenyVista are able to drag these individual colour coded chromosomes onto the pallet where the QTL information is depicted.  ...  SyntenyVista was developed for this purpose as shown in The three columns of shaded boxes on the left of Figure 4 are the sets of chromosomes for the rat, mouse and human genomes.  ... 
doi:10.1142/9789812772503_0005 fatcat:7rtexvj4lvh5ddp2ypflh72izy

VisGenome: visualization of single and comparative genome representations

J. Jakubowska, E. Hunt, M. Chalmers, M. McBride, A. F. Dominiczak
2007 Bioinformatics  
VisGenome extends SyntenyVista (Hunt et al., 2004) with a single genome display and presents homologies alongside QTLs and micro array probes. Our plans are as follows.  ... 
doi:10.1093/bioinformatics/btm394 pmid:17965437 fatcat:si7l2ab5evggdcnpwrjmgzxuga

Experiences of Applying Advanced Grid Authorisation Infrastructures [chapter]

R. O. Sinnott, A. J. Stell, D. W. Chadwick, O. Otenko
2005 Lecture Notes in Computer Science  
In the current implementation the usage of SyntenyVista offers direct visualisation of data sets available via the repository (from ensembl [28] ).  ...  ). • Upon launching SyntenyVista (using WebStart technologies) the users can use data available in the repository (which itself provides an OGSA-DAI front end and exploits IBM Information Integator to  ... 
doi:10.1007/11508380_28 fatcat:s2iijcfbwzgvxfc2r5hnokpcnq

Genomic Spring-Synteny Visualization with IMAS

Chris D. Shaw
2008 2008 Fifth International Conference BioMedical Visualization: Information Visualization in Medical and Biomedical Informatics  
In SyntenyVista [8] , Hunt et al developed methods of displaying similar genes and other loci between chromosomes of human, rat, and mouse.  ...  For the Synteny viewers like SyntenyVista, Cinteny and SynBrowse, secondary order is important, so similarity linkage is drawn using color patches or line segments or a combination of both.  ... 
doi:10.1109/medivis.2008.17 fatcat:t5bdjh7mmbh2dj26e4vhchmfna

Visualizing conserved gene location across microbe genomes

Chris D. Shaw, Katy Börner, Jinah Park
2009 Visualization and Data Analysis 2009  
In SyntenyVista [9] , Hunt et al developed methods of displaying similar genes and other loci between chromosomes of human, rat, and mouse.  ...  For the Synteny viewers like SyntenyVista, Cinteny and SynBrowse, secondary order is important, so similarity linkage is drawn using color patches or line segments or a combination of both.  ... 
doi:10.1117/12.811912 dblp:conf/vda/Shaw09 fatcat:zrtc6hqztjcyxaqd7w5fympeiy

MizBee: A Multiscale Synteny Browser

M. Meyer, T. Munzner, H. Pfister
2009 IEEE Transactions on Visualization and Computer Graphics  
SyntenyVista has a segregated-discrete layout, and Sybil a separate-linear layout.  ... 
doi:10.1109/tvcg.2009.167 pmid:19834152 fatcat:mploapatubg5dmbsbyouyeqeua

VisGenome and Ensembl: Usability of Integrated Genome Maps [chapter]

Joanna Jakubowska, Ela Hunt, John McClure, Matthew Chalmers, Martin McBride, Anna F. Dominiczak
Lecture Notes in Computer Science  
SyntenyVista [13] shows a comparative view of two genomes but is limited with regard to other data such as micro array probes.  ... 
doi:10.1007/978-3-540-69828-9_8 fatcat:3aft4zc63bf2ppg5meboyj6que