Visualizing%20Biosciences

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Visualizing Biosciences

• Genomics Proteomics

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• Scientists Complete Rough Draft of Human Genome
  - New York Times, June 26, 2000
• The problem
• 3 billion base pairs (ACGT)
• 40,000 genes (?)
• How do we decipher them?
• What do they mean?
• How can the information be used?

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• genomics
• The study of all of the nucleotide sequences,
  including structural genes, regulatory sequences,
  and noncoding DNA segments, in the chromosomes of
  an organism.
• proteomics
• Description and functional characterization of
  the full complement of an organisms proteins

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• Some types of BioViz
• Publicly available visualization tools
• Commercial visualization tools
• Genetics Aesthetics

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• Entrez Genome Browser - National Center for
  Biotechnology Information,National Institutes of
  Health - http//www.ncbi.nlm.nih.gov/entrez/query.
  fcgi
• Ensembl Genome Browser - European Molecular
  Biology Laboratory - http//www.ensembl.org/
• TIGR Genome Maps The Institute for Genetic
  Research - http//www.tigr.org/tdb/tgi/map.shtml
• Human Protein Reference Database -
  http//www.hprd.org/

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NCBI Map Viewer
http//www.ncbi.nlm.nih.gov/mapview/
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NCBI Map Viewer
http//www.ncbi.nlm.nih.gov/mapview/
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NCBI Map Viewer
http//www.ncbi.nlm.nih.gov/mapview/
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NCBI BLAST
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NCBI BLAST
http//www.ncbi.nlm.nih.gov/BLAST/
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NCBI BLAST
http//www.ncbi.nlm.nih.gov/BLAST/
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NCBI BLAST
http//www.ncbi.nlm.nih.gov/BLAST/
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NCBI BLAST
http//www.ncbi.nlm.nih.gov/BLAST/
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• Commercial visualization tools
• metalife

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NCBI Map Viewer
http//www.ncbi.nlm.nih.gov/mapview/
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metalife genome viewer
http//metalife.orbitel.bg/
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metalife genome viewer
http//metalife.orbitel.bg/
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metalife genome viewer
http//metalife.orbitel.bg/
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metalife protein viewer
http//metalife.orbitel.bg/
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metalife protein predictor protein interaction
sites
http//metalife.orbitel.bg/
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protein interaction diagram
http//www.hprd.org
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metalife interaction viewer
http//metalife.orbitel.bg/
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metalife interaction viewer
http//metalife.orbitel.bg/
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• Commercial visualization tools
• metalife
• DNAStar

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DNAStar BLAST
http//www.dnastar.com
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DNAStar sequence alignment
http//www.dnastar.com
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DNAStar GenVision
Figure 1. The overall structure of the E. coli
genome. The origin and terminus of replication
are shown as green lines, with blue arrows
indicating replichores 1 and 2. A scale indicates
the coordinates both in base pairs and in minutes
(actually centisomes, or 100 equal intervals of
the DNA). The distribution of genes is depicted
on two outer rings The orange boxes are genes
located on the presented strand, and the yellow
boxes are genes on the opposite strand. Red
arrows show the location and direction of
transcription of rRNA genes, and tRNA genes are
shown as green arrows. The next circle
illustrates the positions of REP sequences around
the genome as radial tick marks. The central
orange sunburst is a histogram of inverse CAI
(1 - CAI), in which long yellow rays represent
clusters of low (lt0.25) CAI. The CAI plot is
enclosed by a ring indicating similarities
between previously described bacteriophage
proteins and the proteins encoded by the complete
E. coli genome the similarity is plotted as
described in Fig. 3 for the complete genome
comparisons.
The complete genome sequence of Escherichia coli
K-12. Blattner et al., Science 2771453-1462,
1997.
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• Genetics Aesthetics
• Visual maps of genomic information.
• e.g. Genomic Cartography by Benjamin Fry,
  Aesthetics Computation Group, MIT Media Lab
• http//acg.media.mit.edu/people/fry/genocarto.html
  

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genomic cartography axonometric introns and
exons
http//acg.media.mit.edu/people/fry/genocarto.html

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genomic cartography handheld genome browser
http//acg.media.mit.edu/people/fry/genocarto.html

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genomic cartography genome valence
http//acg.media.mit.edu/people/fry/genocarto.html

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The future is now?
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The future is now?
http//acg.media.mit.edu/people/fry/genocarto.html

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The future is now?
http//acg.media.mit.edu/people/fry/genocarto.html