1. Bluejay: Customized and Selective Genome Browsing
- A Basic Tutorial -
Last Updated: January 31, 2007
Key concepts:
• The wealth of biological data available is overwhelming as it is now.
• Data visualization and exploration can be easily and intuitively done with Bluejay.
• Knowledge integration is possible through linking various tools together.
What you will be able to do at the end of this tutorial:
• Visually explore entire genomes and create publishable images based on those
explorations using the Sun COE’s Bluejay.
• Explore the implications of linking various bioinformatics tools together to expand the
worldwide knowledge base.
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2. Overview
Bluejay addresses two main issues:
• Visualization of large genomic data sets
• Integration of various knowledge bases
1. Motivation
Biological data sets are growing too fast for them to be useful as they are. As such, visualization
methods need to be employed to understand the data. Furthermore, as the wealth of knowledge
increases with the ever-growing collection of valuable bioinformatics tools, we must also
consider how various sources of information can be linked together to create a comprehensive
understanding of the entire organism.
2. Bluejay Overview
Bluejay is a relatively new browser for visualizing biological sequences. Written in Java with an
easy-to-use “point and click” interface, it has a customizable display of genomic and proteomic
data, with multiple levels of visual manipulation. Bluejay supports several data types, combining
them into a coherent visual model. The user can interact visually with the whole sequence,
functional categories, as well as individual elements. Features of Bluejay include semantic
zooming, several types of customizable image granularity, Scalable Vector Graphics (SVG)
imagery, and session management.
Bluejay was created to interoperate with existing software in a broader bioinformatics context
through the use of XML-based standards and protocols. It serves as a visual front-end to unify
access to distributed resources. It can also be integrated into other software tools.
Bluejay is available as both a secure applet that is suitable for new users, and a downloadable
standalone application for larger datasets and faster throughput.
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3. Bluejay Proxy Server Bluejay Browser
XLink XML SAX parsing into Data DOM
management
Session
management XLink management
Data
XML data
integration XPath-enabled legend creation
Translation User activity Abstract painting of visual models
Non-XML data data
into XML
Java2D painting of SVG imagery
WSDL-SOAP
BioMOBY services
processing
SVG
interactive
graphics
USER
An overview of the Bluejay architecture
3. Proxy Server Side
The proxy establishes communication between data sources (data, websites, and data analysis
services) and the Bluejay browser front-end. It also houses the internal components of Bluejay's
session management.
Before data can be visualized, it has to be standardized. This is accomplished via a data
preprocessing mechanism on the proxy Server side.
4. Browser Side
The browser receives and visualizes incoming XML data, providing the user with a collection of
data manipulation tools to facilitate data queries. It incorporates Scalable Vector Graphics
(SVG) in the creation and saving of documents through an open-source Apache SVG browser
called Batik.
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4. 5. Data Manipulation Tasks
The common tasks that Bluejay can perform can be summarized as follows:
1. Visual display customization
The main canvas and other display components can be customized to suit the user
preferences:
• The Legend can be pulled out of its holder and moved to anywhere on the
screen.
• Drawing preferences (such as background and foreground colors, fonts etc) can
be customized.
• All window components can be resized to suit the user needs.
2. Level-of-detail customization
The level of detail may be changed according to user preferences. This can be
accomplished in three different ways:
• View mode (pie chart/bar chart, single-frame/two-frame/six-frame graphical
view, and textual view),
• Semantic zoom (accomplished by zooming mechanisms), and
• Granularity adjustment (via the context tree).
3. Visual operations
The table below summarizes the scope of visualization operations of Bluejay as well
as the various manipulations that can be performed at each level.
Scope of
Manipulations of data
operation
Entire data set Change between linear and circular models of
the sequence
Switch between normal and reverse-
complement views
Rotate by a desired angle
Cut at a base pair position
Functional Interactive legend
categories Context tree granularity
Individual gene Click on the gene to bring up its data and
element XLinks (links to other data sources)
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5. 6. Bluejay and Knowledge Integration
Combining the knowledge of different biological components and data sources in order to
understand the entire organism is becoming very important, especially in the emerging area of
systems biology. Bluejay takes this eventual expansion and incorporation into account as it links
to various bioinformatics tools, and allows for other tools to link to it.
For example, through extensive XLink support, Bluejay integrates information from other
sources, including MAGPIE and Osprey. Magpie currently hosts 90 publicly available genomes
and uses extremely powerful sequence analysis accelerators, such as the Paracel GeneMatcher2
and TimeLogic DeCypher to produce comprehensive annotations of these genomes. Through
XLinks, Bluejay also links in other resources, such as NCBI web resources, PubMed article
citations, and a wide variety of MOBY services. Thus, Bluejay can be thought of as a visual
front-end to a distributed collection of bioinformatics tools and resources.
On the other side, other bioinformatics tools can launch a Bluejay browser as well. Currently,
MAGPIE provides hyperlinks to Bluejay, launching any of the available genomes in the browser.
Other tools will be able to link Bluejay browsers once the MOBY service broker is operational.
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6. Exercises
The exercise component of this Bluejay tutorial consists of two parts:
• A guided tour of Bluejay that allows you to explore all of the ways that Bluejay can help
you visualize significant data to be found in one of the available genomes.
• A “use what you have learned”part to create a final publishable image of an exploration
you are interested in.
1. Bluejay Guided Tour
Bring up your web-browser (Firefox or Internet Explorer) and go to the website
http://bluejay.ucalgary.ca. Click on the “App Preview” image and then click on “Web Start” in
the “One-click start” column to launch Bluejay.
Note: if you are using Internet Explorer, be sure to add http://bluejay.ucalgary.ca to trusted sites
(Tools Internet Options Security Trusted sites Sites, then click on Add).
Step 1 – Bookmarks and a first glance
Go to the menu Bookmarks Public Organelle Genomes in Magpie Guillardia
theta plastid. Wait for the image to appear. Notice that the browser logo Bluejay bobs
on the branch while the document is loading. What you see is a graphical
representation of a complete Guillardia genome.
Look at the Legend on the bottom left side of the screen.
See if you can locate the different functional categories
on the genome by color. Then single-click different
functional categories to first “ghost” and then hide them
in the main window. For more information about the
Legend, search for it in the Help Browser (Help Help
Browser).
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7. Step 2 – Zooming in for more information
On the top of the screen, below the http address line, is a zoom mechanism.
Play with the zoom to select the desired size of the image.
How much detail can you see? For more information about
the Zoom feature, search for it in the Help Browser.
Step 3 – Context Tree
Go to the Context Tree (found on the left side, top half of
screen). Scroll down and uncheck the “gene” box and then
click on Apply. Notice how the contents of the main window
change to display or hide the parts you have checked or
unchecked. For more information on how the Context Tree
works, search for "Context" in the Help Browser.
Step 4 – Navigation (keyboard shortcuts to make navigation easier)
Bluejay is riddled with unique and sophisticated navigation methods. Below is a short description
of how to efficiently navigate in Bluejay. For example, put your mouse cursor in the main
windows and try the following short-cuts:
Keyboard + mouse button combo Effect
SHIFT key + LEFT mouse button Drags the document around
SHIFT key + RIGHT mouse button Drag zooms the document in or out
CTRL key + LEFT mouse button Drag selects the viewing area for the
document
CTRL key + RIGHT mouse button Drag rotates the document
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8. Step 5 – Navigation (“go-to”)
Select 400% from the zoom drop down menu. Click on the
Navigation tab on the bottom left size of the screen and enter
a specific base pair position in the sequence, or use the slider
to select a base pair to “go to” and then click Apply. Notice
that the main window image reloads to show the sequence
section that surrounds the chosen position.
Step 6 – Looking at the data with a different view
In the View menu, several ways to visualize the entire dataset are available. Pie Chart and Bar
Chart summarizes the data based on percentage of functional categories this dataset contains.
Two Frame view displays the sequence information graphically, and Six Frame view expands the
graphical representation to include all six possible reading frames (three normal and three of the
reverse-complement). Text view provides the sequence data explicitly, highlighting the text
according to the functional categories and consistently with the graphical views. Now try the Pie
Chart, Bar Chart, Single Frame, Six Frame, and Text views to see what the views like.
Step 7 – Hyperlinks in the document
Now reset the view to Two Frame (View Two Frame) if it isn't already in this view. Left click
on one of the genes in the sequence. Notice that a list of links comes up. The first link is one to
the corresponding MAGPIE web page for this gene (if available). The other items in the list (if
any), are BioMOBY Services. In short, BioMOBY services display extra information inherent in
the data set for this gene. For more information on BioMOBY, search for it in the Help Browser.
Step 8 – Viewing the data "behind the scenes"
Go to Document View Raw Data. The newly opened window shows the raw data in BioML
format, which is a kind of XML. It describes the structure of the Guillardia genome using a
markup language (tags). The file is organized as nested tags. For more information about this
feature, search for it in the Help Browser.
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9. Step 9 – Saving the graphics to be printed later
Go to Document Convert Image to SVG. Then select Current Screen. You will next be
prompted to enter a file name and a location to save the SVG file as. (For more information on
what SVG is, see the W3C website (http://www.w3.org/TR/SVG/).) The resulting file will be a
high-quality image that can then be manipulated in imaging software that supports the SVG
format (such as CorelDraw). For more information about this feature, search for it in the Help
Browser.
Step 10 – More views to consider
Go to View Show Shape Tab. Select Linear and then click
Apply. What you see now is a linear representation of the
Guillardia genome. For more information about this feature,
search for it in the Help Browser.
Step 11 – A different orientation
First, make sure that you are in the circular shape (see Step
11 on how to change to circular shape). Go to View
Show Orientation Tab. Select Rotate and change the
degrees box to 45 and then click Apply. The Guillardia
genome has now been rotated 45 degrees clockwise. For
more information about this feature, search for it in the
Help Browser.
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10. Step 12 – Looking at the other strand
In the Orientation tab, select the Rev. Comp. (Reverse
Complement). Click on Apply. Notice that the
complementary DNA strand has now been reversed and has
traded places with the original strand. For more information
about this feature, search for it in the Help Browser.
Step 13 – Limiting what you want to see
Make sure that you are in the linear shape (see Step 11 on
how to change your shape). In the Orientation tab, select
the Cut option. Slide the ruler over to some number and
click Apply. Use the Navigation Tab and mouse zoom
features to see that the top left of the linear view has
shifted and now starts at the base value that was entered.
For more information about this feature, search for it in the
Help Browser.
Step 14 – Comparing genomes
Go to Bookmarks Public Viral Genomes in Magpie Fuselloviridae Sulfolobus spindle-
shaped virus 1 (SSV1). Wait for the image to appear. Next, go to Comparison Add
Sequence Add from Bookmarks, and then follow the same menu chain to load Sulfolobus
spindle-shaped virus 2 (SSV2). You are now in the “comparison” mode and have two similar
genomes displayed together for comparison. Notice the three lines linking the two genomes.
They link the genes from each genome that belong to the same functional categories. Once in
comparison mode, you can choose to add yet another sequence, unload all or one slave
sequences, or specify a slave sequence as the new master sequence, etc. You can do all these
under the Comparison menu.
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11. Step 15 – Setting window preferences
Go to Program Drawing Prefs. to change or customize your color schemes and display
references. Try it out with different text preferences and graphical display elements.
Step 16 – Take notes!
Click on the Notes tab and enter some notes in the text window. In later versions of Bluejay, this
Notes pane will be saved along with your other session-related information. See that they remain
there with the document. For more information about this feature, search for it in the Help
Browser.
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12. 2. Using What You Have Learned
In this part, you will launch Bluejay from an external genomic resource, MAGPIE, and use the
tools presented in Part 1 to create a publication-quality image.
Step 1. Run Bluejay and select a genome of your choice from Bluejay bookmarks.
Step 2. Use the various tools and manipulations introduced in Part 1 above to explore the
genome you have selected.
Step 3. When you have isolated any information that you find interesting, save it as an SVG
image for future reference.
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