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  1. 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. 1
  2. 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. 2
  3. 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. 3
  4. 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) 4
  5. 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. 5
  6. 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 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 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). 6
  7. 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 7
  8. 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. 8
  9. 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 ( 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. 9
  10. 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. 10
  11. 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. 11
  12. 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. 12