Integrated Genome Browser

Owned by Ann Loraine (Unlicensed)
Last updated: Apr 17, 2014 by ktsuttlemyreVersion comment
21 min read

Table of Contents

Goals

At the end of this tutorial, you will be able to:

  • Select a genome
  • Navigate in IGB (zoom and pan)
  • Zoom in on a gene, load sequence, and view its translation
  • Follow "linkouts" to find out more information about a gene
  • Use the Sequence Viewer to view different translation frames, spliced and unspliced sequence, copy and paste sequence
  • Load RNA-Seq data into a track, including read alignments and coverage graphs
  • Use IGB Annotation and Graph tabs to
    • Change track appearance, including
      • Colors and font sizes
      • Track labels
    • Change graph scaling to compare expression in different samples types
  • Record your results using
    • Bookmarks (notes, location, data sets)
    • Image Export function
    • IGB session saving and reloading

What you need

To do this workshop, you'll need

  • A computer with 5 Gb or more computer memory (RAM)
  • A computer with Java 1.5 or higher installed
  • Ability to download and install software from the Internet
  • Internet connection (the faster the better)
  • About two hours to do the tutorial from start to finish

You'll also need a basic understanding of molecular biology concepts. Terms like "DNA", "alternative splicing," "transcription", and "gene" should be familiar to you.

You should also be familiar with sequencing technologies and sequencing-based assays, including ChIP-Seq and RNA-Seq.

Download and install Integrated Genome Browser

There are two ways to get IGB.

The first (easiest) way is to use Java Web Start, a system for downloading and running Java-based software programs from the internet. However, your computer may have been configured to block Java Web Start, in which case we'll use a different method (igb.zip) to download and run IGB.

Check memory

To start, check how much memory is available on your computer. You'll need to know this to decide whether to run big, medium, or small memory IGB.

Make a note of the amount of memory your computer has and proceed.

Try Java Web Start to launch IGB

To launch IGB by Java Web Start, go to http://www.bioviz.org and click Download. You will see three IGB icons:

IGB Java Web Start icons

These icons link to a special type of file called a Java Network Launch Protocol (JNLP) file. A JNLP file contains computer-readable instructions for how to download and start Java-based software programs like IGB. However, because downloading and running programs from the Internet is often not a good idea, many systems administrators block computers from doing this. Which means: Java Web Start might not work for your computer system. But it is a good idea to use it because if your computer is configured to handle JWS applications, you'll automatically get IGB software updates and it's convenient and easy (when it works.)

If you are running Linux you can use icedtea to get similar functionality of Java Web Start.sudo apt-get install icedtea-netxIf you install IGB using Java Web start, then every time you launch the IGB program, Java Web Start will check to see if there is a new version of IGB available. If yes, the new IGB version will download and install it automatically. However, if you ever need to get an older version of IGB, they are available at the BioViz.org site.

IGB rules of thumb

  • If you have 8 Gb or more of computer memory, choose the "Large memory" option.
  • If you have 4 Gb of computer memory, choose "Medium memory" IGB.
  • If you have less than 4 Gb of memory, choose "Small memory" IGB.

When you click the icon, the corresponding JNLP file will download. If all goes well, your browser will launch the Java Web Start plug-in, which will then download IGB from BioViz.org and start it. Java Web Start may also show a window inviting you to create a shortcut icon for IGB on your desktop. If you click "yes", then Java Web Start will put a new IGB icon on your desktop which you can use to start IGB later on.

If this process fails, it's possible your computer might not have enough memory to run IGB. In that case, try a lower memory version.

If that doesn't help, the problem may be that your computer is not configured to allow Java Web Start to run. If this is the case, try downloading igb.zip.

If you can't use Java Web Start, download igb.zip

If Java Web Start didn't work, you can instead download igb.zip, unpack it, and launch IGB by double-clicking an IGB start script.

On the download page, click the link labeled igb.zip and download it. (Or you can use this link: igb.zip)

Save the file and then double-click it to unpack it (on Mac) or use a tool like WinZip on Windows.

When you unpack igb.zip, you'll see a new folder called igb. Open the folder and double-click one of the IGB script designed for your computer platform. There are three start scripts for the three different memory options: small, medium, and big.

  • The IGB start scripts for Mac end with .command
  • The IGB start scripts for Windows end with .bat
  • The IGB start scripts for UNIX end with .sh

When you double-click a start script, a new window will open called a "shell" or "terminal." This window will remain open until you close IGB. If you close the window, IGB will shut down. So you should leave it open until you are ready to quit IGB.

IGB Start screen - click to enlarge

Choose the Arabidopsis thaliana genome on the IGB start screen

When IGB first starts, it will show the IGB start screen. The IGB start screen contains scrollable images depicting different species whose genomes are available through the IGB QuickLoad data distribution site. If you click an image for a species, IGB will load the latest assembly for that species.

For this workshop, we'll work with the June 2009 (TAIR10) release of the Arabidopsis thaliana Columbia-0 genome assembly and the latest annotations. (For more information about this assembly, see http://www.arabidopsis.org.)

To chose the Arabidopsis genome, click the image labeled A. thaliana on the IGB start screen. IGB will then display the Arabidopsis genome and load gene models from the publicly accessible IGBQuickLoad server, which is a Web site with data files configured to supply data for IGB. Some of these files are also useful for bioinformatics analysis you might do using R/Bioconductor, bedtools, and other command-line tools. For example, the IGBQuickLoad site has a data file named TAIR10.bed.gz that contains the full set of TAIR10 gene annotations in BED Detail format, a tab-delimited format developed at UCSC.

The address of the QuickLoad server is http://igbquickload.org/quickload. To find out what files are stored on the IGBQuickLoad.org site, visit http://igbquickload.org/quickload in your Web browser. However, the site is not very interesting to look at in a Web browser. The best way to view the data from an IGBQuickLoad site is in IGB. The site is version controlled and is available for "check out" using svn from publicly accessible subversion repository https://svn.transvar.org/repos/genomes/trunk/genomes/pub/quickload.

Once the gene models load, IGB will show the genome's equivalent of "chromosome 1." To change to a different chromosome, click the *Current Genome* tab. Note that the IGB window consists of three parts. One is the IGB data display area, also sometimes called a "map." This data display area will show the genome sequence, genome annotations, and any other data sets you may add.  Data sets will be put into horizontal rows called "tracks," usually on a file-by-file or data set by data set basis. The other parts are tabs that contain buttons, menus, and other controls for manipulating data in IGB, creating and managing bookmarks, searching, and so on. There is also an alternative view called Sliced View that trims intronic sequence and is useful for viewing data from species (like human) with large introns. We won't cover it here.

IGB after Arabidopsis genome loads

Zoom in a gene model

One of the most important aspect of IGB that distinguishes IGB from other genome browser tools is IGB has many ways to move quickly through a genome. The main purpose of IGB is to make it easy to interpret and explore results from genome-scale experiments, such as data from RNA-Seq, ChIP-Seq or tiling array experiments. An RNA-Seq experiment, depending on the level of replication and the treatment or conditions being investigated, may produce many hundreds or thousands of differentially expressed genes. To evaluate the results and make sure the make sense, you'll likely need to look at many different genes in a single session. For this reason, we've made speedy navigation through the genome a top priority in IGB.

About zooming

Let's start with learning about zooming in IGB. The key thing you need to understand about zooming in IGB is how to focus zooming by clicking on a place in the map.

To zoom in on a location, click the spot where you want to zoom. Note that the zoom stripe, a vertical gray bar, hops to the wherever you click in the display. When you zoom, the zoom stripe will stay in place while the entire scene stretches or contracts around it. To zoom horizontally, drag the horizontal slider at the top right of the display. To zoom vertically, use the vertical slider.

Try it now:

  • Note there is a location to the right of 20,000,000 bp on chromosome 1 that has several blue lines stacked in a column. These represent a highly zoomed-out view of a gene that is alternatively spliced. Click the region nearby to focus zooming.

Click to focus zooming

  • Use the horizontal slider or the "plus" button next to the horizontal slider to zoom in. As you zoom in, the gene models you're aiming for will seem to scoot away. Re-position the zoom pointer by clicking to zoom in on the models.
  • Use the the vertical slider or the "plus" button next to the vertical slider to stretch the display vertically. Note that as you stretch the display vertically, labels and other annotations appear.

To make more room in the display, click the bottom arrow on the left side of the lower tabbed panels to minimize the tabs. Try to focus the display on AT1G61150 centered at around 22,543,000 bases.

Once you've zoomed in on the gene, using the panning (move) controls to further adjust the view. Try to center the gene in the middle of the display.

Zooming shortcuts

IGB has two important zooming shortcuts you should know about.

To quickly zoom to a region:

  • Double click on an exon or gene model to zoom in on it
  • Click-drag the sequence axis to zoom in on a region

Panning the display - move up or down, left or right

Panning the display means moving it left and right, up or down. There many ways to pan the display in IBG, including:

  • Choose the grab cursor (hand icon top left) and click the display to move it (By default, when you start IGB the selection tool (arrow) is choosen.)
  • Click the green arrow panning buttons to move left or right (toolbar)
  • Use the horizontal scroller above the bottom row of tabbed panels
  • Use the vertical scroller on the right side of the window
  • Click the arrow selection tool and click-drag the cursor into the left or right side of the main display window

Try it out now. Move the current zoomed-in scene to the center of the display using IGB panning tools. Try to recreate the following close-up view of AT1G61150

Close-up on a gene (click to enlarge)

How IGB represents genomic features (gene models)

When you've zoomed in far enough, the you can see details of individual gene models. Gene models, by default, contain arrows indicating the direction of transcription and use tall or shorter blocks to represent translated and untranslated parts of a gene model.

Note that the gene we zoomed in on (AT1G61150) has a complex pattern of alternative splicing affecting it's five prime region.

Selection in IGB

IGB is different from other genome browsers you may have used in that IGB allows you to interact with and manipulate gene models and other items in the display. However, to use these functions, you need to understand how to select entire gene models, parts of gene models, and tracks.

How to select a gene

To select an entire gene model, click its label, click slightly outside the gene, or click one of its introns. When you select a gene model, a red outline will appear around it. If you then click the "info" button (top right) or the Selection Info tab, information about the gene model will appear.

How to select part of a gene

To select a part of a gene model, such as an individual exon, click inside the exon. A red outline will appear around the exon when selected. If you then click the "info" button or the Selection Info tab, information about the exon will appear, including its start and end position and strand.

How to multi-select or add to the current selection

You can also select multiple items. When you multi-select, the number of selected items will appear in the box at the top right.  To select multiple items, click the display and then drag the mouse over the items you want to select. When you do this, you'll see a box appear over the region over which you drag the mouse and when you release the mouse button, a red outline will appear around everything you selected. To add to the current selection, click the item you want to select while pressing the SHIFT key.

How to remove an item from the current selection

To deselect an item without losing the other selections, click the item you want to de-select while pressing SHIFT-CONTROL.

How to select a track

Lastly, you can select one or more tracks by clicking or SHIFT-clicking the track labels. This is useful when you want to configure track appearance using the Annotation tab. (More on this later.)

Edge matching

Often you will need to compare boundaries of exons and introns from different gene models that overlap along the genomic sequence axis. To help compare boundaries, IGB implements a visualization technique called "edge matching" in which a highlight is added to the edges of items that have the same start or end as whatever is currently selected.

To see how edge matching works, change to back to the arrow cursor selection tool by clicking the arrow icon next to the hand icon.

Click one of the skinny lines inside one of the gene models to select the entire model. Note that a red outline appears around the selected model. Notice that the boundaries of other exon blocks in the display are highlighted. This highlighting is edge matching.

To make edge matching more noticeable, change the color of the edge matching highlight.

  • Choose File > Preferences
  • Choose Other Options
  • Under Edge Match, click the color swatch to choose a different color. Red is often a good option.

Take a moment to identify exons whose boundaries match or don't match.

You may need to zoom and in out on different parts of the models to find the places where they disagree.

Load sequence to view the conceptual translation for a gene

To see individual base pair translations, you must load the genomic sequence. If you do that, then IGB will be able to translate the gene models, allowing you to compare the translations across different splicing variants for the same gene.

Try it:

  • Zoom out a bit so that the entire gene (AT1G61150) is visible in the IGB window
  • Click the Load Sequence button to load the sequence
  • Zoom in on the start or stop of the taller part of the gene model.
  • Observe that the start and end of the taller parts correspond to start and stop codons respectively.

Take a moment to investigate how alternative splicing affects the coding region of the gene. Where do the translations differ?

Right-click a gene model to get more information about it

Change again the selection cursor (arrow pointer) and then right-click on the skinny middle of a gene to select it. Observe a menu appears (this is called a context menu) with the option to do a google search or go to the Arabidopsis Information Resource (TAIR). Choose the TAIR option and take a moment to look at the record for the gene.

Right-click again and note the option to view the sequence in the Genome Sequence Viewer. Choose View Genomic Sequence in Sequence Viewer.

A new window will open. Note that exons are colored yellow and introns are white, the start and stop codons are outline with green and red boxes respectively, and the coordinate on the left are with respect to the start of the gene model, not the genome.

Take a minute to look over and try out the different Genomic Sequence Viewer menu options. Note that you can select and copy sequence from the Sequence Viewer window, a useful feature if you need to copy the data into a search tool like BLAST at NCBi.

Genome Sequence Viewer (click to enlarge)

Zoom in on the sequence (and select sequence bases)

If you still have the sequence viewer open, close that now. Continue by clicking a location in near the five-prime end of the gene and zoom in horizontally until you can see the sequence bases. Using the selection tool, click-drag over the sequence. Note that a red outline appears around the sequence. Note that the position and number of bases you selected appears in the Selection Info box. Now, right click on your selection and make note of the options. You can either view the sequence in the genomic sequence viewer or simply copy the sequence to the clipboard.

It you choose the option "Copy selected sequence to clipboard," the sequence will be copied to your system clipboard and you can now paste it into a query tool or text document. Go ahead and copy a 5 base sequence using this method.

Search sequence

Now zoom out a bit more and load more sequence data. Click the Advanced Search tab. You can use the Advanced Search tab to search sequences within the currently visible region. You can also do keyword searches. For now, we'll demonstrate the sequence search.

Under Search, choose the Residues option. Paste the five-prime sequence you just copied into the search box and then click the Search button immediately to the left of the search box.

You should now see something that looks like the image below. Note that there is now a new annotation in the Coordinates track showing a match to your query and the match appears in the results table. Double-click the results table to zoom to the selected result.

Now repeat the process - but this time, we'll search for reserve complemented sequence:

  • Zoom in on the three prime end of the gene
  • Select some sequence downstream (three prime) of your previous results
  • Right-click the selected sequence, but this time, choose View Genomic Sequence in Sequence Viewer (Note: if your OS does not have a context menu use the menu bar located at the top of the window instead)
  • Within Sequence Viewer, choose View > Show Reverse Complement
  • Click-drag over the sequence to select it
  • Choose Copy > Copy Selected DNA Sequence
  • Go back to the main IGB window and zoom out again to show the entire gene.
  • Paste the sequence into the Search box. Leave the box "Overlay residues" checked. This ensures previous results won't be erased.
  • Click Search to search for the copied residues.

Note that now IGB will now show a second match symbol near the 3-prime end of the gene. Also note that the symbol is slightly offset from the first, indicating the match is on the minus or bottom strand.

Results after searching for the second sequence

Closeup on the right sequence

Closeup on the left sequence

Keep this in mind for later. It is very useful when designing and/or annotating primers for qPCR or other related molecular biology applications.

You can also use wild card characters (regular expressions) to search for closely related sequence in promoter regions.

Load data sets: T-DNA insertions

For this part of the tutorial, we'll load RNA-Seq data from a remote server. However, you could easily load data from a local file, using the File > Open menu.

Click the Data Access tab at the bottom of the IGB window. Note that the bottom left of the panel contains a listing of available data sets you can load into IGB.

TDNA insertion lines are lines of plants bearing T-DNA (transfer DNA) insertions at known locations in the genome. If a T-DNA insertion is located within the coding region of a gene, there is a good chance that the insertion is null or "knock-out" allele, which makes it useful for analyzing gene function. Researchers interested in studying the function of a particular gene can order T-DNA lines from Arabidopsis stock centers. Being able to visualize T-DNA insertions is important for understanding and predicting their effects on coding sequences, splicing, and transcription.

Select the checkbox labeled TDNA insertion lines. Note that when you select a data set to load, a new track appears in the main display window (above the gene models track) and that a new row is added to the Data Management Table in the Data Access Panel. Zoom out a little bit so that the gene we were looking at before is now about half the size of the window.

To load the data, click the Load Data button. You should now see thin, green marks appear in the TDNA track. Double-click on a TDNA feature to zoom in on it. Note that when you selected (and double-clicked) the TDNA insertion feature, the Selection Info box (top right) displayed the name of the line. To find out more about the line, such as how to order it, right-click the select TDNA feature and choose the Google option. A Web page will open showing Google search results. Follow the links to TAIR to find out how to order the line. Also take a minute to review the other links. Often, if some-one else has worked with a particular TDNA line, you can find out about from a Google search.

Also note that when you select an item, you can then click the "i" (info) button in the top right to view some information about the selected item, such as its name, it's length, its genomic coordinates, and other details about it. If you do this for gene models, you'll often get to see a short description of its function, if known.

If you no longer need to see a track, you can remove it from the display by unchecking it in the Available Data window or by clicking the red X icon next to the name of the track in the Data Management Table.

Remove the TDNA track.

Load RNA-Seq data - coverage graphs

Return to the Available Data window and open the folder named IGB Pollen. This folder contains data sets from an Arabidopsis pollen RNA-Seq data set. For details on the data, see http://www.plantphysiol.org/content/early/2013/04/16/pp.112.211441.abstract.

Open coverage graphs.

First, we'll load coverage graphs, which provide a overview of gene expression. Select the IGB Pollen folder and choose two data sets:

  • RNASeq > SM > Graph > Pollen, coverage.
  • RNASeq > SM > Graph > Drought Control 1, coverage.

Everything in the SM folder comes from reads that mapped exactly once onto the genome. MM stands for "multi-mapping" and contains data from reads that mapped two or more times to the genome.

Once you select the data sets, they will appear in the Data Management Table just as before.

Also make note of the "i" icon next to each data set in the Available Data section. Click on the "i" icon next to the pollen data set. Your Web browser will open a page that lists the contents of the IGBQuickLoad.org Pollen RNA-Seq data folder. All the files you see there are available for download and analysis. Make a note of two files:

  • pollen.alignments_distribution.txt
  • drought_control_1.alignments_distribution.txt

Click each file to view the contents. Note that each file lists the number of alignments for reads that mapped once, twice, three times, and so on. The key point for understanding the pollen RNA-Seq data is that the pollen data set had around 42 million singly-mapped reads (the first row) and the drought control 1 data set (called "seedling 1" in the paper) had around 38 million singly mapped reads. Thus the pollen data set had about 1.3 times more reads than the seedling 1 data set, which you should keep in mind when comparing coverage between genes. So if the apparently "fold-change" between two data sets is only 1.3 in favor of pollen, once you take read depth into account, there is not much evidence for enriched expression in pollen relative to seedling.

Load data

Zoom out to view about half of the chromosome and then click the Load Data button to load the entire coverage graphs for chromosome 1. If you are running IGB using the high memory option, you should be able to load the entire coverage graph for chromosome 1 into the viewer. If your internet connection is relatively fast, the data should load in less than a minute. However, if your connection is slow and you do not want to wait, you can cancel the load by clicking the red "stop" icon in the lower left corner. For this workshop, go ahead and let the data load.

Once both graphs are completely filled into the tracks, click and then SHIFT-click each track label to select both graphs. When a graph (or any other track) is selected, a red outline will appear around in inside of the track label rectangle. Next, choose the Graph tab in the bottom part of the display.

Take a moment to review the various options for modifying and configuring graphs. You can change graph color, change their names, and, more importantly, change their scale. For the remainder of the tutorial, we'll use the scaling options to compare the two graphs:

Change scale and height:

  • Use the Height slider to make the graphs a little taller. Warning: IGB may not appear very responsive - this is because it is attempting to render many data points at once. Be careful.
  • Use the Y axis scale double-headed slider to put them on the same scale. Enter values 3500 for "min" and "9330" for max if you have trouble using the double-headed slider.

You should see something like the following image.

  • Seedling and pollen coverage graphs*

Spend a few minutes to explore the coverage graphs. Note how some genes have extremely high coverage in the two different data sets and that the overall profile of the seedling and pollen data sets is very different. Zoom in on a region with high pollen expression. What gene did you find and what does the TAIR Web site have to say about that gene?

Zoom in on gene U2AF65A (splicing factor) using search box

Use the search box to search for a gene named U2AF65A. Enter "U2AF65A" in the search box and type ENTER. IGB should then jump the gene.

Take a moment to adjust the view so that it will be easier to examine the gene - we'll be looking at this gene in detail for the rest of the tutorial.

  • Click the TAIR10 mRNA track label to select it
  • Click the Annotation tab
  • Under Strand, choose the "+/-" option to put minus and plus strand features into the same view
  • Under Stack Height, click Optimize (We'll cover what this means later.)

Now, click Load Data again to load the coverage graphs for the U2AF65A region. Put the two data sets on the same scale as before and make note of the differences in the coverage graph in the alternatively spliced region.

U2AF65A Coverage Graphs

Do you see any differences in coverage? What part of the gene is affected? (Note: this gene is on the minus strand and transcription proceeds right to left.)

Open pollen and seedling 1 RNA-Seq read alignment data sets

We're finished with the coverage graphs for now, so remove them. Recall that to remove a data set, you can uncheck it from the Available Data panel or click the red "X" next to the data set listing in the Data Management Table.

Go back to the Available Data Panel and choose

  • Open Reads folder
  • Pollen, alignments
  • Control 1, Drought alignments (this is the same as seedling 1 in the paper)

Click Load Data to load the alignments into the viewer. You should see something like the following image from IGB:

U2AF65A after loading reads

Note that within each track, you see a series of blocks and connected blocks. These represent read alignments. Also, note how each track has a row of darker-appearing reads at the top of each track. These darker reads signal that there are many additional reads that can't be shown because there is not enough vertical space.
The reason for this is that there are often many hundreds or even thousands of reads overlapping a region and there is no way you could view them all without changing the vertical scale of the tracks.

Also note that the read sequences are drawn. To view just the differences between the reads and the genome, click the Load Sequence button, which will load the genomic sequence into the Coordinates track and allow IGB to highlight the differences between the reference and the reads.

To see all the read data, we need to configure the IGB display so that each track has enough space, but not too much.

  • To start, make the IGB window taller - as tall as you can make it.
  • Select the TAIR10 track and select the Annotation tab.
  • Click Lock Track Height to set the height of the track and set it to 150 pixels.
  • Click the down arrow on the bottom tabbed panels to hide the tabbed panels - we won't need them for a while.
  • Select BOTH the read tracks by clicking and SHIFT-clicking their track labels.
  • Now click the "Optimize Selected Tracks" icon second from the right in the IGB toolbar.

What you should see now is that all of the reads are now being shown, but there are so many of them that they are "crushed" into the track.

U2AF65A after optimizing stack height reads

Now that the reads are loaded, you can use them to investigate the difference you observed in the two coverage graphs in the preceding section of the tutorial.

To investigate the read alignments in more detail

  • Use the vertical zoomer to stretch the display.
  • Use the vertical scroller to move up and down.
  • Make note of the alternatively spliced region in the three prime (left) end of the gene.

Look at the pollen reads and then the seedling reads. When you finish looking at the pollen reads, click the "-" icon in the top left of the track to collapse it. The track won't be deleted - this just gets it out of the way while you're focusing on the other track.

Which splice variant has the most support in each data set?

Track Operations - FindJunctions

IGB contains a number of functions you can perform on annotation and graph tracks. To find out what functions are available for a given track, right-click on the track label and choose Track Operations.

In this demo, we'll use the FindJunctions feature, which creates junction features from spliced reads on a track-by-track basis. Junction features are a type of annotation the represents an exon-exon junction that was inferred from one or more reads that aligned across an intron. Junction features represent the splicing of exons that flank an intron inferred from the RNA-Seq dta.

To see how it works, right-click on the pollen and then the seedling tracks and choose Track Operations > FindJunctions > Use Default.

This will create two new IGB-generated tracks containing junctions inferred from the read alignments. Note each junction feature is labeled by a number; the number represents the number of reads that supported the junction.

IGB after using FindJunctions feature

In this case, the ratio of junctions in pollen is very different from the ratio in seedling, suggesting that the U2AF65A gene undergoes a pollen-specific splicing pattern.

Taking a picture

If you see a particular scene in IGB that triggers an insight or idea, you should take a picture of it so that you can refer to it later, use in talks or papers, and so on.

To take a picture

  • Choose File > Export Image or click the Export Image icon in the toolbar (it looks like a picture frame)
  • Enter the values for DPI and other attributes, and click OK

Making Bookmarks

To bookmark a scene, click the "Bookmarks" tab located on the right side of the screen. Click the Create Bookmark icon to make a bookmark. A window will then open that allows you to give a name to the bookmark and make notes on it.

Saving your session

IGB supports sessions, meaning: you can save a record of all the data sets you've loaded into IGB. To save a session, choose File > Save Session or click the Save (looks like a floppy disk) icon on the toolbar. The next time when you run IGB, you can open the session file and all the data sets you loaded previously will re-load into the browser.