computer science

Integrated Genome Browser

Integrated Genome Browser is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Integrated Genome Browser rather than just read about it. In short: Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an open-source genome browser, a visualization tool used to observe biologically interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays. History Integrated Genome Browser was first developed at Affymetrix for their scientists and public sector collaborators to visualize data from genome-wide til…

Key takeaways

Integrated Genome Browser belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Integrated Genome Browser to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Integrated Genome Browser from memory before moving on to harder problems.

Reference excerpt

Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an open-source genome browser, a visualization tool used to observe biologically interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.

History Integrated Genome Browser was first developed at Affymetrix for their scientists and public sector collaborators to visualize data from genome-wide tiling arrays. The first iterations of IGB were developed using funding from NIH awarded to company scientists Gregg Helt and Tom Gingeras. In 2004, Affymetrix released IGB as open source software, along with the Genoviz SDK, a graphics library for building genome browser applications. The first release of the code base was done as a compressed file archive. Soon after, the code was imported into a new repository at SourceForge. Since then, all development has proceeded in public under an open source model. In early 2008, a group led by former Affymetrix employee Ann Loraine began developing and maintaining IGB, supported by funding from the National Science Foundation and new investigator funds from UNC Charlotte. Since then, Loraine, her students, and collaborators have added many new features and capabilities, notably support for visualizing high-throughput sequencing data from Illumina and other platforms. In 2014, they migrated the source code to a git repository at Bitbucket. In 2020, Oracle's Java Magazine named the Integrated Genome Browser as one of the 25 greatest Java apps ever written.

Description IGB is built on top of the Genoviz SDK, a Java library that implements key visualization features such as dynamic, real-time zooming and scrolling through a genomic map, a feature of the IGB browser that sets it apart from many similar tools. IGB is also distinguished by the ease with which individual labs can set up data source servers to share data, notably, via REST-style Web services (Distributed Annotation System) and a simple file-system based approach called QuickLoad.

Supported formats IGB reads data in dozens of formats, including BAM, BED, Affymetrix CHP, FASTA, GFF, GTF, PSL, SGR, and WIG. The most up-to-date list is available at the BioViz Wiki. IGB can output visualized data in dozens of formats via the FreeHEP library. These include EPS, PostScript, PDF, EMF, SVG, SWF, CGM, GIF, PNG, and PPM.

References

External links Genoviz SDK at Bitbucket IGB installer download site

Illustrations

Worked examples

Example 1 — a first encounter with Integrated Genome Browser

Start with the simplest possible case. Write down what Integrated Genome Browser claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Integrated Genome Browser before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Integrated Genome Browser ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Integrated Genome Browser

In research: Integrated Genome Browser appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Integrated Genome Browser in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Integrated Genome Browser is common in secondary-school and first-year university syllabi. It links to neighbouring topics Free bioinformatics software, so understanding it makes those chapters shorter.
In everyday life: Look for Integrated Genome Browser outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Integrated Genome Browser in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Integrated Genome Browser means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Integrated Genome Browser out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Integrated Genome Browser in simple terms?

Why does Integrated Genome Browser matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Integrated Genome Browser?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Integrated Genome Browser.