Visualize genomes with Integrated Genome Browser
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1. The Integrated Genome Browser (IGB) is an open-source desktop application for interactively visualizing genomic data. 2. IGB allows users to load different data types like RNA-Seq reads, zoom and filter views, and share data configurations through Quickload files. 3. IGB is continually improved through an open development process involving testing, code reviews, and an issue tracking system. It serves as an extensible platform for third-party genomic visualization apps.
Visualize genomes with Integrated Genome Browser
- 1. Visualizing genomes with Integrated Genome Browser Ann Loraine, Dept. of Bioinformatics & Genomics, UNC Charlotte
- 2. Interactive visualization generates insight • Discover unforeseen trends • Use visualization to sanity-check results • Create data scenes to communicate discoveries
- 3. Example - RNA-Seq experiment investigating effects of dehydration stress on gene expression in Arabidopsis thaliana (model plant) • Extract RNA, made libraries for Illumina sequencing: – controls (well-watered) – treatments (no water) • Sequence libraries, align to gemome wet dry • Count overlapping reads per gene • Check alignments in Integrated Genome Browser
- 4. control 1 control 2 RNA-Seq reads aligned to genome
- 5. control 1 control 2 Control 1 has 622 aligned reads IGB tip: selection info box reports number of selected items IGB tip: click-drag selection tool to multi-select
- 6. control 1 control 2 Control 2 has 681 aligned reads Control 1 has 622 aligned reads IGB tip: selection info box reports number of selected items IGB tip: click-drag selection tool to multi-select
- 7. control 1 control 2 Control 2 has 681 aligned reads Control 1 has 622 aligned reads • Similar read count, different alignment pattern. • Control 2 has lower sequence diversity, artifact of library preparation.
- 8. • Desktop genome browser, implemented in Java • Research Goal: Develop best practices for genomic data visualization Free from BioViz.org
- 9. First developed at Affymetrix for visual analysis of genome tiling array data • Developed in early 2000s – Used GenoViz SDK library to implement fast zooming, interactivity – Developed first at UC Berkeley, then Neomorphic • Released to customers in 2002 (free) • Open source in 2004 • Loraine Lab took over development in 2009 • Funding from NSF, NIH
- 10. Open source license - Common Public License Version 1.0 • Free for everyone • License allows re-use for any purpose – No warrantee, guarantees • Funded by NIH, NSF grants – Users & developers volunteer time, effort IGB User's Guide > Get IGB > License
- 11. Many improvements since first release • Faster, more responsive – Local data caching – Multi-threading • Added more data types – Sequence data *Seq • Improved usability – More intuitive UI • Easy-to-use installers – Installer includes Java virtual machine – Updates when we release a new version Download Windows, Mac, Linux installers from BioViz.org
- 12. Constantly improving development process • Using git, fork and branch workflow – code review – functional review • Issue tracking system integrated with version control • Continuous integration – Test, build, release on every commit – Installers for every branch • Continual testing – each issue Continuous integration using Bitbucket Pipelines branch-specific installers for testing, custom releases developer's fork configured for pipelines
- 13. jira.transvar.org - issue tracking
- 15. 1. Fast, fluid animated zooming Semi-transparent zoom stripe – Focuses zooming – Boundary guide rule when zoomed in
- 16. right-click to search, run BLAST, open new views select & count 2. Highly interactive
- 17. drought stress heat stress control control control 24 hours recovery 3. High resolution images for presentations
- 18. 4. Visual analytics functions - filtering, summarizing
- 19. 5. IGB Quickload protocol supports data sharing & publication • Description files on a Web site or local folder • User adds Quickload URL to IGB • IGB reads description files • IGB lists files in UI • User opens files, loads data
- 20. <?xml version="1.0"?> <files> <file name="http://s3.amazonaws.com/araport/ERR274310/accepted_hits.bam" title="AWS bams/shoot/shoot - ERR274310" description="Aerial part of seedling with mock (NaCl) treatment" url="http://www.ncbi.nlm.nih.gov/Traces/sra/?run=ERR274310" foreground="0x64cc65"/> ... </files> • Quickload site is just a folder with meta-data files (data can be stored elsewhere) • Can be local or on-line • If on-line, can configure passwords annots.xml http://lorainelab-quickload.scidas.org/eplant http://lorainelab-quickload.scidas.org/eplant
- 21. User's Guide explains how at https://wiki.transvar.org
- 22. 6. IGB is extensible - a platform for creating new visual analytics functions for genomic data • IGB is comprised of modules called bundles – jar files with meta-data specifying packages visible to other bundles – Running in an OSGi container • Container controls bundle lifecycle – Loads, unloads bundles – No re-start, re-install required • Developers implement Apps as bundles – deploy bundles in on-line "bundle repositories" – Users install (activate) Apps using IGB App Manager To install and run IGB Apps: 1.Choose Tools > Open App Manager 2.Select an App 3.Click Install
- 23. IGB demo Slides will be available on SlideShare later
- 24. Resources • Team repository (fork this) - http://bitbucket.org/lorainelab/integrated- genome-browser • Issue tracker - http://jira.transvar.org • Users' Guide, Developer's Guide - http://wiki.transvar.org • On-line course (mainly links & reading) - http://canvas.instructure.com/courses/1164217
- 25. John Nicol Hiral Vora David Norris Ivory Blakley Nowlan Freese Allysa Gulledge Mason Meyer Archana Raja Ehsan Tabari Nick Ren Tarun Mall Danny Freese Ashwini Kadam Sanket Patil Deepti Joshi Vikram BishnoiFuquan Wang Devdatta Kulkarni Many thanks to...
Editor's Notes
- #3: Graphical visualization better than text visualization Interactive visualization better than static visualization https://www.coursera.org/learn/dataviz-design/lecture/CrnHW/static-versus-interactive-visualizations
- #5: Rule of thumb for data visualization: Can you tell just from looking at it that something's up? The idea is related to the concept of pre-attentive processing. This is the idea that some visual processing happens unconsciously, without seeming to require analytical effort. In this view, you can see the shape of the read alignments is very different.
- #7: Rule of thumb for data visualization: Can you tell just from looking at it that something's up? The idea is related to the concept of pre-cognitive processing. This is the idea that some visual processing happens unconsciously, without seeming to require analytical effort. In this view, you can see the shape of the read alignments is very different.