lei kong, ph.d. center for bioinformatics peking university abrowse - a general purpose genome...
DESCRIPTION
Information Panel Navigation Bar Annotation Canvas GFF Data Expression Data WIG Data BED DataTRANSCRIPT
![Page 1: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/1.jpg)
Lei Kong, [email protected] for Bioinformatics
Peking University
ABrowse - A General Purpose Genome Browser Framework
![Page 2: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/2.jpg)
ABrowse
• Data Visualization User Interface
• Data Retrieve and Analysis
• User Space
• ABrowse Customization
![Page 3: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/3.jpg)
Information Panel
Navigation Bar
Annotation Canvas
GFF Data
Expression Data
WIG Data
BED Data
![Page 4: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/4.jpg)
Display Information in Sub-windows
![Page 5: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/5.jpg)
Multiple Sub Views in One Page
![Page 6: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/6.jpg)
The main canvas can be embedded into html pages of other sites.
![Page 7: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/7.jpg)
ABrowse
• Data Visualization User Interface
• Data Retrieve and Analysis
• User Space
• ABrowse Customization
![Page 8: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/8.jpg)
A Uniform Query Box for Location and Sequence Searching
![Page 9: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/9.jpg)
Sequence Search
![Page 10: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/10.jpg)
Full Text Search and Complex Query
![Page 11: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/11.jpg)
Compatible with BioMart
![Page 12: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/12.jpg)
Submit data to external bioinformatics platforms
![Page 13: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/13.jpg)
Providing Web Services Interface
![Page 14: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/14.jpg)
ABrowse
• Data Visualization User Interface
• Data Retrieve and Analysis
• User Space
• ABrowse Customization
![Page 15: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/15.jpg)
ABrowse Provides Track Evaluation Function
![Page 16: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/16.jpg)
Adding/Managing Comments fora Single Entry
![Page 17: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/17.jpg)
More flexible, user may create an instant note by selecting an area on the genome
![Page 18: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/18.jpg)
Uploading User tracks
![Page 19: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/19.jpg)
User May Create/Share Bookmark
![Page 20: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/20.jpg)
ABrowse
• Data Visualization User Interface
• Data Retrieve and Analysis
• User Space
• ABrowse Customization
![Page 21: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/21.jpg)
Annotation Database Layer
Bioinformatic Computational
Applications (e.g., Galaxy, Taverna,
WebLab)
Data Query Web Interface
User Interaction Layer
Visualization Engine
Data Query Engine
Data Processing Layer
SOAP-based Web Service for Data
Retrieval
User-Space Engine
BioMart Engine
Browsing Canvas User-Space Web Interface
Genome Browser Web Interface
ABrowse Architecture
![Page 22: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/22.jpg)
ABrowse for Site Administrator• We provide step by step installation guide.
• We provide a set of utilities to help site administrators to import data.
![Page 23: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/23.jpg)
ABrowse is Highly Configurable
• global.abrowse.xml for globle settings
• genome_name.abrowse.xml for each species, for example:– arabidopsis.abrowse.xml– japonica.abrowse.xml– indica.abrowse.xml
![Page 24: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/24.jpg)
Each single track could have more than one type of view
![Page 25: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/25.jpg)
ABrowse is loosely coupled with DBMS and table schema.
• Site admin may specify SQL sentence for each track view.– ABrowse demands the tables have 3 columns
contains chromosome location including, chr name, chr start and chr end information.
![Page 26: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/26.jpg)
Controlling the Action of Clicking an Entry
![Page 27: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/27.jpg)
ABrowse for Developer• By writing rendering classes, developers could
add new view types for tracks.
……
……
……
![Page 28: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/28.jpg)
Conclusion
• ABrowse provides an intuitive approach for users to navigate genome interactively.
• ABrowse supports full text search and bulk data retrieve function.
• A multiple functional user space is supported by ABrowse.
• As a framework, ABrowse is easy to install and highly configurable.
![Page 29: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/29.jpg)
Web Access StatisticsM
ay-1
1
Jun-
11
Jul-1
1
Aug-
11
Sep-
11
Oct-1
1
Nov-
11
Dec-1
1
Jan-
12
Feb-
12
Mar
-12
0
5,000
10,000
15,000
20,000
25,000
30,000
35,000
http://www.abrowse.org/
![Page 30: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/30.jpg)
RhesusBase
CottonDB
Rice-Map
![Page 31: Lei Kong, Ph.D. Center for Bioinformatics Peking University ABrowse - A General Purpose Genome Browser Framework](https://reader035.vdocuments.net/reader035/viewer/2022062413/5a4d1b547f8b9ab0599a8952/html5/thumbnails/31.jpg)
Acknowledgement
• WANG Jun, Ph.D. Student• Prof. GAO Ge• Prof. LUO Jingchu
We appreciate great help from• BioMart• Galaxy • TAIR• VISTA