User Guide

Quick Start

Location search

Sequence search

Full text search

Field specified search

Multiple Chromosomes Annotation Browsing

Data Analysis support

BioMart-compatible query

Web Service query

Computational analysis support

User Registration & User Space

User registration

Make evaluation for track

Add comment for entry

Browsing history record

Sequence query result record

Upload & Manage My Tracks

Quick Start ^

ABrowse provides different query methods for quick navigation: location search, sequence search, full text search and field specified search. User can browse query result in the center panel, smoothly draging and zooming in/out. Moreover, it's convenient to change between normal view and basepair view.

Location search

User can input an exact location to browse an interested region in two formats: (1)chr:start-end, like "chr2:190,542-230,976". (2)chr:start+length, like "chr2:190,542+1000". By specifying interested annotations by setting "Track Options" switch, user can browse desired data types.

Sequence search

User can input fasta format sequences directly to initialize a search. ABrowse will map the input to the whole genome, and return the mapped locations.

Full text search

Full text search is supported by input concerned words directly.

Field specified search

Field specified search is supported for both annotation data and user-supplied comment data. User can retrieve desired data directly from this interface.

Multiple Chromosomes Annotation Browsing ^

ABrowse allows user to smoothly browse multiple chromosomes annotation simultaneously which is convenient for genome comparison. User can use the magic wand in the middle of navigation arrows to select a region and zoom in in the main canvas or in a sub window. (Click the magic wand to activate selecting status, then click a point as the start point and release the mouse. Now move to the end point and click it, then the rectangle area between the start point and end point is selected.)

Moreover, browsing tracks are listed in the "Current Tracks" panel, and user can reorder them according to comparison analysis. (Clicking the up-down arrow beside the track name, and drag it to the desired location.)

Data Analysis support ^

BioMart-compatible query

User can execute BioMart-compatible batch query under the BioMart schema for data retrieval. Select a dataset and interested fields, then set the query conditions, user can get the desired result.

Web Service query

The main aim of ABrowse Web Service is to provide programmatic access to the underlying database in order to help users in integrating ABrowse into their applications. To ensure software from various sources work well together, this integration technology is built on open standards such as Simple Object Access Protocol (SOAP), a messaging protocol for transporting information, Web Services Description Language (WSDL), a standard method of describing Web Services and their capabilities. Currently, ABrowse Web Service is compatible with Taverna workbench of myGrid project.

The ABrowse WSDL specifies the contract between external developers and the ABrowse Web Services. The Web Service Description Language (WSDL) is an XML format for describing network services. And a WSDL binding describes how the service is bound to a messaging protocol, particularly the SOAP messaging protocol. The ABrowse WSDL file is:Web Service WSDL File.

Interface Description:

Method Name Parameters Result Type

getGenomes() No parameter String Array of all genomes

getTracks() String genome String Array of all tracks

getAnnotationNumberFromRegion() String genome, String track, String chromosome, String start, String end, String length_greater_than, String length_less_than, String strand Integer of result number

getAnnotationFromRegion() String genome, String track, String chromosome, String start, String end, String length_greater_than, String length_less_than, String strand Two-dimension String Array of annotations (maximum results upto 2000 entries at a time)

getAnnotationFromID() String genome, String track, String ID Two-dimension String Array of annotations (maximum results upto 2000 entries at a time)

getComment() String genome, String track, String entryID, String account Two-dimension String Array of comments (maximum results upto 2000 entries at a time)

fullTextSearch() String queryString Two-dimension String Array of annotations (maximum results upto 2000 entries at a time)

Web Service interface JavaDoc: ABrowse interface JavaDoc

Test Case (in Java code): ABrowseWSClient.tar.gz

Test case in soapUI can be found in the soapUI test page.

Computational analysis support

All the sequence data and query data in ABrowse can be sent to external bioinformatic analysis platform WebLab or Galaxy for further computation in one click. User can submit data in four ways:

(1)Select a region in the graphic chromosome and submit the selected sequence. (Click the magic wand to activate selecting status, then click a point as the start point and release the mouse. Now move to the end point and click it, then the rectangle area between the start point and end point is selected.)

(2)Submit nucleotide/protein/genomic sequence in "Entry Detail" directly.

(3)Submit BioMart batch query result directly to external bioinformatic analysis platforms.

(4)Submit comment search result directly to external bioinformatic analysis platforms.

User Registration & User Space ^

ABrowse provides user space for customized data.

User registration

User can register a ABrowse account freely. As a registered user, user can add own annotaion, make track evaluation, save important analysis status and save sequence query result.

Make evaluation for track

ABrowse allows user to make track evaluation by adding stars and comments. One user can add comments many times, while only one time for star evaluation.

Add comment for entry

User can add comments for entries with private/public privilege. If it's private, then only the contributor can read it. If it's public, then everybody can read it. Therefore public comments are useful for sharing and exchanging knowledge among members, while private comments can be taken as personal online work notes.

Besides pre-computed entry, ABrowse provide "My Instant Note" (Demo Video) for every registered user, supporting user to select a region on-the-fly and attach comment for it. Then user can add comment for any length of region freely, ranging from a single nucleotide SNP position to a long QTL region. (Click the magic wand to activate selecting status, then click a point as the start point and release the mouse. Now move to the end point and click it, then the rectangle area between the start point and end point is selected. Choose the last item "Add region to my instant note", and add comment to the region, then it will be added in the "My Instant Note" track instantly.)

Browsing history record

By recording browsing status as a "landmark", user can quickly jump to preserved important analysis status. Moreover, login user can share landmark with specified users. (This function is available for both registered user and guest.)

Sequence query result record

Sequence search results can be saved automatically for further analysis. (This function is available for both registered user and guest.)

Upload & Manage My Tracks

Login user can upload own data from web interface. After setting the track name, genome name, file format, privilege and file path, user can upload local file to the ABrowse genome browser instantly and do further analysis under the context of the other tracks. Uploaded tracks will be listed in the "My Tracks" panel, and user can delete it if it's unnecessary.

Tips:

ABrowse supports data transport in compression files. Please set the "network.http.accept-encoding" to "gzip,deflate" in your browser to enable compression files accepting, which will speed up your browsing.

If you are using the Safari browser, please remove the "Block pop-up windows" option

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