UTGB Medaka User Manual

​The University of Tokyo Medaka Genome Browser (UTGB Medaka) is a web-based genome database browser, which provides various information related to medaka genomes, including assembly sequences, genes, clones, homologus genome sequences to other species, etc.

The distinctive features of ​UTGB Medaka are as follows:

• Highly-sophisticated web interface with drag & drop and resize supports of database tracks.
  • In UTGB Medaka, we aggressivly incorporated the latest web application technologies, including ​Google Web Tooklits (GWT), to enhance the user experience. Traditional web applications have to redraw the entire page in order to move or resize some components within the displayed page, which requires frustrating page reloading. But in ​UTGB, drag & drop and resize operations can be performed quite smoothly, since we can relocate components (such as tracks) in a page locally by using JavaScript? engine, which requires no page reloading. The modern web browsers (e.g., IE, Firefox, Safari, etc.) are already equipped with JavaScript? engine, so you can use the ​UTGB Medaka immediately.

• Quick responce via AJAX (Asynchronous JavaScript? + XML) technology. AJAX is a kind of back-ground internet connection, which can utilize the idle network while you are viewing a page. For example, our keyword search engine can quickly show your interested sequence positions from the input keywords. You can search genome posisions using gene names, clones, EnsembleID, GO:Id, etc.

• Customizable views: Your configuration, such as a set of displayed tracks, track frame sizes, etc. can be saved as a file on your PC, and you can restore the browser state from the saved file.

Browser Interface

The UTGB's interface has several tracks that can be used to browse genome sequences, genes, SNPs, etc. For the details of available tracks, see UTGBMedaka/Track.

Track Frame

Icons

	Configuration button	Open the configuration panel for the track
/	Adjust the height of the track	Resize the track frame height according to the track image size
/	Minimize/Open? track button	Minimize the height of the track frame
	Close Button	Closes unnecessary tracks