Lab 1.41 GelScape and GelBank David Wishart University of Alberta Edmonton, AB

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Presentation transcript:

Lab 1.41 GelScape and GelBank David Wishart University of Alberta Edmonton, AB

Lab 1.42 GelScape Web-enabled gel viewing and annotation tool Allows users to post, share and compare gels in a free, platform independent manner A Java Applet with extensive Perl and HTML Tested and operable on most platforms (UNIX, Linux, Windows, MacOS X) using most browsers (IE and Netscape > 4.5) Conceptually aligned with web mail Developed by Nelson Young & Casper Chang

Lab 1.43 GelScape Reference

Lab 1.44 GelScape Supports... 1D and 2D gel image uploading (gif and jpg) from local machine Non-local (server-side) storage of annotated gels Image resizing (zooming) Spot marking and unmarking Spot annotation (via Swiss Prot ID, mass fingerprint, hand annotation)

Lab 1.45 GelScape Supports... MW and pH grid drawing and dragging Spot edge detection and spot integration Interactive, image map spot annotation display Gel comparison (overlay, transparency) Gel legend display Image saving, image uploading (to GelBank), image printing (preview)

Lab

Lab 1.47 Sign in...

Lab 1.48 First Screen...

Lab 1.49 Select a Gel Image...

Lab Or Select Pre-existing Image

Lab Annotate/View Mode

Lab Kinds of Annotation Modes

Lab Swiss-Prot Mode (Fast)

Lab Mass Fingerprint (Fast)

Lab Click on a Marked Spot

Lab Setting Axes, pH & MW Grids

Lab If You Change Grid – Save!

Lab Zooming

Lab Zooming

Lab Peak Picking/Integration

Lab Peak Picking/Integration

Lab Toggle the Spot Box

Lab Click Box – Adjust Threshold

Lab Viewing A Gel Legend

Lab Printing a Hard Copy

Lab Saving Gels (3 Modes)

Lab Comparing Gels (3 Modes)

Lab Gel Warping

Lab Gel Warping

Lab GelBank A public, web-accessible database that stores annotated gels produced from GelScape Accessible directly from GelScape Gel Images are stored as clickable HTML Image Maps Supports gel querying from level of organism, organ/tissue, Swiss-prot ID and protein name Relatively few entries so far

Lab Federated 2D Gel Databases Remotely queryable via the web Attainable through SWISS-PROT search Linked to other 2D databases via web Image mapped 2D gel spots to support graphical image query Directly reachable from within 2D gel analysis software Appel, R.D. et al. Electrophoresis 17: (1996)

Lab GelBank Remotely queryable via the web Attainable through SWISS-PROT search Linked to other 2D databases via web Image mapped 2D gel spots to support graphical image query Directly reachable from within 2D gel analysis software Appel, R.D. et al. Electrophoresis 17: (1996)

Lab GelBank

Lab GelBank

Lab Let’s Try it...