1. Click anywhere to go on to the next slide This demonstration is best viewed as a slide show, enabling you to simulate a session and make changes in cursor position more obvious. To do this, click Slide Show on the top tool bar, then View show. Tour of ViroBIKE Analysis of Metagenome Aggregates ViroBIKE (Biological Integrated Knowledge Environment) combines: Knowledge: All completed viral genomes known to NCBI Many viral metagenomes Analytical Tools: A powerful graphical language that permits creative expression to those with no programming experience It is accessible through a virological community web site: http://ixion.csbc.vcu.edu/virobike

2. In this tour, you'll see how to: Tour of ViroBIKE Analysis of Metagenome Aggregates Slide 4 8 17 24 32 37 80 85 92 You can go to any slide in this tour at any time by typing the slide number and pressing Enter. Log onto ViroBIKE Speak BioBIKE (the language of ViroBIKE) Find the number of contigs in a metagenome Find the average contig size in a metagenome Find the average GC content within a metagenome Visualize the distribution of GC content amongst the contigs of a metagenome

3. Coming Attractions! If you like this tour, you might also try Sequence Comparison, where you'll see how to: Display the sequence of a metagenome contig Find similar sequences amongst metagenomes Find similar sequences amongst known viruses Find similar sequences amongst everything in GenBank Make a sequence alignment Make a phylogenetic tree

4. The public can access everything at the community web site (except member names and e-mails), but only registered users can write to it. For now you're public. Access ViroBIKE through the blue bar. URL: htpp://ixion.csbc.vcu.edu/virobike

5. Click the link to the public access login screen.

6. Enter anything you like as a login name, but no spaces or symbols. No password necessary. Click New Login Your name (no spaces)

7. You can leave the blue bar to access other resources, but screen space is scarce, so grab it and move it offscreen to the left. Construct the code you want to execute here! For a visual guide to the VPL, click here

8. Function palette Results window Construct the code you want to execute here! For a visual guide to the VPL, click here The BioBIKE environment is divided into three areas as shown. You'll bring functions down from the function palette to the workspace, execute them, and note the results in the results window Workspace

9. Construct the code you want to execute here! For a visual guide to the VPL, click here Two very important buttons on the function palette: On-line help (general) Something went wrong? Tell us! HELP! PROBLEM

10. Construct the code you want to execute here! For a visual guide to the VPL, click here Two very important buttons in the workspace: Undo (return to workspace before last action) Redo (Get back the workspace you undid)

11. Construct the code you want to execute here! For a visual guide to the VPL, click here Our Story Suppose you have a special interest in a sequence, a contig, derived from the metagenome taken from the Arctic Ocean. The metagenome is called p-arct. How many sequences does that metagenome contain? Clicking on or hovering over any palette button brings down choices of functions or data to bring into the workspace. Click on the LISTS-TABLES button to reach a function that will count how many sequences are within the list of sequences that make up the metagenome p-Arct.

12. Construct the code you want to execute here! For a visual guide to the VPL, click here

13. Construct the code you want to execute here! For a visual guide to the VPL, click here

14. A COUNT-OF function box is now in the workspace. Before continuing with the problem, let's consider what function boxes mean.

15. General Syntax of BioBIKE Function-name Argument (object) Keyword object Flag The basic unit of BioBIKE is the function box. It consists of the name of a function, perhaps one or more required arguments, and optional keywords and flags. A function may be thought of as a black box: you feed it information, it produces a product.

16. Function-name (e.g. SEQUENCE-OF or LENGTH-OF ) Argument: Required, acted on by function Keyword clause: Optional, more information General Syntax of BioBIKE Flag: Optional, more (yes/no) information Function-name Argument (object) Keyword object Flag Function boxes contain the following elements:

17. General Syntax of BioBIKE Function-name Argument (object) Keyword object Flag … and icons to help you work with functions: Option icon: Brings up a menu of keywords and flags Clear/Delete icon: Removes information you entered or removes box entirely Action icon: Brings up a menu enabling you to execute a function, copy and paste, information, get help, etc

18. Back to our story… we wanted to count the number of contiguous sequences in our favorite metagenome p-Arct. Click on the gray argument box to activate it for entry, either from the keyboard or by insertion.