Adding a personal touch

There's one major menu option we haven't taken you through yet and that's My MetNet. When you hover over the option with your mouse cursor, the tooltip gives you a hint of what's in store. This is the option that gives you access to the personalization features of our site. Go ahead, click it. You know you want to...
In order to use the personalization features of MetNet Online, you need to authenticate yourself with your username and password. If you don't have an account yet, you can create a new account from this page as well.
Upon successful login, take a moment to go back to the main page for the site. You'll see some additional icons appear that let you interact with our personalization features.
Go ahead and browse to your favorite pathway. You'll see a star appear next to the menubar that lets you choose visualization options. This is another sign that authentication was successful and that you can start using the personalization features. The star lets you bookmark what you're viewing. It doesn't get added to your browser bookmarks though, but to your "My MetNet" bookmarks. You can still use browser bookmarks as well if you want to, by the way. It's just that your browser will treat them like any other bookmarks, while MetNet Online can do some pretty neat things with them, as we'll see later on in this tutorial.
Go ahead and click the star to bookmark your current pathway. You'll get a notification that tells you that bookmarking was successful. If you click the bookmark-icon a second time by the way, the system will inform you that you already bookmarked the pathway.
Now go back to the main page. See those four new icons still? Click on the star again, this time to access an overview of all your bookmarks.
You see that there are three types of data that you can bookmark: pathways, interactions and entities. You'll also notice that in our example, we have α-D-glucose bookmarked. This is handy, because in the future now we can reference to it directly, without having to wade through the hundreds of search results anymore. Not every search yields that many results of course, but it's still a perfectly justified use of bookmarks.
Let's say that we're interested in starch metabolism. We've looked up the different starch-related pathways (biosynthesis and degradation). We could bookmark each pathway and combine them in some way, but then we would see an integrated clutter of transcription, translation and other peripheral events in which we're just not interested for the time being.
So, instead of bookmarking complete pathways, we can scroll down to where the interactions in the pathway are shown and bookmark only these interactions of interest to us.
In this case, we select all the enzymatic reactions and click the bookmark icon that accompanies the table.
A notification message informs us that we've bookmarked all the enzymatic reactions that we've selected.
Let's go to our other pathway of choice: starch biosynthesis.
Repeat the procedure: instead of bookmarking the entire pathway, scroll down to the individual interactions.
Select all enzymatic interactions and bookmark them. Watch the notification window to make sure they're all bookmarked.
Now when you go back to your bookmark overview page, you'll see your enzymatic reactions under the "Interactions" heading. By clicking on the link "visualize these interactions into a single network", you can open the by now familiar visualization interface.
This is the integrated network. Note that in the information frame (underneath the thumbnail), no reference is made this time to original pathways. The system only shows the integrated interactions, it doesn't keep track of where they originally came from. By the way, you can see this integrated network for yourself here.
Biological pathways are connected. What if you want to interact with the pathways that have to do with a set of genes or metabolites? Well, just like interactions and pathways, you can also bookmark entities.
In this screenshot we've bookmarked every variant of Gibberellic Acid. We're interested to get an overview of GA metabolism and regulation.
Lists are a new concept that is being introduced at this point. They hold collections of entities of interest.

You can convert all of your currently bookmarked entities into a single list for convenient management and future lookup.

After naming your list and clicking the "Create list" button, you can a confirmation message. But where did the list go?
Choose "My Lists" on the menubar and you get an overview of all of your lists. Note our newly created list at the bottom. We're told how many entities are in it, and the trashcan icon next to it allows us to delete the list, should we no longer want it. There are multiple ways to create lists by the way, we've only shown you one here.
When you click on the name of the list to see more detail, you see this screen. The icon in front of each entity means that the entity is recognized as a MetNet entity. Should you use other ways to create lists, you will occasionally encounter entities that are not in our database. We're still interested in pathways, so we click on the "Common pathways" tab.
Because people want to see different things, we provide different orders to link your entities with pathways. There are three different view available. The first view shows you alphabetized pathways that were found to be relevant to the entities. Per pathway, the relevant entities are shown.
The second view shows entities, followed by relevant pathways per entity. You'll recognize the table format: yes, you can select multiple pathways in this interface and integrate them into a single network.
The final view shows an undifferentiated list of pathways that are linked to one or more of the entities in your list. This is more of a quantitative view, as it doesn't tell you how many entities were found in the pathway, or how many pathways a particular entity is found in.
List are good. Use them to keep track of related entities, or differentially expressed genes. And as always: feel free to share new applications with us so we can pass them on to other scientists.

This concludes our tutorial on how to use the personalization features of the MetNet Online website. You can select another tutorial if you wish.


Copyright Wurtele lab