BioMoby Dashboard

Dashboard is a Graphical User Interface helping Biomoby service providers to develop and deploy their Biomoby services. Because of its extensibility, however, it may (and I hope it will) contain also panels that are useful even for pure Biomoby end-users when they wish to call Biomoby services. One of them is the Simple Client that can call any service and has an extensible set of viewers for displaying results.

How to start Dashboard

At the moment, the only way to start Dashboard on your machine is to have a jMoby CVS local copy (how to do it). Once it is built, type:
ant dashboard
Later, you can also use the following (the reason for runing at least once the above is that it creates a dashboard configuration file - more about it below):
On Windows, similarly
ant dashboard
The first time, Dashboard connects to a default Biomoby registry, and fills its local cache with the Biomoby objects, and other entities. It may take few minutes, depending on the network connection. Next time, it starts almost immediately. You can (and time to time, you should), however, synchronise the local cache with the registry (there is a button Update for this purpose).

After started the first time, most of the fields will be empty. But once filled, the values will be remembered as your user preferences, and next time you start Dashboard, they will appear in the text fields.

Other ways how to get Dashboard are coming:

How to use Dashboard

Dashboard has several panels, but not all of them are immediately visible. You have to go to Setting --> Panels selection and choose the panels you would like to be loaded (Dashboard remembers it so you do not need to repeat it next time).

Each panel, and the Dashboard itself, has its own Help page, accessible either from the Help menu, or by pressing F1 anywhere (sorry, there is not any Back button in the help pages). This document has links to the panel help pages. Note however, that if the links (those by the panel figures below) do not work, the documentation was not built properly. If it happens in your own local installation of jMoby, just run an Ant task:

ant docs
From panel to panel, you can also navigate by pressing ALT-n where "n" is a panel number (the first panel has number 1).

All console windows serve as terminals - they display messages (and they are read-only, unless they have a different colour, then you can edit them, but it is rare). You can also save their contents, or copy & paste it (use the usual copy key combination CTRL-C). You can also increase and decrease their font. The verbose mode is rarely used, but you can control the append mode.

Most of the lists react also on the RIGHT-CLICK with the pop-up menus. You can also copy from a list by selecting a line and CTRL-C.

When using File choosers, be careful not to accidentally rename files (this cannot happen when using Java 1.5 and above).

Your user preferences (the last entered values) are stored in files. On Unix, in your home directory under a sub-directory .java, on Windows in the Registry, on Mac I don't know. If some remembered values bother you (e.g. they are too long), you can always find them in the preferences and remove them manually (but there is a plan to have this function available from Setting).

The sub-panels are often divided by a divider and can be re-sized by dragging the divider. You can drag the divider to any position as long as neither contained component goes below its minimum size. This is not the case with the two small arrows that appear on the divider - they let you collapse (and then expand) either of the components with a single click completely.

Dashboard Panels Gallery

The individual panels have their own help documents - click on the links below.

Registry Browser panel

Registration panel

MoSeS Generator panel

Simple Client panel

Registry Statistics panel

Debugging panel

Customize the available repositories / Adding a new Repository

This explains how you can manipulate the available repositories in your Dashboard.

Customize the available repositories

To manipulate which repositories shall be available in your Dashboard application you can edit the moby-live/Java/src/config/dashboard/ file.
Search for the dashboard.wanted.registries, which is per default not active. If you activate it by removing the # before the line you can remove the repositories by deleting the corresponding entry.
For example this is the original one:
#dashboard.wanted.registries = default,Calgary,INB,IRRI,testing
if you now want only to have the official BioMoby central and its test repository:
dashboard.wanted.registries = default,Calgary,testing
after that just start dashboard again with ant dashboard

Adding a new Repository

IMPORTANT: We do not encourage people to set up their own repository as every can use the official BioMoby central repository. But if in any case you have to set up an own repository this explains how to make it visible in Dashboard.

The easiest way is to type the URL and the URI in the Endpoint and Namespace (URI) input fields in Dashboard, respectively. Dashboard does remember your inputs and you can select your entries later again.

If you want to have it as an entry in the dropdown box you have to edit the moby-live/Java/src/org/biomoby/registry/meta/ file and add there your repository based on the template of the others. This should be only done if you know what you are doing !
After that you should add the name of your repository also to the dashboard.wanted.registries property inside the moby-live/Java/src/config/dashboard/

If you then restart dashboard you will see now your repository coming up.

Plans and issues

The latest developers notes and plans, even sometimes how they are prioritized, can be found in Dashboard Notes. Please be aware that it is completely informal, sometimes quite technical document (I am just trying not to write the NOTES in Czech, and usually I succeed ). But still it is the best place to see what is "under the hood" and what is coming...

Main known issues

Sometimes (but not often) when Dashboard starts, it displays an error message about a NullPointerException somewhere in the MetalUI interface. It continues to work fine but it is annoying... (Anybody would help to fix this?)

The tree that builds new data type (in Registration panel, under Data Type registration sub-panel) sometimes does not pain itself properly and needs to be refreshed.

Sometimes, I had problems with the Statistics Panel when a list of services was re-loaded. I think I fixed it, but one never knows... Please let me know if you witness anything strange.

Frequently Asked Questions

There are no stupid questions, there may be only stupid answers...



Dashboard starts empty - no panels there...

There are two ways how to start Dashboard (see How to start Dashboard) - but the first time it must be started from the Ant - typing:
ant dashboard
The reason is that the Ant creates a Dashboard configuration file (dashboard-config.jar) which defines what panels to include (and other things, such as Dashboard title). Details about configuration are in a separate document.

Where are the user preferences stored?

On Linux in %HOME/.java/.userPrefs/org/biomoby/service/dashboard.

On Windows in Registry: HKEY_CURRENT_USER/Software/JavaSoft/Prefs/org/biomoby/services/dashboard.

On Mac: I don't know...


The initial development was done by Martin Senger thanks to the funding from the Generation Challenge Programme and from International Rice Research Institute. Many other Biomoby developers contributed by their comments, suggestions and code.

Some viewers in the SimpleClient panel were inspired, sometimes highly inspired, by similar viewers in Taverna.

Most of the icons were shamelessly stolen from the open-source project Eclipse.

Martin Senger
Last modified: Thu Feb 14 15:02:09 2008