|Bioclipse dialog to upload chemical|
structures to an OpenTox repository.
Us chem- and bioinformaticians have it easy when it comes to Open Science. Sure, writing documentation, doing unit testing, etc, takes a lot of time, but testing some new idea is done easily. Yes, people got used to that, so trying to explain that doing it properly actually takes long (documentation, unit testing) can be rather hard.
Important for this is a platform that allows you to easy experiment. For many biologists this environment is R or Python. To me, with most of the libraries important to me written in Java, this is Groovy (e.g. see my Groovy Cheminformatics book
) and Bioclipse
). Sometimes these hacks grow to be full papers, like with what started with OpenTox
) which even paved (for me) the way to the eNanoMapper project
But often these hacks are just for me personal, or at least initially. However, I have no excuse to not make this available to a wider audience too. Of course, the source code is easy, and I normally have even the smallest Bioclipse hack available somewhere on GitHub
(look for bioclipse.* repositories
). But it is getting even better, now that Arvid Berg
(Bioclipse team) gave me the pointers to ensure you can install those hacks, taking advantage from Uppsala's build system
So, from now on, I will blog how to install Bioclipse hacks I deem useful for a wider audience, starting with this post on my Wikidata
/Linked Data Fragments hack I used
to get more CAS registry number mappings to other identifiers.Install Bioclipse 2.6.2
The first thing you need is Bioclipse 2.6.2
. That's the beta release of Bioclipse, and required for my hacks. From this link you can download binary nightly builds for GNU/Linux, MS-Windows, and OS/X. For the first two 32 and 64 bit build are available. You may need to install Java and version 1.7 should do fine. Unpack the archive, and then start the Bioclipse executable. For example, on GNU/Linux: $ tar zxvf Bioclipse.2.6.2-beta.linux.gtk.x86.tar.gz $ cd Bioclipse.2.6.2-beta/ $ ./bioclipseInstall the Linked Data Fragments manager
The default update site already has a lot of goodies you can play with. Just go to Install → New Feature...
. That will give you a nice dialog like this one (which allows you to install the aforementioned Bioclipse-OpenTox feature):
But that update site doesn't normally have my quick hacks. This is where Arvid's pointers come in, which I hope to carefully reproduce here so that my readers can install other Bioclipse extensions too.Step 1: enable the 'Advanced Mode'
The first step is to enable the 'Advanced Mode'; that is, unless you are advanced, forget about this. Fortunately, the fact that you haven't given up on reading my blog yet is a good indicated you are advanced
. Go to the Window → Preferences
menu and enable the 'Advanced Mode' in the dialog, as shown here:
When done, click Apply
and close the dialog with OK
.Step 2: add an update site from the Uppsala build system
The first step enables you to add arbitrary new update sites, like update sites available from the Uppsala build system
, by adding a new menu option. To add new update sites, use this new menu option and select Install ￼￼→ Software from update site...
By clicking the Add
button, you go this dialog where you should enter the update site information:
This dialog will become a recurrent thing in this series, though the content may change from time to time. The information you need to enter is (the name is not too important and can be something else that makes sense to you):
- Name: Bioclipse RDF Update Site
- Location: http://pele.farmbio.uu.se/jenkins/job/Bioclipse.rdf/lastSuccessfulBuild/artifact/site.p2/
After clicking OK
in the above dialog, you will return to the Available Software
dialog (shown earlier).Step 3: installing the Linked Data Fragments Feature
The Available Software
dialog will now show a list of features available from the just added update site:
You can see the Linked Data Fragments Feature
is now listed which you can select with the checkbox in front of the name (as shown above). The Next
Because the Linked Data Fragments Feature
extends Bioclipse with a new, so-called manager (see doi:10.1186/1471-2105-10-397
and type in the console view man ldf
which should result in something like this:
You can also type man ldf.createStore
to get a brief description of the method I used to get a Linked Data Fragments wrapper for Wikidata in my previous post
, which is what you should reread next.
Have fun and looking forward to hear how you use Linked Data Fragments with Bioclipse!