I’m collecting any interesting blog entries, wall posts, videos, articles etc. about osteoarthritis on a Google Plus Page called… “Osteoarthritis”

It’s here: https://plus.google.com/111374778904939177742/posts

Please circle the page if you’re interested!

This website is powered by WordPress with a modified Arjuna-X theme.

WordPress provides a “child theme” facility that allows you to customise a theme without altering the source code. This means when you update your theme you still inherit all the good new stuff but you don’t over write your changes.

I’ve put my child theme “arjuna-x-child” up on github for anyone to copy/learn from.

It is not that complicated.

It changes the page background color/gradient.  A brighter background gives more contrast to the text and makes it easier to read.

It adds a custom banner to the header. For the banner to work correctly you need to add a logo in the theme options section. The image should be 89 x 960 pixels.

It changes the footer a little and corrects a current bug causing the comments not to be displayed.

There is also a wp content filter that adds a menu to pages with links to subpages.

That’s it. You can find it here: http://github.com/glawlor/arjuna-x-child 

is here:

It is the initial commit with the original class and a test. You’ll have to add the test image to VTK_DATA_ROOT/Baseline/Graphics/TestCollisionDetection.png

Feel free to improve the code – there are some prompts in the source where speed increases could be achieved. The class is accurate rather than quick.

Tk Icon

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Tk takes flak for not being pretty, so a while ago I did up a quick shaded version of the Tk icon logo. I noticed a couple of 404’s to an old link so I’m redirecting to here for posterity:

Download the SVG file

New look website

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To kick off 2011, bioengineeering-research.com has been converted to a WordPress powered site*. To complement the static pages, I’ll be blogging about software and research developments too.

Happy New Year!

* writing raw html had become a pain…

I wrote a collision detection class for VTK – vtkCollisionDectionFilter – back in 2003, as a simple way to simulate joint articulation. Its been open sourced since 2006 in my vtkbioeng project on sourceforge.

The package has been downloaded a little over 1000 times and checked-out of cvs a little under a 1000 times. Judging by emailed questions most people are after the collision detection source code. (Btw, the highest percent of downloads are from China at 25%).

After an emailed nudge from David Doria,  it was time to try and submit the class for inclusion in the official repo, so I’ll be creating a branch on github and putting an updated class, examples, and test up there. Gerrit also seems like a good submission review process, so I’ll have a go with that too.

Why did it take so long to submit? Firstly, the class was open sourced in a cmake ready package – developers could easily compile it themselves if they wanted the class. Unfortunately this meant that users of precompiled binaries of VTK couldn’t access the class. Secondly, there is an implicit promise to support a  submitted class far into the future – scary stuff and not to be taken lightly. As against this, I co-wrote a submitted class vtkGL2PSExporter with Prabhu Ramachandran and while checking up on it the odd time, it has not given me any grief.

As a version 2.0 of the proposed branch, I’ll be looking at an abstract superclass for collision detection with subclasses implementing the current class, a wrapper class around the Bullet physics library, and perhaps a multi-body subclass too (in version 3.0)

If all goes to plan, an article to the VTK journal would be a good endpoint.

A mini-seminar among post-grads took place in DIT on 30th June to talk about the software application Arthron and where it fits in with current research.

There was an interesting split between the needs of researchers who just wanted to use the application and those that wanted to develop the software.

Both groups wanted a way to customize projects – so we’ll come up with some sort of project template format and an interface for creating and updating them.

Developers wanted a way to query the internal structure of the application. That exists but a robust developer API should be published rather than the ad hoc methods used at the moment.

The next big step is enabling real-time sharing of data – all the project data, not just the pretty stuff, so that collaborators came immediately take up where others leave off.

Innovation Alliance, known as the “UCD/TCD innovation alliance” in UCD and the “TCD/UCD innovation alliance” in Trinity, got going in earnest with the Engineering Design Innovation Open Forum on the 27th April. Postgrads, postdocs, and PI’s show-cased some of their research projects to further the 4th level partnership between Dublin’s largest universities. Since the colleges have been rivals in the past, the word “unprecedented” was used an… unprecedented number of times.

PTRLI cycle 5 program was common talking point that came up.

We presented a demo of the Arthron software package. See here