Wednesday, May 27, 2009

A novel information retrieval model for high-throughput molecular medicine modalities

Finally this paper in Cancer Informatics is indexed by PubMed. This paper describes the early "model formulation" phase of my PhD work. As I approach the end, and obtain more shareable results, I will include more Biomedical Informatics resources on this website.

More information about the paper:


Significant research has been devoted to predicting diagnosis, prognosis, and response to treatment using high-throughput assays. Rapid translation into clinical results hinges upon efficient access to up-to-date and high-quality molecular medicine modalities.We first explain why this goal is inadequately supported by existing databases and portals and then introduce a novel semantic indexing and information retrieval model for clinical bioinformatics. The formalism provides the means for indexing a variety of relevant objects (e.g. papers, algorithms, signatures, datasets) and includes a model of the research processes that creates and validates these objects in order to support their systematic presentation once retrieved.We test the applicability of the model by constructing proof-of-concept encodings and visual presentations of evidence and modalities in molecular profiling and prognosis of: (a) diffuse large B-cell lymphoma (DLBCL) and (b) breast cancer.

Friday, April 10, 2009

I am very inspired by Tyler's online pledge to lose 100 pounds. Visit his website and help him meet his goal. I wish I was brave enough to document my training/weight-loss goal.

Wednesday, April 8, 2009

Magnetic Movie

Magnetic Movie from Semiconductor on Vimeo.

The secret lives of invisible magnetic fields are revealed as chaotic ever-changing geometries . All action takes place around NASA's Space Sciences Laboratories, UC Berkeley, to recordings of space scientists describing their discoveries . Actual VLF audio recordings control the evolution of the fields as they delve into our inaudible surroundings, revealing recurrent ‘whistlers' produced by fleeting electrons . Are we observing a series of scientific experiments, the universe in flux, or a documentary of a fictional world?

More info here

An Animate Projects commission for Channel 4 in association with Arts Council England.

Wednesday, January 28, 2009


If I am to say one thing this month on my blog, I would praise the CakePHP Framework. I love it. The documentation leaves a lot to be desired, but for me the fun of coding in CakePHP is looking at the code and figuring out how well everything is put together and how intuitive the framework is.