‘Developing software to help scientists in the lab’
Imtiaz Khan is a Bioinformaticist at the Cardiff University School of Medicine and develops software that helps researchers to capture and convey their day-to-day laboratory activities.
The regenerative powers that stem cells promise may one day abolish a range of human diseases and disabilities.
Cells and tissues of our body experience damage or degradation due to heart attack, injuries, neurodegenerative diseases like Alzheimer’s and other age related diseases. Such damaged or degenerated cells can be replaced by cells that are regenerated from stem cells.
However, the primary source of stem cells has, until recently, been the human embryo, which has obviously sparked a number of ethical, social and religious concerns. Addressing these, in recent years scientists have invented mechanisms to genetically programme adult skin cells and transform them into embryonic-like stem cells, known as induced pluripotent stem (iPS) cells.
Simplistically it is like putting the adult cells into a time-machine, taking them back to the embryonic stage and then taking them forward in a directed path to grow appropriate cells or tissues, such as heart tissues or nerve cells. The whole process is carried out in laboratory and currently researchers are at the very early stages of developing this technology.
To turn the promise of stem cells into therapeutic reality, we need to develop stable and reproducible processes to ensure safe stem cell products. This will require the development of reliable and well-documented laboratory processes that can be shared and assessed across different laboratories.
My research focuses on developing software that helps researchers to overcome some of these challenges. In collaboration with the Broad Institute of Harvard and MIT, USA, I lead the development of ProtocolNavigator (http://protocolnavigator.org/), which is a “digital laboratory”. Here researchers carry out their experiments as normal, but the software automatically documents the details of their activity and draws the process, or “workflow”, of their experiments on a digital canvas as an interactive map.
ProtocolNavigator has been tested within a Wales-based stem cell research consortium. The notable impact this software has demonstrated is the visual understanding and the ability to compare multiple processes – enabling researchers to easily identify any subtle differences between different experiments.
Bringing coherent documentation and understanding is the first step towards developing safe protocols for generating stem cells for therapeutic purposes. Wales is at the forefront of stem cell research (Sir Martin Evans of Cardiff University won the 2007 Nobel prize for his work on stem cells) and we believe that this work will add scientific, therapeutic and commercial value to stem cell research both in Wales and beyond.
Imtiaz may be contacted at: firstname.lastname@example.org
This article first appeared in the Western Mail on 25th November 2013, as part of the Welsh Crucible series of research profiles.