Dec 6 2011

Advanced Simplicity?

Last week I attended Giles Colborne’s talk on ‘Advanced Simplicity’, hosted by the EBI Interfaces Forum at the EBI, Hinxton.  What struck me in particular in his talk was the clear parallel between what he refers to as ‘mainstreamers‘ and ‘experts‘ and the ‘biologists‘ and ‘informaticians‘ that use bioinformatics services at the EBI. People doing wet lab experiments, maybe spending 10-20% of their time at the computer, and dry programmers with 100% of the time on the computer.

Giles Colborne talks about experts and mainstreamers when it comes to understanding 'usability'

The way things break down into two categories sounds simple, but the huge challenge comes when one has to come up with designs for online services that must suit both audiences simultaneously.  One way to do this, Giles suggests, is to hide more complex functionalities, so its only the experts that discover them; he used a hidden sliding panel on a remote control as an example of this in practice. On the flipside then, it means that the major routes into the most frequently accessed services should be made even easier, so the mainstreamers can’t help but find them.

One way to tackle this problem is to make sure we design for – and test solutions with – individuals from both worlds.  Applying realistic scenarios in usability testing can help hugely to understand whether you have achieved the right balance.  I also involve both audiences in initial user research and workshops to make sure the requirements for each are understood.

From my experience, designing for the generalist is harder and more important, because they are much more liable to give up and lose hope of finding what they want.  The investment in energy to find what they are after is greater, because they don’t come there very often.  In contrast, the expert always seems to find a way to get what they want, whether the route to it is clear or not.

Overall, I find it reassuring that people like Giles have struggled, and continue to struggle, with this careful balancing act.  I look forward to reading more from Giles on how I can improve UX for both of these important segments of our audience.

By jcham • Uncategorized • 0

Nov 22 2011

Which of my papers received the most citations?

After a year or two, I thought it was time to check on the citations of the papers I wrote during my doctorate.

I used ISI Web of Knowledge to do this – which is a nifty little service.  You add in an author name and it gives you information on the number of citations achieved for each paper by that author.  You can display the results dynamically as bar chart graphs, and can adjust the settings for different displays.  It works best for peer-reviewed journal articles or book chapters, as far as I can tell.  There is a time lag too, as recently published work doesn’t appear in the database immediately.

Interestingly, this search showed that the review papers we wrote on proteomic bioinformatics were the most popular, receiving 21 and 23 citations for the 2007 and 2009 reviews, respectively.  The MRMaid paper, which was published in Molecular Cellular Proteomics (MCP) journal also received 18 citations.  I think it’s usual for reviews to be cited more frequently than research papers.  All round, not too bad…

By jcham • Uncategorized • 0

Nov 21 2011

Writing for the Web Course with Caroline Jarrett

On Friday 25th November, I will be attending Caroline Jarrett’s course on writing for the web, which is being held at the EBI.

I don’t know about you, but I don’t tend to think enough before I write – so I’m hoping after this course I’ll have a neat check list of dos and don’t s, to which I will refer, before I click ‘Publish’.  The result for you, the reader, should be some much better quality postings on this site – and generally a happier experience!

By jcham • Uncategorized • 0

Nov 2 2011

Bioinformatics PhD opportunity at Cranfield University

Below is an advert for a PhD in bioinformatics with my former PhD supervisor – he is a great guy, highly recommended.

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PhD Bioinformatics Opportunity at Cranfield University, UK
We are currently seeking a highly motivated individual to take up a PhD studentship in the Bioinformatics Group at Cranfield University in the UK.
The Project
Developments in analytical technologies are resulting in ever larger amounts of dynamic biological data becoming available, in both the public domain and within individual companies. These data include molecular information from transcriptomics, proteomics and metabolomics as well as phenotypic information such as that from patient records and clinical trials. This ever increasing mass of data is only useful if relevant biological information can be reliably extracted from it, and it is this challenge that forms the core of this PhD project.
The aim of the PhD will be to apply, evaluate, and further develop Bayesian methods for the extraction of disease-specific biological knowledge from large heterogeneous biological datasets. In recent years Bayesian approaches have been shown to have a number of benefits over traditional “frequentist” statistical approaches. The project will begin with the development of a protocol for information extraction, starting with well understood data and gradually adding more data from different sources to refine and augment the extracted information. Our overall goal is to discover new biological knowledge of relevance to diabetes.
The Skills Required
The project is entirely computer based, so we are looking for someone with excellent computer skills, including proven expertise in programming, data analysis and databases. A good BSc or MSc in Bioinformatics or other data-centric subject is essential. Specific experience of Bayesian methods would be beneficial, but not essential as there will be opportunities to learn about this during the PhD.
About Cranfield Bioinformatics Group
Cranfield Bioinformatics Group was established in 2000 and has since established a track record in the development of algorithms and software for the analysis of large molecular data sets. Our PhD graduates have all gone on to successful careers in bioinformatics, with employers including the European Bioinformatics Institute, the Sanger Institute, GlaxoSmithKline and Johnson & Johnson. You can find out more at about the group at http://www.cranfield.ac.uk/health/bioinformatics.
The Funding
The studentship is sponsored by Sanofi-Aventis. There are no fees to pay, and the student will receive a tax-free stipend of ~£14,000 per year. The project includes a budget for computer equipment and conference travel. Please note that funding is only available to applicants who are already citizens of the European Union. The project duration will be three years, and the project supervisor will be Dr Conrad Bessant.
How to Apply
For more information, or to make an application, please email Dr Bessant, c.bessant@cranfield.ac.uk.

By jcham • Uncategorized • 0