ENSEMBLE

A new tool has been added to the Ensemble projects page. This page is based on the Molecule of the Month series from the Protein Data Bank. It demonstrates how information can be dynamically integrated from the Protein Data Bank – an online repository of structural information about large biological molecules – to create 2D and 3D renderings of molecular structures, using Exhibit and Jmol, a java-based 3D chemical structure viewer. The tool can also search the scientific literature via Pubmed for recent articles related to proteins of interest.

At present, it is best viewed using Firefox.

Molecule of the Month from the Protein Data Bank

The first major public output of the Ensemble pilot projects (coinciding with the official launch of the main project on 1st October) is the Plant Evolution Timeline.  This was developed as part of the pilot work of the project by Ben Roberts and Nicola Peart at CARET with support and feedback from members of the University of Cambridge Department of Plant Sciences.

This tool is designed primarily to aid Plant Scientists studying at the University of Cambridge with their learning of plant evolution. The tool is used to provide an overview of course content and major themes for 1^st and 3^rd year students during the first few lectures of their courses, and will also be suitable for use within small group supervisions and for revision purposes. The public version of the timeline offers all of the interactive features but does not link to the specific lecture content of the Cambridge courses.

Nicola Peart, one of the team responsible for the development of the Timeline, describes how:”[the timeline] is useful for helping students assemble a large range of data sources at a range of scales and relevance. It is also useful for teachers illustrating links between data that are difficult to visualise without a tool like this. It is also [helps] researchers to see how different people might draw connections between data, or to inspire further research into variables that may or may not correlate.”

The timeline itself is produced using a modified version of the Timeplot tool developed as part of the SIMILE project at MIT, together with some site-specific Javascript and PHP scripting to handle authentication.  There are instructions and links to other related resources.

The Plant Evolution Timeline

A team of researchers, staff and students will begin work developing pilots and ‘demonstrators’ of Semantic Web technologies, including the SIMILE toolkit, to a range of teaching and learning applications as part of the run-up to the launch of the Ensemble project. Three UROP (Undergraduate Research Opportunities Programme) students will work with staff at the Centre for Applied Research into Educational Technologies (CARET) in Cambridge during the summer to develop applications in Plant Sciences, Earth Sciences, Local History and in Education and Learning Support. Their work will appear on this website over the next few months.