We have developed a large collection of videos on YouTube developed to explain how to use our software Jalview as well as other tools from the group such as the JPred structure prediction suite. The videos also provide background to multiple sequence alignment, structure prediction and introduce resources for school children. The majority of these videos were developed by Dr Suzanne Duce.
This video introduces the team that work on Jalview and also showcases the Discovery Centre building that we work in!
This video introduces the current team in our long-term collaboration with Gordon Simpson on the analysis of RNA processing in plants and funded by BBSRC. Watch to the end to find out what is in the box!
The video was made by filmaker Steve Soave.
This short video was created to explain alternative polyadenylation and to introduce our polyAdb database to a general audience. The work on polyadenylation is from a long-term collaboration with Gordon Simpson on the analysis of RNA processing in plants and funded by BBSRC.
The video was created for us by Vivomotion.
GenomeScroller is an art/science/outreach project that highlights the size of the human genome and how much we do and don't know about it. It was conceived and written by Dr Chris Cole and Dr Nick Schurch with contributions from Dr Richard Bickerton for the 3D structure animations and enthusiastic support from Geoff Barton.
This two minute video highlights three versions of GenomeScroller:Version 1 used 9 interlinked screens and was exhibited in the atrium of the Wellcome Trust Building at the School of Life Sciences, University of Dundee for three weeks in September 2010. Version 2 modified this to three screens, with the main scrolling display run by two projectors and a separate screen to show the timetable. Version 2 was exhibited in the foyer of the Medical Sciences Institute at the School of Life Sciences, University of Dundee in November 2012, while Version 3 was adapted to run on a single 16 screen video wall at the Digital Arts Week in Singapore during May 2013.
GenomeScroller is a live exhibit not a canned video. This presented a number of technical challenges. In particular, the 16 screen video wall version pushed the limits of what the hardware could sustain to get a fast enough frame rate with all screens running at full HD resolution. A video would require 300 MB of storage per second to display as shown in the exhibit. This is approximately 1 TB (terabyte) per hour, or 168 TB for the week...
Credits: Although Nick and Chris did the bulk of the work with Richard providing the 3D graphics of proteins and small molecules on all versions of GenomeScroller, others also made contributions: Version1: had input from Pete Richardson of the Duncan of Jordanstone College of Art and Design in discussion of the original concept and design and construction of the plinths. Version 3: benefitted from help by Stefan Arizona and his PhD student Zeng Wei at Singapore to get the Scroller working well on the video wall. All versions: Jim Procter helped a lot with advice on Java programming, while the Community of Processing users was invaluable with their advice.
The music on this video was written to reflect the seemingly never-ending nature of the Genome and contains repeating four-note broken chords to emphasise the four bases of DNA. The audio only version is on SoundCloud.
GenomeScroller has its own website with further information and images.
This interview with Geoff Barton was made to provide background to the new Centre for Translational and Interdisciplinary Research (CTIR, now known as the Discovery Centre) which the Group moved into in July 2014. A short clip from this interview is used on the CTIR website.
Geoff discusses the impact of the human genome sequencing project and the knock-on effects this has had for research in biology.
This interview with Geoff Barton was done by students at the OSCAT 2012 conference.
Geoff Barton: Visualizing Protein and Nucleic Acid Sequence Alignments from VIZBI on Vimeo.
This talk by Geoff Barton goes from alignments handwritten on paper in the 1980s through various developments such as Alscript and AMAS to the features and options in Jalview and ends with thoughts on the visualisation challenges we face today and will need to meet in the future.
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