special issue of Nature Methods was to create a practical resource giving biologists an overview of current computational methods and tools used for visualizing biological data. The issue consists of five commissioned reviews - covering visualization of genomes, alignments & phylogenies, macromolecular structures, image data, and systems biology data - plus a commentary article summarizing key challenges and perspectives in visualizing biological data.
VIZBI, an international conference series on 'Visualizing Biological Data', bringing together researchers using visualization to study genomes, transcripts, proteins, cells, organisms, and populations. VIZBI reviews the state of the art and highlights future challenges - it is held annually in March, alternating between Europe and the USA, and is funded by EMBO and NIH to run until at least 2016.
2010 and 2011 are freely available on video, as are many of the slides used by the speakers. In addition, the posters from 2010 and 2011 are also available.
ISMB 2010, a group of us initiated the first ‘Killer App Award’ to recognize excellence in creating new tools or systems that are of direct, practical benefit to experimental life scientists. The second ‘Killer App Award’ at ISMB 2011 was very popular, and the Award is set to become a regular ISMB tradition.
ISMB is a serious, world-class scientific meeting of around 2,000 bioinformaticians - we certainly don't need to have wild, fun parties: but then again, why not?! Since 2008 I have been leading a series of ISMB parties - for many participants, this large, annual social event is the highlight of the conference, and it has now become an ISMB tradition.
Aquaria is a new, free web resource for biologists that simplifies the process of gaining insight from protein structures. For any protein sequence, Aquaria shows all related structures; with one click the sequence can be mapped onto the structure; one more click and the structure is colored by features, e.g., domains, SNPs, or posttranslational modification sites. See our article in Nature Methods.
Reflect is a free service that tags gene, protein, and small molecule names in any web page within a few seconds; clicking on a tag opens a popup with detailed information. It can be used with any browser, or via an API. See our webinar and our articles in Nature Biotechnology & J. Web Semantics. Reflect was developed at EMBL and the University of Copenhagen.
Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect has now been adopted by Cell Press and ScienceDirect, and has used by many life scientists to analyze seven million documents in the past year.
Martini is a free, easy-to-use tool for characterizing differences between two sets of genes. Martini differs from comparible tools in that it is based on keywords extracted from Medline abstracts and it supports a much wider range of species; testing it against several similar tools using several benchmarks, it was generally more detailed, precise, and accurate. See our article in Nucleic Acid Research; Martini was developed at EMBL.
article in PLoS ONE, we analyzed global gene expression changes in people with Progeria and found that the protein Rb is a key factor in Progeria, and that targetting this protein may help premature aging. This was a collaboration with the Djabali lab at Columbia University, NY.
24 June 2015
Lecture on Visualization of Macromolecular Structures at 2015 EMBL Australia PhD Course, Perth, Australia.
10–11 July 2015
Paper track presentation on Integrated Visual Analysis of Protein Structures, Sequences, and Feature Data at BioVis 2015, the 5th symposium on biological data visualization, Dublin, Ireland.
12 July 2015
Birds of a Feather meeting on Web Molecular Graphics at ISMB 2015, 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology, Dublin, Ireland.
13 July 2015
Tech Track talk on Aquaria: Simplifying discovery and insight from protein structures at ISMB 2015, 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology, Dublin, Ireland.
10 August 2015
Keynote talk on Data Mining to Knowledge at BIOKDD'15, the 14th International Workshop on Data Mining in Bioinformatics, Sydney, Australia.
10 September 2015
Keynote talk on Big Data Visual Analytics in the Life Sciences at BDVA, the 1st International IEEE International Symposium on Big Data Visual Analytics, Hobart, Australia.
23–24 November 2015
Keynote talk at B3 2015, the Big Biology and Bioinformatics Symposium, Brisbane, Australia.
9–11 March 2016
VIZBI 2016, the 7th international meeting on Visualizing Biological Data at EMBL, Heidelberg, Germany - funding from EMBO.
25–27 March 2015
VIZBI 2015, the 6th international meeting on Visualizing Biological Data the Broad Institute, Cambridge MA, USA - funding from NIH.
17 November 2014
Keynote talk on Visualising Biological Systems for Research and Outreach at Biological Data Visualization: where science meets arts, Ghent, Belgium.
17 September 2014
Plenary talk on Visualising Biological Systems for Research and Outreach at ICSB 2014, the 15th International Conference on Systems Biology, Melbourne, Australia.
11–12 July 2014
BioVis 2014, the 4th IEEE symposium on biological data visualization, Boston, MA, USA.
5–30 May 2014
Vivid Ideas event: Unlocking the Protein Data Bank: A Masterclass with David Goodsell, Sydney, Australia.
5–29 May 2014
Vivid Ideas signature event on On Making Science Beautiful, Sydney, Australia.
5–7-9 May 2014
Faraday Discussion on Molecular Simulations & Visualizations, Nottingham, UK.