Nature Methods special issue

Our goal in this 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 conference series

Data visualization is increasingly important in life science as data grows in volume and complexity. In 2010 we launched 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.

VIZBI videos and posters

To ensure that the broader community of life scientists can benefit from VIZBI, the talks from 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 Killer App Award

At 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 party series

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.

Reflect augmented browsing tool

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.

Elsevier Grand Challenge

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 gene-set analysis tool

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.

Premature aging & Rb protein

Progeria is a rare premature aging disorder caused by a mutation in Lamin A, a protein integral to the nuclear membrane. In a recent 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.

SRS 3D structure retrieval service

SRS 3D is a free add-on to SRS helping scientists find and use 3D structures. For any protein sequence, SRS 3D 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 Bioinformatics; SRS 3D was first developed at Lion Bioscience, and it was open sourced by BioWisdom in 2008.

Coming Soon

5–7 March 2014
VIZBI 2014, the 5th international meeting on Visualizing Biological Data at EMBL, Heidelberg, Germany - funding from EMBO.

Recently

27–29 October 2013
Invited talk on Visualising Biological Data: Current Perspectives at CMLS 2013, the 4th International Symposium on Computational Models for Life, Sydney, Australia.
27–29 October 2013
Proceedings talk on Visual analytics of phosphorylation time-series data on insulin response at CMLS 2013, the 4th International Symposium on Computational Models for Life, Sydney, Australia.
21–25 October 2013
EMBL-Australia Masterclass on Protein Sequence Analysis, The Kinghorn Cancer Centre, Garvan Institute, Sydney.
13–14 October 2013
Primer talk on "Visualizing Networks and Interactions" at BioVis 2013, the 3rd IEEE symposium on biological data visualization, Atlanta, GA, USA.
13–14 October 2013
Proceedings talk on "The Molecular Control Toolkit: controlling 3D molecular graphics via gesture and voice" at BioVis 2013, the 3rd IEEE symposium on biological data visualization, Atlanta, GA, USA.
16 September 2013
Three minute interview on the future impact of data visualisation in biology, recorded at the Danish Design Center in Copenhagen, Denmark.
16 September 2013
Invited talk on Visualizing Biological Data, part of the 'Big Data Crossover Evening' at the Danish Design Center in Copenhagen, Denmark.
2 September 2013
Invited talk on Very large scale data visualization at ICSB 2013, the 14th International Conference on Systems Biology, Copenhagen, Denmark.
30 May 2013
"Connect with Science", how creativity impacts science & science communication; part of VIVID Sydney.
20–22 March 2013
VIZBI 2013, the 4th meeting on visualizing biological data at the Broad Institute, Cambridge MA, USA - funding from NIH.
26 February 2013
Invited talk on "Visualizing biological data" at IEEE PacificVAST (Visual Analytics Science & Technology), Sydney, Australia.
9-14 September 2012
Dagstuhl seminar on Biological Data Visualization, Schloss Dagstuhl - Leibniz-Zentrum für Informatik GmbH, Wadern, Germany.
12 October 2012
Invited talk on "How to exploit prior knowledge: From text mining to crowdsourcing" at AGD 2012 (Annual Meeting 'Arbeitsgemeinschaft für Gen-Diagnostik'), Potsdam, Germany.
14–15 October 2012
BioVis 2012, the 2nd IEEE symposium on biological data visualization, Seattle, WA, USA.
12 June 2012, 12 noon
Garvan science leaders seminar on Visualizing Biological Data, Garvan Institute for Medical Research, Sydney, Australia.
30 March 2012, 12 noon
Seminar on Visualizing biological data, Room 471, Level 4, Molecular Bioscience Building, G08, The University of Sydney, Australia.
22 March 2012
Plenary speaker, Bioinformatics FOAM 2012, Langham Hotel, Melbourne, Australia.
15 March 2012
Invited speaker at tayviz, Dundee University, UK.
6–8 March 2012
VIZBI 2012, the 3rd international conference on Visualizing Biological Data at EMBL, Heidelberg, Germany - funding from EMBO.
23–24 October 2011
BioVis 2011, the 1st IEEE symposium on biological data visualization, Providence, RI, USA.
19 July 2011
2nd Killer App Award at ISMB 2011, Vienna, Austria.
18 July 2011
Workshop on Data Visualization and User Interfaces, at ISMB 2011, Vienna, Austria. PDFs of the presentations are available here.
16–19 March 2011
VIZBI 2011, the 2nd workshop on visualizing biological data at the Broad Institute, Cambridge MA, USA - funding from NIH.