Dr Seán O’Donoghue

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 reviews covering visualization of genomes, alignments & phylogenies, macromolecular structures, image data, and systems biology data - plus a commentary article summarizing challenges and perspectives.

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 is held annually in March, alternating between Europe and the USA, and is funded by EMBO and NIH.

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 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 wildly 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 a 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 is used by life scientists to analyze 20,000 documents per day.

Martini gene-set analysis tool

Martini is a free service that automatically characterizes functional differences between two sets of genes. In comparison to similar tools, Martini supports a wider range of species, and gives more detailed, precise, and accurate functional characterization. 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; targeting this protein may help premature aging. This was a collaboration with the Djabali lab at Columbia University, New York.

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.