Seán O'Donoghue

VIZBI conference series

Data visualization is increasingly important in life science as data grows in volume and complexity. VIZBI is an international conference series on 'Visualizing Biological Data.' The conference brings together researchers in genomics, transcriptomics, proteomics, cells, organisms, and populations. VIZBI reviews the state of the art methods and future challenges. It is held annually in March, alternating between Europe and the USA, and is funded by EMBO.

VIZBI videos and posters

To ensure that the broader community of life scientists can benefit from VIZBI, the posters from 2018 and 2017 are freely available on the website, as are many of the slides used by past speakers.

Minardo

We have developed Minardo, a novel layout strategy to visualise large-scale data with time profiles applied to the time-series data. Minardo has been used thus far to demonstrate a Snapshot of the Insulin Cell Signalling Pathway, and Phosphoregulation of Mitosis. In future work, we plan to develop Minardo into a web-based application tool, allowing interactive visualisation and ease of collaboration.

Rondo

Rondo is a tool developed with a circular layout, to enable molecular biologists to interactively explore chromosome conformation data sets from a wide range of technologies, across numerous human and mouse cell lines. Rondo was used to study genomic rearrangements in cancer.

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.

Aquaria: insight from structures

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.

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.

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.

Coming Soon

13-15 March 2019
The annual conference on Visualising Biological Data (VIZBI 2019), EMBL, Heidelberg Germany.

Recently

26-28 July 2018
Speaker at EMBO Workshop 'In situ methods in Cell Biology and Cellular Biophysics,' Berlin Germany.
2-6 July 2018
Invited speaker at Winter School in Mathematical & Computational Biology, Brisbane Australia
25 May - 16 June 2018
Beautiful and Dangerous, a Vivid Lights installation by the VIZBI lab, Sydney Australia
28 May 2018
31 May 2018
Presenter at Data Visualization Masterclass, Sydney Australia
1 June 2018
4 June 2018
Keynote speaker at workshop on 'Molecular Graphics and Visual Analysis of Molecular Data,' EuroVis 2018, Brno Czech Republic.