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EMBL-Australia Masterclass
on Protein Sequence Analysis

Registration closes tomorrow!

The Kinghorn Cancer Centre, Garvan Institute, Sydney
21-25 October 2013


The Masterclass is a great opportunity to learn up-to-date, practical methods in protein sequence analysis directly from a range of internationally recognized experts in bioinformatics who are actively developing and applying  these methods. Students will receive both an overview of recent research results that provide the theoretical basis for modern methods in protein sequence analysis, as well as hands-on practical training in bioinformatics tools that apply these methods to gain new insight into underlying biological functions and processes. The tools used and practical exercises taught will cover:

  • Using standard bioinformatics resources and databases, such as BLAST, Reflect, and UniProt.
  • Identifying and understanding protein sequence families and protein modules, using resources such as ClustalX, Jalview, InterPro, PFAM, and SMART.Identifying and understanding short linear motifs, using resources such as ELM, PhosphoELM, and Switches.ELM.
  • Identifying and understanding intrinsic disordered regions, using resources such as IUPRED and ANCHOR. Identifying and understanding protein repeat motifs and compositional bias, using resources such as ARD2, HIPPIE, PFAM, and STRING.
  • Identifying and understanding protein-protein interactions and residues involved in intermolecular contacts, using resources such as Cytoscape, IntAct, MINT, STITCH, STRING, and structureViz/Chimera.
  • Using 3D structures to gain insight into protein function, using resources such as ePDB/PDB, Jalview, and structureViz/Chimera.

Target audience

The Masterclass is designed for graduate and postgraduate level bench biochemists and molecular biologists who need to use computational sequence analysis for their research, as well as for bioinformaticians at an early stage of their career.


What does it cost?

Student                  $800
Academic/CSIRO     $950
Industry                 $1,500

What’s included?

Morning and afternoon teas, lunch, a group dinner, access to online course material. Accommodation is not included with the registration fee.

Where to stay?

Students from outside of Sydney will need to organize their own travel and accommodation. We have arranged a special rate with the Holiday Inn Potts Point of $165 per night for a single room plus breakfast, or $180 per night for a double or twin room plus two breakfasts. The Holiday Inn is within easy walking distance of the Garvan. To take advantage of this offer, contact Holiday Inn InHouse Reservations via or phone (02 9368 4045), quoting the group confirmation code KCC-599590. This offer will expire once either 20 rooms have been booked by Masterclass participants, or after 6 October 2013.

What to bring?

Each student is required to bring their own laptop to the Masterclass. This allows the students to work in their own environment and for some exercises to use their own data and get feedback on their research from the experts. Most tools covered will be web-based, however some additional plug-ins or software will need to be installed. Details will be given via email following registration.


Places are strictly limited to 35 students, and will be allocated on a first-come first-served basis. During registration, you are required to provide a short abstract about your work and during the course, you will have the opportunity to briefly present yourself and your work to the class.

Registration has closed, please fill this form out if you want to be placed on a wait list.

Click to download the Programme

Click to download the Poster                                


For information on registration and logistics contact Melissa Vincent, Garvan Institute, Australia.




Trainer Biographies


Miguel Andrade is a group leader at the Max Delbrück Center for Molecular Medicine, Berlin, Germany. He received his Ph.D. in Biochemistry at the Universidad Complutense de Madrid in 1994. He trained at the postdoctoral level at the European Molecular Biology Laboratory in Heidelberg and Cambridge with Chris Sander and Peer Bork. His postdoctoral studies involved the development and application of computational methods for the analysis of gene and protein function and structure. From 2003 to 2007, he was Assistant Professor in the Department of Medicine of the University of Ottawa and Scientist and Head of the Bioinformatics Group of the Ottawa Health Research Institute in Ottawa, Canada, where he was promoted to Senior Scientist in 2006. In September 2007 Miguel moved to the Max Delbrück Center for Molecular Medicine in Berlin to start the Computational Biology and Data Mining group. His group ( focuses on the development and application of computational methods that are used to research the molecular and genetic components of human disease.

Aidan Budd is a member of staff at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, where he works as a computational biologist in the group of Toby Gibson. He is interested in the evolution and prediction of short protein linear motifs, and in the evolution of individual gene families. Additionally, Aidan is involved in teaching and organising practical courses for researchers, mostly focusing on multiple sequence alignment, phylogenetics, and exploration of protein modular architecture - along with introductory courses for secondary school teachers in bioinformatics. After studying for his undergraduate degree in Zoology at Cambridge University, Aidan worked as a research assistant with Torsten Krude in the lab of Ron Laskey at the Gurdon Institute in Cambridge. He went on to obtain his PhD at EMBL Heidelberg focusing on the evolution of gene families expected to have similar evolutionary histories. Between completing his PhD and rejoining EMBL, Aidan worked as the commissioning editor for life science books at Wiley-VCH in Weinheim, Germany.

Holger Dinkel is a member of staff at the European Molecular Biology Laboratory (EMBL). He is a Biologist by training and a computer scientist by passion, fascinated by the biology of short linear motifs. He started working on these small protein modules during his PhD by studying the interplay between linear motifs and globular domains. Since 2009 he has been working at the European Molecular Biology Laboratory as a software engineer, developing methods to study short linear motifs. He is also taking care of the ELM, Phospho.ELM and Switches.ELM databases & web services. He is focused on the technical aspects of science and loves to use & teach Linux, Python, git, Django and more.


Sean O'Donoghue is an OCE Science Leader in Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO), and a group leader at the Garvan Institute of Medical Research in Sydney. Previously, he worked in the Structural and Computational Biology programme at the European Molecular Biology Laboratory (EMBL), and at Lion Bioscience AG, both in Heidelberg, Germany. He has been involved in developing a range of bioinformatics methods, including ARIA, a method widely used for calculating 3D structures from NMR data. Since then, he has initiated and is leading several projects, including: the SRS 3D service for integrating 3D structure, sequence, and sequence features; the VIZBI initiative, aimed at improving the global standard of bioinformatics visualization method; and the Reflect service for annotating biochemical terms in web pages. The Reflect service won the Elsevier Grand Challenge, and since it was published in mid-2009 in Nature Biotechnology, the user-base of the service has grown rapidly, and it is currently used by life scientists to process thousands of documents per day.

Zsuzsanna Dosztanyi is a Senior Research Fellow at the Institute of Enzymology in Budapest, Hungary. Her research is focussed on understanding the structural and functional properties of intrinsically disordered proteins and their involvement in various diseases. Current research goals are: modeling the thermodynamic basis of order and disorder in proteins; recognizing functional sites within disordered proteins; understanding the specific roles of protein disorder in cancer. Various theoretical and computational approaches are utilized including simplified biophysical models, bioinformatic prediction methods and system biology approaches.


Toby Gibson is at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. He studied Biology at Edinburgh University and did his PhD with Bart Barrell at the LMB, Cambridge. He is a computational biologist: i.e. a biologist who finds computers to be useful adjuncts to biological research. He is a co-developer of the widely used Clustal series of multiple sequence alignment software. He oversees the development of ELM, the Eukaryotic Linear Motif resource devoted to protein sequence motifs involved in cell signalling and regulation. Toby is currently fascinated by the developing structure-function paradigm for the massively interacting hub proteins such as P53, IRS-1, sundry AKAPs and many, many more. These are characterised by large natively unstructured protein segments that are repositories of abundant "linear motifs" - short regulatory sites that interact with other proteins. These low affinity interacting modules allow for co-operative and combinatorial regulatory interactions in the assembly of large regulatory protein complexes in response to signals received at the cell membrane. Multiple input parameters can be sampled by direct interaction so that regulatory decisions are made by in-complex molecular switching often returning multiple outputs into the regulatory networks. This discrete switching model contrasts with the more prevalent and diffusionist signalling cascade metaphor. The latter perspective would seem to be in need of replacement by a model that allows for more spatially and temporally discrete operations.

Lars Juhl Jensen is a research professor at the Novo Nordisk Foundation Center for Protein Research in Copenhagen, where he heads a disease systems biology group. He is also a co-founder of the company Intomics, which specializes in performing state-of-the-art data mining and systems biology analyses for pharmaceutical and biotech companies. His main scientific interest is to understand the principles that govern complex biological systems such as the cell cycle, signaling networks, and diseases. Most of his work work is based on integration of data from high-throughput experiments, sequence analysis, and automatic literature mining. He also maintains a blog, microblogs on Twitter, shares scientific papers and blog posts via Google Reader, and answer questions on BioStar.


 Scooter Morris is Executive Director of the Resource on Biocomputing, Visualization, and Informatics at the University of California, San Francisco, USA. His major interests are in the visualization of diverse biological data in ways that can communicate important properties about underlying properties. The major vehicle for that visualization has been Cytoscape, an open source platform for integration and visualization of biological data - particularly biological data that can be mapped onto networks of various different kinds.  Some examples of his work in this area include: (1) chemViz, extends the capabilities of Cytoscape into the domain of cheminformatics. (2) clusterMaker, which unifies a number of different clustering techniques commonly used by biologists for segregating proteins into groups, performing expression profiling, and more recently epistatic mini-array profiles (EMAPs). (3) structureViz, which provides a linkage between the network view commonly used for visualization of pathways, protein-protein interaction networks, or protein similarity networks and the structural view commonly used by structural biologists to manipulate, analyze, and compare macromolecular structures. In addition to the plugins mentioned above, he participate in the ongoing development of Cytoscape as a member of the core development team, contributing a number of plugins and extensions to Cytoscape to improve the general functionality as well as usability.