Seminar: Elucidating the Microbiome: Adventures across our microbial earth: Assoc Prof Jack Gilbert

When?

12:30pm 13 May 2014

Where?

AgriBio, La Trobe University, 5 Ring Rd Bundoora|Melbourne|Vic|3083|AU

Who?

Dr Jack Gilbert is an Environmental Microbiologist at Argonne National Laboratory, Associate Professor in the Department of Ecology and Evolution at University of Chicago, and senior fellow of the Institute of Genomic and Systems Biology.  He is currently working on microbial communities in natural, urban, built and human ecosystems. He is Principal Investigator for the Earth Microbiome Project (www.earthmicrobiome.org), Home Microbiome Project (www.homemicrobiome.com), Gulf Microbial Modelling Project (www.microbial-models.com), Hospital Microbiome Project (www.hospitalmicrobiome.com), and the Chicago River Microbiome Project.

For more information: contact Pauline Mele (03 9032 7083)

Metagenomics@Melbourne symposium

Registration is now open for the Metagenomics@Melbourne symposium! 

This FREE event will be held at Bio21 Institute on November 27 (12:30-6pm) and will include:

• talks from 4 interstate speakers
• short talks from 10 local speakers
• lunch, afternoon tea and evening refreshments.

The aim of the symposium is to bring together Melbourne researchers with an interest in metagenomics and microbiome research, to learn more about the science and the practicalities of working in this area, to identify potential collaborators and to build local networks. Topics covered will include 16S bacterial profiling as well as metagenomic deep sequencing, with applications ranging from human clinical microbiome studies to ecological studies and marine ecosystems. Our sponsors, including sequencing technology companies and local service providers, will be on hand to provide technical advice which may help with upcoming grant applications.

We have a fantastic lineup of guest speakers from outside Victoria:

• Ian Paulsen, Macquarie University
• Gene Tyson UQ Centre for Ecogenomics
• Aaron Darling, i3 Institute UTS
• Brendan Burns, UNSW

In addition, we will hear from local researchers about their recent experiences in microbiome and metagenomics research in Victoria, including:

• Rob Moore, CSIRO
• Shu Mei Teo, University of Melbourne (Pathology)
• Tim Stinear, University of Melbourne (Microbiology & Immunology)
• Stuart Dashper, University of Melbourne (Oral Health CRC)
• Tony Papenfuss, WEHI
• Carl Kirkwood, MCRI
• Andre Mu, University of Melbourne (Earth Sciences; Microbiology & Immunology)
• Liz Ross, DEPI and La Trobe University
• Rebekah Henry, Monash University (Civil Engineering)
• Peter Kriesner, University of Melbourne (Genetics)

Cytoscape workshop, melbourne

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and
integrating these networks with annotations, gene expression
profiles and other state data.   Cytoscape is currently the primary package used throughout the world for visualizing and analyzing Biological networks of many types.  The Cytoscape consortium recently released the first major revision of Cytoscape in 10 years: Cytoscape 3.0 and the next release, Cytoscape 3.1 was just released in beta and promises several new, exciting features for integration and visualization of biological networks.

Places limited!

Click to read more...

Seminar: Dr Guy Cochrane Team Leader - European Nucleotide Archive @ EMBL-EBI

WHAT

Pathogen sequence data management: scaling and accelerating an infrastructure (~20 min)

Rapid technological advances have increased dramatically the availability of whole genome sequencing technology for the investigation of pathogens, including their biology, their ecology in host and environmental settings and their monitoring in the context of public health programmes. The public data resources responsible for persisting and making available these important data face radically increased rates of data deposition and novel patterns of access to the data. EMBL-EBI's European Nucleotide Archive, the European node of the International Nucleotide Sequence Database Collaboration, is undergoing a major engineering programme to support rapid sharing of pathogen read and assembly data based upon simplified data structures, fully automated processing pipelines and a range of user APIs and web interfaces to support those working in this area. In the talk I will present the context for such a system and the roadmap to delivering new services upon the system.

Biological data fluidity (~40 min)

Rapidly advancing high-throughput platform technologies, and their application to ever broader areas of study, have brought the life sciences into their data-intensive era. No longer solely at the hands of large specialist facilities, access to these technologies, and hence the capacity to generate data at volume, is widely dispersed around the world. At the same time, making use of these data requires analyses that are both compute-intense and operate across multiple dispersed datasets and connect with distant reference and comparator data.
    The concept of 'data fluidity', in which data flow more appropriately and easily, is an important part of the informatics response to the challenges of this era. Data fluidity addresses the streamlining of flows of data around local and global networks through such methods as data compression, streaming, partitioning into manageable units appropriate and sufficient for analysis and efficient transfer.
    In the talk, I will describe these challenges and present two methods applicable to sequence data that are being developed in this area: CRAM, a framework for sequence data compression and direct access to read data and the Webin data streamer, a UDT-based network transfer protocol.

WHEN

Monday 14 October @ 11:00-12:30 (1½ hours)

WHERE

Lecture Theatre 3, Building 105, Faculty of BusEco

111 Barry St (corner of Pelham St), CARLTON.

Maps: University |  Google

Software Carpentry Bootcamp for Bioinformaticians

September 24-26 in Adelaide and 1-3 October in Melbourne

Bootcamp Aims

To improve the productivity of bioinformaticians through teaching good programming/software skills/practices.

Target Audience

Bioinformaticians that want to improve their skills and knowledge of good programming/software practices. We may accept applicants from outside this target audience if space permits.

Expected Skills/Experience

You may be from a biological, mathematical or computer science background but should be able to identify as a bioinformatician/computational biologist. As such, you will be expected to have working knowledge of a UNIX/Linux operating system and at least one programming/scripting language in which you would consider yourself competent.

Click here for more detail...