About SBI Australia
SBI Australia has been established at ARMI as the first node of Japan’s internationally recognised Systems Biology Institute.
The node connects and promotes collaboration between Japanese and Australian research and industry partners, and facilitates the sharing of scientific technology, resources and expertise.
SBI Australia develops and supports the Australian systems biology research community, through the provision of training and advice, facilitation and making national and international linkages.
In the short time since its establishment, SBI Australia has attracted national and international attention. SBI Australia has a number of exciting linkages and projects already underway and is actively seeking grants and funding for all of its programs.
At SBI Australia, there are four core elements to how systems biology research is viewed:
1. Use all the available knowledge.
Building on the knowledge of the life sciences, systems biology brings in expertise from fields such as mathematics, engineering, computer science, physics and chemistry. Using all the available tools scientists can, for example, make powerful computations that are not humanly possible, develop mathematical models that help researchers to not only understand but also predict behaviour, and uncover what makes a system robust or vulnerable to threats such as disease or pests.
2. Be creative.
The purpose of integrating all the disciplines is to not just transfer solutions from one place to another. Sometimes, the solution does not exist – and thinking about a problem from a completely new perspective may provide the creative breakthrough that is needed.
3. Collaborate internationally.
Around the world, people are doing exciting, cutting edge research. The large-scale challenges of systems biology rely on an international network to bring the best skills and knowledge together. Only in this way will it be possible to solve these grand challenges.
4. Focus on what matters, and make it count.
There are many problems affecting society today – human health and wellbeing, pressures around sustainable living, food and water security, and quality of life for people everywhere. Systems biology enables researchers to tackle many of these global problems, and to make a real difference by focusing on research that has a rapid translation to real outcomes.
Research at SBI Australia focuses on these four goals, and as an initiative of EMBL Australia, scientists use national and international linkages to find new and creative solutions to problems in human health and the environment, with the purpose of rapid translation to applied outcomes. As host of SBI Australia, Monash University has gained a competitive advantage and reputation in the systems biology space, both nationally and internationally.
WHAT IS SYSTEMS BIOLOGY?
The international community has not yet reached agreement on a formal definition of systems biology. However, fundamentally the goal is implied by the name: to understand complex biological systems, as a system.
This distinction contrasts with many valuable endeavours in life sciences research that seek to understand biological phenomena, but not necessarily as a system. Two classic examples from biology include: 1) identifying if a mutation in a gene causes disease; and 2) discovering how the structure of a protein enables it to receive and transmit important messages in the body. Both of these are valuable discoveries, but scientists also want to understand how the disease progresses, and how those messages are used in the body.
What defines systems biology (at least in the view of SBI) is the intention to understand complex biological systems in terms of the system itself – the rules and principles that govern, regulate and define the system. Systems biology is also defined by the integration of life sciences research with the knowledge, skills and technology of all the research disciplines, including mathematics, engineering, computer science, physics, chemistry and even linguistics, to tackle this incredibly difficult task.
Systems biology research
As scientific Program Leader, Dr Mirana Ramialison leads the initiative and through her research group uses the exciting technologies of systems biology to study how organs form, specifically the heart.
Mirana’s experience in both traditional experimental biology and computational biology enables her to investigate heart formation with a view to finding treatments for congenital heart disease.
In addition to using the zebrafish as a model organism, Dr Ramialison was the recipient of a Monash Strategic grant to establish the Medaka fish model organism in Australia to look for DNA mutations relevant to human disease.
|A/Prof Mirana Ramialison||Scientific Program Leader|
|Dr Samik Ghosh||Research Fellow – Adjunct|
|Prof Hiroaki Kitano||Adjunct Professor|
|Dr Yukiko Matsuoka||Research Fellow – Adjunct|
|Dr Yuan-Fang Li||Senior Lecturer|
|Dr Lan Nguyen||Senior Research Fellow and Laboratory Head|
|Dr Hieu Nim||Post-doctoral Fellow|
|Adrian (Abbas) Salavaty||PhD Student|
TrawlerWeb is a web-based and extended version of our previously published method Trawler (Nat Methods 4:563ñ5, 2007; Nat Protoc 5:323ñ34, 2010), which allow for the identification of enriched motifs and binding sites in DNA sequences obtained from next-generation sequencing experiments.
Web service: http://trawler.erc.monash.edu.au
Source code: https://github.com/Ramialison-Lab-ARMI/Trawler-2.0
MonaGO is a dynamic web-based visualisation system for performing gene ontology (GO) enrichment analysis and visualising the results, by representing the streamlined outputs using intuitive chord diagram-based clustering visualisation.
Web service: https://monago.erc.monash.edu
Source code: https://github.com/liyuanfang/MonaGO
3D-cardiomics is an online interactive interface which allows for further exploration of the spatial gene expression data of the heart in three-dimensional space, with essential features including the interactive 3D exploration, gene search, clustering, and differential expression analysis.
Web service: http://3d-cardiomics.erc.monash.edu/
Source code: https://github.com/Ramialison-Lab-ARMI/3DCardiomics
IVI (Integrated Value of Influence) is a novel integrative algorithm that synergises the effects of the most important network centrality measures and simultaneously removes their inherent biases with the purpose of identifying the most influential nodes within networks.
CRAN R package: https://cran.r-project.org/package=influential
Source code: https://github.com/asalavaty/influential
Corresponding publication: https://doi.org/10.1016/j.patter.2020.100052
Partners and funding agencies: The Australian Research Council, the US Food and Drug Administration, the Australian Regenerative Medicine Institute
Until recently, we thought that the heart was controlled by its muscle cells. Systems biology is helping us to understand that cardiac fibroblasts, which give structure to the heart, may also be central to the heart’s function.
With funding from the ARC, we’re building mathematical models to investigate how cardiac fibroblasts regulate the function of healthy adult hearts.
We’re also working with the US Food and Drug Administration on a study of the effects of anti-cancer drugs in the heart, joining forces with colleagues at the Australian Regenerative Medicine Institute to combine our knowledge of cardiac fibroblasts with their expertise in in vivo cardiac research.
Embryogenesis and assisted reproductive technologies
Partners and funding agencies: Monash IVF, EMBL Australia, RIKEN (Japan)
SBI Australia is bringing together experts in biology, chemistry, computer science and maths to understand how embryos develop, and we’re working with clinicians at Monash IVF to bring this research to patients quickly. The end goal: generating better embryos for implant.
We’re looking at the mechanisms governing cell fate decisions – which direct embryonic stem cells to become one cell type or another – with Australian and Japanese colleagues from research, industry and clinical practice.
SBI director Hiroaki Kitano and EMBL Australia group leader Nico Plachta are building models which colleagues at Monash IVF are using with their own patient data to improve their understanding of likely success and risk in IVF.
Partners and funding agencies: The Canon Foundation, UC Merced (USA), UNAM (Mexico)
We’re working to understand how coral reacts to environmental stress by mapping the complex symbiotic relationships between coral and algae. We want to understand why some corals are more tolerant to certain stresses in their environment, and to learn about the trade-offs which make those corals more susceptible to other stresses.
In collaboration with researchers in California, Mexico, Japan and Queensland, our work could help to protect and even restore reefs damaged by climate change.
Garuda Alliance and Flint
Partners and funding agencies: The Garuda Alliance
SBI Australia will facilitate access to high performance computing and resources for systems biology such as Garuda and Flint.
The Systems Biology Institute was a founding partner of the Garuda alliance – a group of university and industry bodies developing an open standard to share information between the software we use to describe the models we use in systems biology.
Flint is a simple interface which gives researchers without expert programming knowledge easy access to computing resources around the world. SBI and Monash will connect Flint to the Monash-NeCTAR Research Cloud – a five-year, $4 million project to bring new tools and expansive computing resources to research organisations in Melbourne’s south-east.