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Fighting Cancer Cancer touches so many of us; with one in two Australians being diagnosed with cancer by their 85th birthday, medical research is the key to finding better treatments.
Cancer research progress at Garvan Institute of Medical Research is slowed by the limited access researchers have to the supercomputers they need to crunch complex research data. For a long time, cancer has been thought of by its tissue of origin — for example lung, breast or pancreatic cancer.
But cancer is Crm strategy of vodafone disease of the DNA, and so with the advances in genome sequencing, world leading researchers at Garvan Institute of Medical Research are interested in creating a library of cancers, grouped based on their genetic mutations.
Analysing Mutations To do this, researchers need to analyse the genomic mistakes DNA mutations of thousands of different cancer patients and group them based on their genetic profiles not the tissue in which the cancer originated.
The sequencing of just one genome generates tens of gigabytes of data. So huge computing power is needed to complete this analysis. But at Garvan and around the world access to supercomputers is limited and costly.
At the moment the app is available on Android only. To tackle this problem the Garvan Institute of Medical Research has developed a novel in-house computational algorithm to estimate how functionally close the mutated genes between two patients could be, which can then be used to group tumours based on their mutation profiles, regardless of which tissue the cancer originated.
It has been adapted to run on Android Smartphones for DreamLab. Inside DreamLab The algorithm calculates a number of statistics of the interactions between two sets of genes i.
These patterns can help researchers identify subgroups of patients who share similar mutation profiles, and could therefore potentially respond to the same therapies. The combination of a large community DreamLab userscoupled with big data analytic algorithms, makes this revolutionary form of research possible.
Once a user has downloaded and set up the DreamLab app, the app will then authenticate against Amazon Cognito and use a set of temporary, limited privilege credentials to request a research job out of Amazon SQSand then download a small research payload out of S3 hundreds of KB with job session state for each phone being managed by Amazon DynamoDB.
The result is then sent back from the phone to S3, for the Garvan team to analyse. Informally, this is similar to solving a crossword puzzle with everyone working on a different clue. The nature of the project required an architecture that supports large volumes of data and spiked traffic, whilst remaining cost effective.
The architecture also needed to support the ability to maintain the state of any data item, whilst simultaneously being updated across more than one client. Amazon Simple Storage Service S3 is an optimal service for the storage of data.
It has no upper limit in the amount of data that can be stored, and due to its distributed nature it has high redundancy. It also has the added functionality of being able to fire events when an item is added. Amazon Simple Queue Service SQS is a queuing system of unlimited size, supporting the requirement of high traffic and data.
The app facing queues utilise the data visibility setting, to ensure that other devices do not fetch an item whilst various operations are taking place. Whilst the data schema for this system could benefit from a relational database syste,m the benefits of the scale and price of DynamoDB outweigh these.
Amazon Cognito and STS provide substantial security with only a minimal requirement for custom development.
Amazon Elastic Compute Cloud EC2 servers run all the custom code that is used to maintain the other systems. This custom code is scheduled to run regularly with CRON jobs. We investigated AWS Lambda, a service that runs custom code on an event notification, however Lambda is currently not available in Australia.
This is so that the communication is over a custom domain that Vodafone uses to zero rate data charges for Vodafone Australia customers in Australia. By the Numbers The Garvan Institute currently hasbase datasets files.
Each file is 2 MB uncompressed, and KB compressed. In the DreamLab project, each of the base datasets will be downloaded by three users for result validation purposes. Garvan also has 5, analysis tasks, with a size of 1 KB uncompressed and bytes compressed.Digital transformation is the profound transformation of business and organizational activities, processes, competencies and models to fully leverage the changes and opportunities of a mix of digital technologies and their accelerating impact across society in a strategic and prioritized way, with present and future shifts in mind.
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