UC-NGI-SW-persson
From EGI Knowledge Base
Use Case title: Bioinformatics on the Grid
Short description: Life sciences have undergone an immense transformation during the recent years, where advances in genomics, proteomics and other high-throughput techniques produce floods of raw data that need to be stored, analysed and interpreted in various ways. Bioinformatics is crucial by providing tools to efficiently utilise these gold mines of data in order to better understand the roles of proteins and genes and to obtain ideas for new experiments. There are several use cases where the European computer grids will be of great importance for bioinformatics area.
Database distribution on the grid. In bioinformatics, databases are crucial and it is important to have them distributed to the grid nodes. In addition, there are frequent updates of the databases (ranging from monthly to daily). The new European bioinformatic infrastructure ELIXIR will support life science research and its translation to medicine and the environment, the bio-industries and society. ELIXIR will establish a trans-national infrastructure for biological information and service providers, building upon existing national/regional infrastructures and networks. ELIXIR will also promote and further development in the use of distributed annotation technologies for large scale European collaborations in the life science databases and promote the formation of an associated European framework for training and outreach.
Gridifying of bioinformatics software. There is work necessary for gridifying and efficiently parallelisation of frequently used bioinformatics algorithms. There is also a need for increased communication between the programmes. The just initiated Nordic Biogrid project has gridifying of bioinformatics software on its task list. Within the EU project EMBRACE people work on improving communication between different bioinformatic programmes and to create seamless workflows. This will be increasingly important when using the grid.
Actors involved: Bioinformatics projects like ELEXIR, EMBRACE and Biogrid, EGI and National Grid Initiatives.
Steps:
- Establish contacts with the Bioinformatics projects
- Identify the main user needs
- Establish strategies and models to define, manage and operate the services
- Ensure the uptake of the services by the infrastructure-, service providers and end-users
