Project work programme
The project work programme has been organised into 9 work packages. Short descriptions of these follow.
WP1 Executable management
A personalized executable registry from which users can select executables for use in a simulation or workflow is being provided. This registry provides access to personal executables, as well as executables available in experiment and public registries. The project is providing access to software development tools to support the modelling and code creation work. In particular, tools or instructions to support deployment are being provided, Matlab and CMISS are being supported and integrated into the project infrastructure, and the use of CellML and other component repositories is being facilitated.
WP2 Workflow management
Workflow management mirrors and complements executable management, providing facilities to add, edit, delete, publish, search, review and select workflows, including additional workflow relevant metadata as appropriate. Integration with the myGrid workflow designer and workflow engine through the associated myIB project is providing facilities to create and execute these workflows.
WP3 Job submission
This work package is enabling users to set up input parameters for an executable or workflow run and to submit jobs to project-accessible resources (e.g. NGS or HPC machines). A job submission portal enables users to submit jobs without having to understand how these target resources work. In time, this will support specification of routing for input/output data, computational steering inputs and outputs, checkpointing and failure handling, etc. Appropriate metadata/provenance data will, where possible, be created automatically. Users will be able to check the status of a job (or workflow) during execution and to steer jobs individually or in collaboration with other users. Different users may want personalised job submission interfaces, or alternative interfaces depending on the type of jobs being run. In particular, a Matlab-based interface to the job submission services is being provided. Software released by the Open Middleware Infrastructure Institute (OMII) is being evaluated for use in the project's job submission facility.
WP4 Data management
The project is developing services to allow users to manage their data space. This consists of local storage, temporary (job lifetime+) storage on project-accessible resources (e.g. NGS compute machines, remote scratch space), medium-term (experiment lifetime+) storage (e.g. on NGS data machines) and finally long-term (archive) storage (e.g. on the Atlas Datastore). Backup and curation for specified types of data will be automatic. It is intended that all data will be accompanied by appropriate provenance metadata. A naming scheme/namespace is being developed. We will enable users to 'publish' data for use by other scientists, as well as search, review and select datasets according to their access rights. Users will be able to review who has accessed their data for audit purposes and be able to set up access rights to their datasets to ensure data is not misused.
WP5 Visualisation
Users are being given access to a range of appropriate visualisation methods and tools for displaying their data. Metadata associated with the data will be used to guide tool choice. Visualisation methods are available as services, selectable by users. Visualisation of results will be possible by one or more (possibly remote) users, both in real time and at the end of a simulation. Users are able to create movies from timeslice data and can control viewing of simulation results either through rotation or movement in the data space or by varying display parameters such as colour. Remote users' viewpoints may be fixed (everyone sees the same) or steerable (each user can change their view independently of the others).
WP6 Computational steering
Users are being given the ability to steer a job or workflow and alter the model input parameters. This is being enabled through real-time visualisation of results and subsequent parameter changes based on user input or parameter boundaries. Users will be able to spawn jobs while steering a simulation to enable the results of multiple simulations with a range of parameter values to be viewed.
WP7 Collaboration
The work plan in this area is currently being developed in collaboration with the associated Integrative Biology VRE project.
WP8 User interface
The work plan in this area is currently being developed in collaboration with the associated Integrative Biology VRE project.
WP9 Security
Providing adequate security for data and code in the project is a high priority. Integrity and confidentiality must be maintained while providing managed access to data and codes. This raises issues of tolerance to component failure, a matter for overall system design and implementation of project components. Integrity of data requires active mechanisms to ensure that key data can be protected against modification, while confidentiality requires access control on who can see and use the data. The unit of security in the project is the in-silico experiment comprising a set of users, resources, data and computations that form a coherent collection. The integrity of each experiment has to be maintained, protecting against modification from outside, and within the experiment the different components have to be allowed to interact without being able to compromise each other. Each experiment will have a designated principal investigator, responsible for defining the security requirements for that experiment.