Scalable Software Services for Life Science

About

Three Main Objectives for ScalaLife:

  1. We develop new hierarchical parallelization approaches explicitly based on ensemble and high-throughput computing for new multi-core and streaming/GPU architectures, and establish open software standards for data storage and exchange.
  2. We implement, document, and maintain such techniques in pilot European open-source codes such as the widely used GROMACS & DALTON, a new application for ensemble simulation (DISCRETE), and large-scale bioinformatics protein annotation.
  3. We have created a Competence Centre for scalable life science software to strengthen Europe as a major software provider and to enable the community to exploit e-Infrastructures to their full extent. This Competence Network provides training and support infrastructure, and establishes a long-term framework for maintenance and optimizat ion of life science codes.

Action Plan:Protein

The goals of the project are being achieved by

  • Analyzing the properties of the pilot applications and develop scalable techniques

  • Optimizing the interfaces and data formats used for life science applications

  • Integrating the new concepts into the pilot applications, maintaining, and releasing them

  • Validating the results by analyzing their impact on end applications running on European e-Infrastructures

  • Widely disseminating the results and train members of the European life science software communities, and

  • Collecting and making widely available the knowledge and best practices developed by the project to the community and providing expert services 

Main Pillars:

Networking activities:

The networking activities are designed to ensure the management of the project and its consortium, provide appropriate dissemination of ScalaLife’s goals and achievements throughout the course of the project, ensuring the project has appropriate impact on the life science software community and fostering a collaborative spirit among so far disconnected activities in the community; and provide an effective training service to foster the exploitation of scalability techniques, interfaces and data formats developed by the project in the life science software community and to increase the uptake and usage efficiency of the software packages improved by the project. The networking activities also play an important role in identifying potential target communities for the competence centre through outreach, training, and general web presence.

Service activities:

The service activities in ScalaLife are aimed to offer an integrated service to the life science software community providing software integration and maintenance, application validation, and the life science competence centre, which is in the centre of the project. We maintain world leading life science software packages and integrate new scalability techniques as well as interfaces and data format producing deployable releases of the software packages. We offer these packages on European e-Infrastructures and validate them with real application cases. The Life Science Software Competence Centre acts as “one-stop-shop” for groups seeking advice and help with life science software through providing documentation, best practices, and expert advise.

Joint Research activities:

We explore scalability techniques for life science software starting with the pilot applications and will develop and push standards for handling both storage and exchange of the ever-increasing amount of simulation data in life science. In the context of ScalaLife, an incremental route for existing applications is formulated. We also investigate the usage of ensemble computing techniques to overcome the scaling limitations inherent in some applications and investigate the usage of acceleration technologies. We help to establish the standards in the field and act as a driving force to avoid humans to be the rate limiting step in modeling/bioinformatics projects.

User communities:

Apart from the three pilot applications, ScalaLife interfaces to the Life Science Software community through the life science software competence centre. The centre is distributed to make best use of the different competences available with the partners involved in the centre and to provide a good geographic coverage over Europe. The competence centreis the key vehicle to ensure the project results taken up widely by the life science software community and by working with different groups help overcoming the fragmentation of knowledge in this field. Communities receiving expert support are and will be selected on their expected impact to the European Life Science community judged using factors like user base, geographic spread, potential for improvement etc.

International aspects:

The ScalaLife Consortium brings together top research centres and institutes from around EU27 and a focused SME on application acceleration. The consortium is balanced among technology providers, resource providers, application developers, and life science researchers. Strong links with European e-Infrastructures provided by DEISA/PRACE and EGI are established to ensure the project’s impact on e-Infrastructures. Apart from the life science researchers represented in the consortium the partners have excellent links to other life science research groups from Europe and overseas which facilitates the planned expansion of the project’s scope in the second half of the project.