Scalable Software Services for Life Science

Join ScalaLife Competence Centre

Life Science researchers are welcome to join the ScalaLife community! And there are many ways for participation!

Whether you are a user of the core applications, a life science research goup or a life science software developer ScalaLife is open to collaborate with you. Please contact us if you are interested by sending a mail to scalalife@pdc.kth.se.

If your research work relies on extensive usage of one of the core applications, the Competence Center Knowledgebase can assist you in the execution of your project. The tutorials and best practices guides will be useful to both novice and advanced users with information on program installation, optimal usage of HPC resources and analysis of the simulation results. Help and advice from the community can be obtained through the forums after registration on the website.

Research groups can apply for exclusive support by application experts at the Competence Center. If accepted in the project, they will receive help with issues concerning the deployment of software codes and optimal utilization of available hardware resources. Additional support with analysis of the computational output is also available. The experts might request to be included as authors of subsequent published works depending on the level of their involvement in the project. This will be discussed during the application process. Interested groups should send a short description of the nature and importance of their research work as well as need for expert support. The application requests should be submitted to the project contact address scalalife (at) pdc.kth.se. The acceptance will depend on the available manpower.

The Competence Center provides information on methods for software code profiling and optimization for HPC systems. This information will be particularly useful to developers of Life Science applications who want to improve the performance of their codes. Community help with optimization techniques can be found through the forums.

Including new software packages as core applications

Research groups which are developing custom applications can apply for their inclusion in the core application base of ScalaLife. If accepted, the Competence Center can

  • Provide expert support with analysis on their performance and scalability on different HPC platforms
  • Popularize the software through ScalaLife's outreach initiatives including conference talks, web presence, newsletter bulletins etc.

Developers will be asked to

  • If needed, deploy precompiled binaries of the applications on selected HPC systems. If the license of the application permits it, provide biannual source code snapshots for official ScalaLife releases. It will be very useful to have necessary input sets and models for testing and benchmarking.
  • Provide through the Competence Center knowledgebase information to users such as tutorials, best practices guides, presentation slides or similar. This information can also be links to already existing one on other sites.
  • Provide support to users of their software through the forums and participate in training events organized as part of the project

As a proponent of open source software and standards, the ScalaLife project requires that the core applications should adhere to the following license requirements.

 

License requirements for core applications in the ScalaLife project

  1. The core applications can preserve their original licenses which they've had at the time of joining the project. Applications with strong restrictions on modification and re-distribution of source code need internal evaluation before joining. At the very least, pre-compiled binaries should be available free of charge to the academic scientific community.
  2. Newly developed source code should be licensed under the terms of BSD, X11(MIT) or similar licenses that permit complete freedom for re-usage.
  3. Extension of previous modules should be at least LGPL to allow commercial applications to link against it. Same holds for code which relies on existing components.