National Centers for Biomedical Computing Software and Data

National Centers for Biomedical Computing Software and Data Integration Working Group Peter Lyster (Chair) NCBC Workshop Wednesday December 16 (2005)

Software and Data Integration: National Infrastructure • Open dialogue through NA-MIC Wiki http: //namic. org/Wiki/index. php/SDIWG: Software_ and_Data_Integration_Working_Group

Charter of SDIWG—from wiki The RFA states the goal of creating “the networked national effort to build the computational infrastructure for biomedical computing for the nation”. In furthering this, the goals of the SDIWG in concert with the Project Team are: • To advance the domain sciences, and promote software interoperability and data exchange. • To capture the collective knowledge of software engineering and practices among the Centers and publish this knowledge widely.

What did we say last year?

Mission statement for the software and data integration working group under the NCBC Building the computational infrastructure for biomedical computing for the nation: • (1) Improvements and efficiencies in software development and maintenance that may be achieved through promotion of shared software engineering practices, interoperable software, reuse of software components at various stages of granularity, and the use of common software repositories where appropriate for software development and distribution. • (2) Explore opportunities for networking data relating to data acquisition, data and metadata interchange standards and formats, data models and ontologies, knowledge bases, grid computing, data distribution, security and confidentiality, IP, and the interfaces between algorithms, models, and data. Effective use of Web services. • (3) Address areas of overlap and interaction with other NIH and governmentfunded efforts. • (4) Address substantial issues related to the physical world modeling—this involves how models are defined, manipulated, visualized and interchanged.

Issues, Progress, in the first year • Demonstration projects • Collaborative software development environment (yellow pages, knowledge environment, full development environment or Framework) • NIH-forge • Emerging efforts in the community (Neuroscience Information framework— NIF, Clearinghouse idea, …)

• Explore NIH-forge, Frameworks, or Clearinghouse-common federated software repositories • Data repositories: issues include the temporal order of creation, maintenance, and their independence/dependence. • Interoperability: the broad issues are developed in the ca. BIG Compatibility Guidelines. One suggestion is the use of interoperability demonstrations as a driver. • The use of Pipelines (e. g. , LONI Pipeline). This may be used to foster software reuse and flexible composition of applications. • Explore interactions with other non-Roadmap Initiatives

What did we say last year?

Mission statement for the software and data integration working group under the NCBC Building the computational infrastructure for biomedical computing for the nation: • (1) Improvements and efficiencies in software development and maintenance that may be achieved through promotion of shared software engineering practices, interoperable software, reuse of software components at various stages of granularity, and the use of common software repositories where appropriate for software development and distribution. • (2) Explore opportunities for networking data relating to data acquisition, data and metadata interchange standards and formats, data models and ontologies, knowledge bases, grid computing, data distribution, security and confidentiality, IP, and the interfaces between algorithms, models, and data. Effective use of Web services. • (3) Address areas of overlap and interaction with other NIH and governmentfunded efforts. • (4) Address substantial issues related to the physical world modeling—this involves how models are defined, manipulated, visualized and interchanged.

Building the computational infrastructure for biomedical computing for the nation: • (1) Improvements and efficiencies in software development and maintenance that may be achieved through promotion of shared software engineering practices, interoperable software, reuse of software components at various stages of granularity, and the use of common software repositories where appropriate for software development and distribution.

Building the computational infrastructure for biomedical computing for the nation: • (2) Explore opportunities for networking data relating to data acquisition, data and metadata interchange standards and formats, data models and ontologies, knowledge bases, grid computing, data distribution, security and confidentiality, IP, and the interfaces between algorithms, models, and data. Effective use of Web services.

Building the computational infrastructure for biomedical computing for the nation: • (3) Address areas of overlap and interaction with other NIH and government-funded efforts. • (4) Address substantial issues related to the physical world modeling—this involves how models are defined, manipulated, visualized, and interchanged

Related issues How similar/different are the Cores among the NCBC Centers? • • • Software engineering methods Shared software repositories Software dissemination methods Effective use of web services Shared data models

Down the Road • Generation of an inventory of relevant areas where SDI is important for the NCBC • Make connections with similar efforts in large-scale computational science and their lessons learned • Analyze barriers to forming the national infrastructure • Plan leveraged demonstration projects • Plan for team infrastructure to continue development and implementation of activities among NCBC Centers and with other NIH and government-funded efforts

Activities in the coming year • Working group interaction with NCBC Centers to explore integration • Road trips • Involvement in upcoming meetings: ISMB, AMIA, SC 05… • Portal

Software and Data Integration Working Group NIH Staff Peter Lyster (NIGMS, Chair) Michael Ackerman (NLM) Carol Bean (NCRR) Art Castle (NIDDK) German Cavelier (NIMH) Larry Clarke (NCI) Elaine Collier (NCRR) Jennifer Couch (NCI) Peter Covitz (NCI) Valentina Di Francesco (NIAID) Dan Gallahan (NCI) Peter Good (NHGRI) John Haller (NIBIB) Donald Harrington (NIBIB) Peter Highnam (NCRR) Michael Huerta (NIMH) Donald Jenkins (NLM) Jennie Larkin (NHLBI) Yuan Liu (NINDS) Michael Marron (NCRR) Richard Morris (NIAID) Bret Peterson (NCRR) Salvatore Sechi (NIDDK) Karen Skinner (NIDA) Michael Twery (NHLBI) Terry Yoo (NLM)

The End • (Miscellaneous slides to follow)