Fourteen years of R/qtl: Just barely sustainable

R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest release contains 35k lines of R code and 24k lines of C code, plus 15k lines of code for the documentation. Challenges in the development and maintenance of the software are discussed. A key to the success of R/qtl is that it remains a central tool for the chief developer's own research work, and so its maintenance is of selfish importance.Comment: Previously submission to First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE), http://wssspe.researchcomputing.org.uk; revised for submission to the Journal of Open Research Software, http://openresearchsoftware.metajnl.com

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon which their works are built. To highlight some of these issues and share experiences, the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) was held in November 2013 in conjunction with the SC13 Conference. The workshop featured keynote presentations and a large number (54) of solicited extended abstracts that were grouped into three themes and presented via panels. A set of collaborative notes of the presentations and discussion was taken during the workshop. Unique perspectives were captured about issues such as comprehensive documentation, development and deployment practices, software licenses and career paths for developers. Attribution systems that account for evidence of software contribution and impact were also discussed. These include mechanisms such as Digital Object Identifiers, publication of “software papers”, and the use of online systems, for example source code repositories like GitHub. This paper summarizes the issues and shared experiences that were discussed, including cross-cutting issues and use cases. It joins a nascent literature seeking to understand what drives software work in science, and how it is impacted by the reward systems of science. These incentives can determine the extent to which developers are motivated to build software for the long-term, for the use of others, and whether to work collaboratively or separately. It also explores community building, leadership, and dynamics in relation to successful scientific software

Data-Driven Application Maintenance: Views from the Trenches

In this paper we present our experience during design, development, and pilot deployments of a data-driven machine learning based application maintenance solution. We implemented a proof of concept to address a spectrum of interrelated problems encountered in application maintenance projects including duplicate incident ticket identification, assignee recommendation, theme mining, and mapping of incidents to business processes. In the context of IT services, these problems are frequently encountered, yet there is a gap in bringing automation and optimization. Despite long-standing research around mining and analysis of software repositories, such research outputs are not adopted well in practice due to the constraints these solutions impose on the users. We discuss need for designing pragmatic solutions with low barriers to adoption and addressing right level of complexity of problems with respect to underlying business constraints and nature of data.Comment: Earlier version of paper appearing in proceedings of the 4th International Workshop on Software Engineering Research and Industrial Practice (SER&IP), IEEE Press, pp. 48-54, 201

Autonomous platform for life-critical decision support in the ICU

Part 2: PhD Workshop: Autonomic Network and Service ManagementInternational audienceThe Intensive Care Unit is a complex, data-intensive and critical environment in which the adoption of Information Technology is growing. As physicians become more dependent on the computing technology to support decisions, raise real-time alerts and notifications of patient-specific conditions, this software has strong dependability requirements. The dependability challenges are expressed in terms of availability, reliability, performance, usability and maintenance of the system. Our research focuses on the design and development of a generic autonomous ICU service platform. COSARA is a computer-based platform for infection surveillance and antibiotic management in ICU. During its design, development and evaluation, we identified both technological and human factors that affect robustness. We presented the identified research questions that will be addressed in detail during PhD research