Leonardo Murta

Towards supporting the life cycle of large scale scientific experiments

One of the main challenges of scientific experiments is to allow scientists to manage and exchange their scientific computational resources (data, programs, models, etc.). The effective management of such experiments requires a specific set of cardinal facilities, such as experiment specification techniques, workflow derivation heuristics and provenance mechanisms. These facilities may characterise the experiment life cycle into three phases: composition, execution, and analysis. Works concerned with supporting scientific workflows are mainly concerned with the execution and analysis phase. Therefore, they fail to support the scientific experiment throughout its life cycle as a set of integrated experimentation technologies. In large scale experiments this represents a research challenge. We propose an approach for managing large scale experiments based on provenance gathering during all phases of the life cycle. We foresee that such approach may aid scientists to have more control on the trials of the scientific experiment.

Odyssey-VCS: a flexible version control system for UML model elements

Many current version control systems use a simple data model that is barely sufficient to manipulate source-code. This simple data model is not sufficient to provide versioning capabilities for software modeling environments, which are strongly focused on analysis and architectural design artifacts. In this work, we introduce a flexible version control system for UML model elements. This version control system, named Odyssey-VCS, deals with the complex data model used by UML-based CASE tools. Moreover, it allows the configuration of both the unit of versioning and unit of comparison for each specific project, respecting the different needs of the diverse development scenarios.

ArchTrace: Policy-Based Support for Managing Evolving Architecture-to-Implementation Traceability Links

Traditional techniques of traceability detection and management are not equipped to handle evolution. This is a problem for the field of software architecture, where it is critical to keep synchronized an evolving conceptual architecture with its realization in an evolving code base. ArchTrace is a new tool that addresses this problem through a policy-based infrastructure for automatically updating traceability links every time an architecture or its code base evolves. ArchTrace is pluggable, allowing developers to choose a set of traceability management policies that best match their situational needs and working styles. We discuss ArchTrace, its conceptual basis, its implementation, and our evaluation of its strengths and weaknesses in a retrospective analysis of data collected from a 20 month period of development of Odyssey, a large-scale software development environment. Results are promising: with respect to the ideal set of traceability links, the policies applied resulted in 95% precision at 89% recall

noWorkflow: Capturing and Analyzing Provenance of Scripts

We propose noWorkflow, a tool that transparently captures provenance of scripts and enables reproducibility. Unlike existing approaches, noWorkflow is non-intrusive and does not require users to change the way they work --- users need not wrap their experiments in scientific workflow systems, install version control systems, or instrument their scripts. The tool leverages Software Engineering techniques, such as abstract syntax tree analysis, reflection, and profiling, to collect different types of provenance, including detailed information about the underlying libraries. We describe how noWorkflow captures multiple kinds of provenance and the different classes of analyses it supports: graph-based visualization; differencing over provenance trails; and inference queries.

Towards odyssey-VCS 2: improvements over a UML-based version control system

Models are becoming first class artifacts in Software Engineering. Due to that, an infrastructure is needed to support model evolution in the same way we have for source-code. One of the key elements of such infrastructure is a version control system properly designed for models. In previous work, we presented Odyssey-VCS, a version control system tailored to fine-grained UML model elements. In this paper, we discuss the main improvements that we are incorporating on the second release of this system, which are: support for UML 2, reflective processing, explicit branching and auto-branching, generic merge algorithm, support for pessimistic concurrency policy, and support for hooks.

ProvManager: a provenance management system for scientific workflows

Running scientific workflows in distributed and heterogeneous environments has been a motivating approach for provenance management, which is loosely coupled to the workflow execution engine. This kind of approach is interesting because it allows both storage and access to provenance data in a homogeneous way, even in an environment where different workflow management systems work together. However, current approaches overload scientists with many ad hoc tasks, such as script adaptations and implementations of extra functionalities to provide provenance independence. This paper proposes ProvManager, a provenance management approach that eases the gathering, storage, and analysis of provenance information in a distributed and heterogeneous environment scenario, without putting the burden of adaptations on the scientist. ProvManager leverages the provenance management at the experiment level by integrating different workflow executions from multiple workflow management systems. Copyright

Odyssey-SCM: An integrated software configuration management infrastructure for UML models

Model-driven development is becoming a reality. Different CASE tool vendors support this paradigm, allowing developers to define high-level models and helping to transform them into refined models or source code. However, current software configuration management tools use a file-based data model that is barely sufficient to manipulate source code. This file-based data model is not adequate to provide versioning capabilities for software modeling environments, which are strongly focused on analysis and architectural design artifacts. The existence of a versioned repository of high-level artifacts integrated with a customized change control process could help in the development and maintenance of such model-based systems. In this work, we introduce Odyssey-SCM, an integrated software configuration management infrastructure for UML models. This infrastructure is composed of a flexible version control system for fine-grained UML model elements, named Odyssey-VCS, and two complementary components: a customizable change control system tightly integrated with the version control system, and a traceability link detection tool that uses data mining to discover change traces among versioned UML model elements and provides the rationale of change traces, automatically collected from the integrated software configuration management infrastructure.

Continuous and automated evolution of architecture-to-implementation traceability links

Abstract A traditional obstacle in the use of multiple representations is the need to maintain traceability among the representations in the face of evolution. The introduction of software architecture, and architecture-based development, has brought this need to architectural descriptions and corresponding source code. Specifically, the task is to relate versions of architectural elements to versions of source code configuration items, and to update those relations as new versions of the architecture and source code are produced. We present ArchTrace, a new approach that we developed to address this problem. ArchTrace distinguishes itself by continuously updating traceability relations from architectural elements to code elements through a policy-based extensible infrastructure that allows a group of developers to choose a set of traceability management policies that best match their situational needs and/or working styles. We introduce the high-level approach of ArchTrace, discuss its extensible infrastructure, and present our current set of ten pluggable traceability management policies. We conclude with a retrospective analysis of data collected from a twenty month period of development and maintenance of Odyssey, a component-based software development environment comprised of over 50,000 lines of code. This analysis shows that our approach is promising: with respect to the ideal set of traceability links, the policies applied resulted in a precision of 95% and recall of 89%.

Experiment Line: Software Reuse in Scientific Workflows

Over the last years, scientists have been using scientific workflows to build computer simulations to support the development of new theories. Due to the increasing use of scientific workflows in production environments, the composition of workflows and their executions can no longer be performed in an ad-hoc manner. Although current scientific workflow management systems support the execution of workflows, they present limitations regarding the composition of workflows when it comes to using different levels of abstractions. This paper introduces the concept of experiment line which is a systematic approach for the composition of scientific workflows that represents an in-silico experiment. An experiment line is inspired on the software engineering reuse discipline and allows the composition of scientific workflows at different levels of abstractions, which characterizes both the in-silico experiment and different workflow variations that are related to the experiment.

OdysseyShare: an environment for collaborative component-based development

Automated support such as the one provided by software development environments (SDEs) is a key requirement for the systematization of large-scale component-based software development. However, to provide a component-based SDE, adequate software development process, methods and tools that consider component-based development (CBD) activities must be previously defined. Moreover, CBD can be a highly distributed and collaborative activity that needs group interaction support. In this paper, we describe OdysseyShare environment, a collaborative component-based SDE under development at the Computer Science Department of COPPE/UFRJ. It supports activities involved in modeling, construction, reuse and group interaction by providing an integrated set of tools and a repository of reusable components.