André Luiz de Oliveira

GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data.

This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.

A Model-Based Approach to Support the Automatic Safety Analysis of Multiple Product Line Products

Software product lines (SPL) have been successfully used in the development of automotive and avionics critical embedded systems. Hazards and their causes may change according to the selection of variants in a particular SPL product. Thereby, lower-level assets like fault trees and FMEA (Failure Modes and Effects Analysis) cannot be reused because they are dependent upon the selection of product variants. In this paper, model-based safety analysis techniques and SPL variability management tools are used together to reduce the effort of product safety analysis by: reusing SPL hazard analysis, and providing automatic safety analysis for each SPL product. Therefore, we propose a model-based approach to support the generation of safety analysis assets for multiple safety-critical SPL products. The proposed approach is illustrated using the Hephaestus variability management tool and the HiP-HOPS model-based safety analysis tool to generate fault trees and FMEA for the products of an automotive hybrid braking system SPL. Applying the approach reduced the effort to perform product safety analysis.

Supporting the Automated Generation of Modular Product Line Safety Cases

The effective reuse of design assets in safety-critical Software Product Lines (SPL) would require the reuse of safety analyses of those assets in the variant contexts of certification of products derived from the SPL. This in turn requires the traceability of SPL variation across design, including variation in safety analysis and safety cases. In this paper, we propose a method and tool to support the automatic generation of modular SPL safety case architectures from the information provided by SPL feature modeling and model-based safety analysis. The Goal Structuring Notation (GSN) safety case modeling notation and its modular extensions supported by the D-Case Editor were used to implement the method in an automated tool support. The tool was used to generate a modular safety case for an automotive Hybrid Braking System SPL.

Investigating framework product lines

Frameworks are tools that promote the reuse of pieces of software within specific domains. An intrinsic property of frameworks is the large amount of intertwined code found across its several modules. This configures an architecture whose modules can hardly be decoupled. Consequently, an application derived from a framework usually carries on the full framework architecture, irrespective of the subset of application requirements. This compromises the maintainability, evolution and reusability of both framework and applications derived from it. To deal with this problem, this paper introduces the concept of Framework Product Lines (FPL). In a FPL, each member - or configuration -- is a framework that contains only a subset of the FPL features according to the application requirements and rules that constrain their composition. Thus, this paper presents the framework product lines concept and shows its use for evolving an application framework towards FPL. Results show preliminary gains in terms of reusability and maintainability in both evolved framework and applications derived from it.

Model-based safety analysis of software product lines

Software product lines (SPLs) provide an engineering basis for the systematic reuse of artefacts used for development, assessment, and management of critical embedded systems. Hazards and their causes are safety properties that may change according to the selection of variants in a particular SPL product. Therefore, safety analysis assets such as fault trees and failure modes and effects analysis (FMEA) cannot be directly reused because they are dependent upon the selection of product variants. In this paper, model-based safety analysis techniques and SPL variability management tools are used together to reduce the effort of product safety analysis by: reusing SPL hazard analysis, and providing automatic safety analysis for each SPL product. The benefit of applying the approach is the reduction of effort to perform product safety analysis. The proposed approach is illustrated using the Hephaestus variability management tool and the HiP-HOPS model-based safety analysis tool to generate fault trees, and FMEA for products of an automotive hybrid braking system SPL. The safety assessment artefacts generated by the approach provide feedback for the SPL development process helping safety engineers to make decisions earlier in the development lifecycle.

Evaluating the Effort for Modularizing Multiple-Domain Frameworks Towards Framework Product Lines with Aspect-oriented Programming and Model-driven Development

Multiple-Domain Frameworks (MDFs) are frameworks that unconsciously involve variabilities from several domains and present two main problems: i) useless variabilities in the final releases and ii) architectural inflexibility. One alternative for solving this problem is to convert them into Framework Product Lines (FPL). FPL is a product line whose members are frameworks rather than complete applications. The most important characteristic of FPLs is the possibility of creating members (frameworks) holding just the desired variabilities. However, the process of converting an MDF into an FPL is very time-consuming and the choice for the most suitable technique may improve significantly the productivity. The main focus of this paper is an experiment that evaluates two techniques that are usually considered for dealing with features: model-driven development and aspect-oriented programming. Our experiment was conducted comparing the effort in converting an MDF called GRENJ into an FPL called GRENJ-FPL The results showed significant differences regarding the time spent and the occurrence of errors using both techniques.

Variability Management in Safety-Critical Software Product Line Engineering

Safety-critical systems developed upon SPLE approach have to address safety standards, which establish guidance for analyzing and demonstrating dependability properties of the system at different levels of abstraction. However, the adoption of an SPLE approach for developing safety-critical systems demands the integration of safety engineering into SPLE processes. Thus, variability management in both system design and dependability analysis should be considered through SPLE life-cycle. Variation in design and context may impact on dependability properties during Hazard Analysis and Risk Assessment (HARA), allocation of functional and non-functional safety requirements, and component fault analysis. This paper presents DEPendable-SPLE, a model-based approach that extends traditional SPLE methods, to support variability modeling/management in dependability analysis. The approach is illustrated in a case study from the aerospace domain. As a result, the approach enabled efficient management of the impact of design and context variations on HARA and component fault modeling.