MOTIVATION: The rapid expansion of Bioinformatics research has led to a proliferation of computational tools for scientific analysis pipelines. However, constructing these pipelines is a demanding task, requiring extensive domain knowledge and careful consideration. As the Bioinformatics landscape evolves, researchers, both novice and expert, may feel overwhelmed in unfamiliar fields, potentially leading to the selection of unsuitable tools during workflow development. RESULTS: In this article, we introduce the Bioinformatics Tool Recommendation system (BTR), a deep learning model designed to recommend suitable tools for a given workflow-in-progress. BTR leverages recent advances in graph neural network technology, representing the workflow as a graph to capture essential context. Natural language processing techniques enhance tool recommendations by analyzing associated tool descriptions. Experiments demonstrate that BTR outperforms the existing Galaxy tool recommendation system, showcasing its potential to streamline scientific workflow construction. AVAILABILITY AND IMPLEMENTATION: The Python source code is available at https://github.com/ryangreenj/bioinformatics_tool_recommendation.

This work follow the verification as planning paradigm and propose to use model-checking techniques to solve planning and goal reasoning problems for autonomous systems with high-degree of assurance. It presents a novel modelling framework — Goal Task Network (GTN) that encompass both goal reasoning and planning under a unified formal description that enables the use of assurance tools. The paper provides a systematic method that highlights how an industrial model checker (PAT) can be used to solve goal reasoning and planning problems modelled by GTNs. Further, this paper also introduces the design of an automated system framework for Goal Reasoning And Verification for Independent Trusted Autonomous Systems (GRAVITAS). The proposed framework is demonstrated in an experiment that simulates a survey mission performed by the REMUS-100 autonomous underwater vehicle.