Related papers: An extensible web interface for databases and its …
We introduce Natlog, a lightweight Logic Programming language, sharing Prolog's unification-driven execution model, but with a simplified syntax and semantics. Our proof-of-concept Natlog implementation is tightly embedded in the…
This paper proposes a visual analytics framework that addresses the complex user interactions required through a command-line interface to run analyses in distributed data analysis systems. The visual analytics framework facilitates the…
Objective: Quantitative real-time PCR is widely used for gene expression analysis, yet inconsistencies in data storage and reporting limit reproducibility. While MIQE guidelines define the minimal information required for publication, they…
Building interactive tools to support data analysis is hard because it is not always clear what to build and how to build it. To address this problem, we present Precision Interfaces, a semi-automatic system to generate task-specific data…
Deep Web databases contain more than 90% of pertinent information of the Web. Despite their importance, users don't profit of this treasury. Many deep web services are offering competitive services in term of prices, quality of service, and…
Clinicians are interested in better understanding complex diseases, such as cancer or rare diseases, so they need to produce and exchange data to mutualize sources and join forces. To do so and ensure privacy, a natural way consists in…
Phylogenetic analysis, which allow to understand the evolution of bacterial and viral epidemics, requires large quantities of data to be analysed and processed for knowledge extraction. One of the major challenges consists on the…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper…
Digital health tools have the potential to significantly improve the delivery of healthcare services. However, their adoption remains comparatively limited due, in part, to challenges surrounding usability and trust. Large Language Models…
Text-to-SQL systems facilitate smooth interaction with databases by translating natural language queries into Structured Query Language (SQL), bridging the gap between non-technical users and complex database management systems. This survey…
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in…
Large Language Models (LLMs) have shown remarkable proficiency in natural language understanding (NLU), opening doors for innovative applications. We introduce StreamLink - an LLM-driven distributed data system designed to improve the…
Unlike most user-computer interfaces, a natural language interface allows users to communicate fluently with a computer system with very little preparation. Databases are often hard to use in cooperating with the users because of their…
Unification of logic variables instantly connects present and future observations of their value, independently of their location in the data areas of the runtime system. The paper extends this property to "interclausal logic variables", an…
Both logic programming in general, and Prolog in particular, have a long and fascinating history, intermingled with that of many disciplines they inherited from or catalyzed. A large body of research has been gathered over the last 50…
We present BioRAGent, an interactive web-based retrieval-augmented generation (RAG) system for biomedical question answering. The system uses large language models (LLMs) for query expansion, snippet extraction, and answer generation while…
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…