Related papers: An extensible web interface for databases and its …

Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…

The rise of the programmable web offers new opportunities for the empirically driven social sciences. The access, compilation and preparation of data from the programmable web for statistical analysis can, however, involve substantial…

The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data.…

Chemical databases store information in text representations, and the SMILES format is a universal standard used in many cheminformatics software. Encoded in each SMILES string is structural information that can be used to predict complex…

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted…

Deep learning models have become fundamental tools in drug design. In particular, large language models trained on biochemical sequences learn feature vectors that guide drug discovery through virtual screening. However, such models do not…

We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large…

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although…

We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…

The bond graph approach to modelling biochemical networks is extended to allow hierarchical construction of complex models from simpler components. This is made possible by representing the simpler components as thermodynamically open…

Many real world systems need to operate on heterogeneous information networks that consist of numerous interacting components of different types. Examples include systems that perform data analysis on biological information networks; social…

Building interactive data interfaces is hard because the design of an interface depends on the data processing needs for the underlying analysis task, yet we do not have a good representation for analysis tasks. To fill this gap, this paper…

Following the ideas of the Remote Procedure Call model, we have developed a logic programming counterpart, naturally called Prolog Remote Predicate Call (Prolog RPC). The Prolog RPC protocol facilitates the integration of Prolog code in…

The number of databases as well as their size and complexity is increasing. This creates a barrier to use especially for non-experts, who have to come to grips with the nature of the data, the way it has been represented in the database,…

Indexing massive data sets is extremely expensive for large scale problems. In many fields, huge amounts of data are currently generated, however extracting meaningful information from voluminous data sets, such as computing similarity…

This document introduces PlDoc, a literate programming system for Prolog. Starting point for PlDoc was minimal distraction from the programming task and maximal immediate reward, attempting to seduce the programmer to use the system.…

We present CleanQ, a high-performance operating-system interface for descriptor-based data transfer with rigorous formal semantics, based on a simple, formally-verified notion of ownership transfer, with a fast reference implementation.…

Output-intensive scientific applications are highly sensitive to low storage throughput. While existing scientific application stacks are optimized for traditional High-Performance Computing (HPC) environments with high remote storage and…

To fully expedite AI-powered chemical research, high-quality chemical databases are the foundation. Automatic extraction of chemical information from the literature is essential for constructing reaction databases, but it is currently…