Related papers: An extensible web interface for databases and its …
Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…
Important advances in pillar domains are derived from exploiting query-logs which represents users interest and preferences. Deep understanding of users provides useful knowledge which can influence strongly decision-making. In this work,…
The aim of this article is to introduce a reporting framework for reproducible, interactive research applied to Big Clinical Data, based on open source technologies. The framework is constituted by the following three axes: (i) data, (ii)…
We provide an overview of efforts to apply and extend Schema.org for archives and archival description. The authors see the application of Schema.org and extensions as a low barrier means to publish easily consumable linked data about…
The integration of Large Language Models (LLMs) into interactive systems opens new opportunities for adaptive user experiences, yet it also raises challenges regarding accessibility, explainability, and normative compliance. This paper…
A lexical database tool tailored for phonological research is described. Database fields include transcriptions, glosses and hyperlinks to speech files. Database queries are expressed using HTML forms, and these permit regular expression…
Motivation: Our goal was to combine the capabilities of Spark and GOR into a single computing framework for use in analysis of large scale genome data. Results: We have created a relational query engine that unites SparkSQL and GORpipe into…
Information extraction and data mining in biochemical literature is a daunting task that demands resource-intensive computation and appropriate means to scale knowledge ingestion. Being able to leverage this immense source of technical…
This paper is an introduction to natural language interfaces to databases (NLIDBs). A brief overview of the history of NLIDBs is first given. Some advantages and disadvantages of NLIDBs are then discussed, comparing NLIDBs to formal query…
This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducibility and the avoidance of pitfalls. It details practical applications from website management using…
Background: Increasingly, decision-making in healthcare relies on computer models, be it clinical prediction models at point of care or decision-analytic models at the policymaking level. Given the important role models play in both…
E-graphs have emerged as a versatile data structure with applications in synthesis, optimization, and verification through techniques such as equality saturation. This paper introduces Python bindings for the experimental egglog library…
Many cultural institutions have made large digitized visual collections available online, often under permissible re-use licences. Creating interfaces for exploring and searching these collections is difficult, particularly in the absence…
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and…
Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are…
Summary: The AptaBlocks Web Interface is focused on providing graphical, intuitive, and platform independent access to AptaBlocks, an experimentally validated algorithmic approach for the in-silico design of oligonucleotide sticky bridges.…
Recent advances in Generative AI have transformed how users interact with data analysis through natural language interfaces. However, many systems rely too heavily on LLMs, creating risks of hallucination, opaque reasoning, and reduced user…
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…
Over the past decade there has been a significant growth in bioinformatics databases, tools and resources. Although, bioinformatics is becoming more specific, increasing the number of bioinformatics-wares has made it difficult for…
Tau Prolog is a client-side Prolog interpreter fully implemented in JavaScript, which aims at implementing the ISO Prolog Standard. Tau Prolog has been developed to be used with either Node.js or a browser seamlessly, and therefore, it has…