Related papers: An extensible web interface for databases and its …
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
Log analysis represents a critical sub-domain within AI applications that facilitates automatic approaches to fault and error management of large-scaled software systems, saving labors of traditional manual methods. While existing solutions…
In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view…
In this work, we develop an intelligent user interface that allows users to enter biomedical queries in a natural language, and that presents the answers (possibly with explanations if requested) in a natural language. We develop a rule…
Today's database systems have shown to be capable of supporting AI applications that demand a lot of data processing. To this end, these systems incorporate powerful querying languages that go far beyond the mere retrieval of data, and…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
Contemporary database systems, while effective, suffer severe issues related to complexity and usability, especially among individuals who lack technical expertise but are unfamiliar with query languages like Structured Query Language…
Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…
Many fields of science rely on relational database management systems to analyze, publish and share data. Since RDBMS are originally designed for, and their development directions are primarily driven by, business use cases they often lack…
Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity…
Datalog-based languages are regaining popularity as a powerful abstraction for expressing recursive computations in domains such as program analysis and graph processing. However, existing systems often face a trade-off between efficiency…
This paper is about the technical design of a large computational lexicon, its storage, and its access from a Prolog environment. Traditionally, efficient access and storage of data structures is implemented by a relational database…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Transparency regarding the processing of personal data in online services is a necessary precondition for informed decisions on whether or not to share personal data. In this paper, we argue that privacy interfaces shall incorporate the…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
The runtime system of dynamic languages such as Prolog or Lisp and their derivatives contain a symbol table, in Prolog often called the atom table. A simple dynamically resizing hash-table used to be an adequate way to implement this table.…
ECLAIR is a Prolog-based prototype system aiming to provide a functionally complete environment for the study, development and evaluation of programming language analysis and implementation tools. In this paper, we sketch the overall…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…