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This paper presents gnss_lib_py, a Python library used to parse, analyze, and visualize data from a variety of GNSS (Global Navigation Satellite Systems) data sources. The gnss_lib_py library's ease of use, modular capabilities, testing…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to…
Cancer complexome comprises a heterogeneous and multifactorial milieu that varies in cytology, physiology, signaling mechanisms and response to therapy. The combined framework of network theory and spectral graph theory along with the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
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…
In this paper we introduce DISROPT, a Python package for distributed optimization over networks. We focus on cooperative set-ups in which an optimization problem must be solved by peer-to-peer processors (without central coordinators) that…
The development of spiking neural network simulation software is a critical component enabling the modeling of neural systems and the development of biologically inspired algorithms. Existing software frameworks support a wide range of…
As a result of a hundred million years of evolution, living animals have adapted extremely well to their ecological niche. Such adaptation implies species-specific interactions with their immediate environment by processing sensory cues and…
External control of agent-based models is vital for complex adaptive systems research. Often these experiments require vast numbers of simulation runs and are computationally expensive. NetLogo is the language of choice for most agent-based…
We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate…
Living plants, while contributing to ecological balance and climate regulation, also function as natural sensors capable of transmitting information about their internal physiological states and surrounding conditions. This rich source of…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
Control of complex processes is a major goal of network analyses. Most approaches to control nonlinearly coupled systems require the network topology and/or network dynamics. Unfortunately, neither the full set of participating nodes nor…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
In modern electronic medical records (EMR) much of the clinically important data - signs and symptoms, symptom severity, disease status, etc. - are not provided in structured data fields, but rather are encoded in clinician generated…
Networks provide a meaningful way to represent and analyze complex biological information, but the methodological details of network-based tools are often described for a technical audience. Graphery is a hands-on tutorial webserver…
Integrating deep learning techniques, particularly language models (LMs), with knowledge representation techniques like ontologies has raised widespread attention, urging the need of a platform that supports both paradigms. Although…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Functional near-infrared spectroscopy (fNIRS) is a non-invasive optical technique that measures brain activity by estimating blood oxygenation using near-infrared light. Traditionally, PsychoPy is used in many studies to send task-specific…