Related papers: Biodose Tools updates for criticality accidents an…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…
BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitting (i.e., nonlinear regression). BioNetFit is compatible…
The README file serves as a critical source of information for gaining an overview and helping developers onboard to an Open Source Software (OSS) project. Yet, documentation issues persist; in particular, ``outdated'' documentation is…
Motivation: Novel machine learning and statistical modeling studies rely on standardized comparisons to existing methods using well-studied benchmark datasets. Few tools exist that provide rapid access to many of these datasets through a…
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with…
Online medical literature has made health information more available than ever, however, the barrier of complex medical jargon prevents the general public from understanding it. Though parallel and comparable corpora for Biomedical Text…
Automatic synthesis of hardware components from declarative specifications is an ambitious endeavor in computer aided design. Existing synthesis algorithms are often implemented with Binary Decision Diagrams (BDDs), inheriting their…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
The recent trend of using Large Language Models (LLMs) as tool agents in real-world applications underscores the necessity for comprehensive evaluations of their capabilities, particularly in complex scenarios involving planning, creating,…
Bayesian inference affords scientists with powerful tools for testing hypotheses. One of these tools is the Bayes factor, which indexes the extent to which support for one hypothesis over another is updated after seeing the data. Part of…
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set…
In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…
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…
The iotools package provides a set of tools for Input/Output (I/O) intensive datasets processing in R (R Core Team, 2014). Efficent parsing methods are included which minimize copying and avoid the use of intermediate string representations…
This paper presents Fossil 2.0, a new major release of a software tool for the synthesis of certificates (e.g., Lyapunov and barrier functions) for dynamical systems modelled as ordinary differential and difference equations. Fossil 2.0 is…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text exhibits a fundamentally different uncertainty structure from general text: dense low-confidence…
Species distribution models (SDMs) are one of the most common statistical methods to assess species occupancy and geographic distribution patterns. With the increasing complexity of ecological data, many methodological approaches have been…
Automated filtering of toxic conversations may help an Open-source software (OSS) community to maintain healthy interactions among the project participants. Although, several general purpose tools exist to identify toxic contents, those may…
Due to their flexibility and superior performance, machine learning models frequently complement and outperform traditional statistical survival models. However, their widespread adoption is hindered by a lack of user-friendly tools to…