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Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
Trusted execution environments (TEE) such as Intel's Software Guard Extension (SGX) have been widely studied to boost security and privacy protection for the computation of sensitive data such as human genomics. However, a performance…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Algorithmic fairness has received considerable attention due to the failures of various predictive AI systems that have been found to be unfairly biased against subgroups of the population. Many approaches have been proposed to mitigate…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generation genome sequencing methods used in precision medicine…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
The rapid evolution of software libraries poses a considerable hurdle for code generation, necessitating continuous adaptation to frequent version updates while preserving backward compatibility. While existing code evolution benchmarks…
There is a strong recent emphasis on trustworthy AI. In particular, international regulations, such as the AI Act, demand that AI practitioners measure data quality on the input and estimate bias on the output of high-risk AI systems.…
To address a looming crisis of unreproducible evaluation for named entity recognition, we propose guidelines and introduce SeqScore, a software package to improve reproducibility. The guidelines we propose are extremely simple and center…
Chromatin conformation capture technologies such as Hi-C have revealed that the genome is organized in a hierarchy of structures spanning multiple scales observed at different resolutions. Current algorithms often focus on specific…
We present Glyph - a Python package for genetic programming based symbolic regression. Glyph is designed for usage let by numerical simulations let by real world experiments. For experimentalists, glyph-remote provides a separation of…
Public omics databases like the Gene Expression Omnibus and the Sequence Read Archive offer substantial opportunities for data reuse to address novel biomedical questions. However, it is still difficult to find samples and studies of…
A flexible and highly-extensible data assimilation testing suite, named DATeS, is described in this paper. DATeS aims to offer a unified testing environment that allows researchers to compare different data assimilation methodologies and…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
PySLSQP is a seamless interface for using the SLSQP algorithm from Python. It wraps the original SLSQP Fortran code sourced from the SciPy repository and provides a host of new features to improve the research utility of the original…
GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a…
The usage of the high-level scripting language Python has enabled new mechanisms for data interrogation, discovery and visualization of scientific data. We present yt, an open source, community-developed astrophysical analysis and…
The rapid proliferation of high-quality synthetic data -- generated by advanced AI models or collected as auxiliary data from related tasks -- presents both opportunities and challenges for statistical inference. This paper introduces a…