Related papers: Twelve years of SAMtools and BCFtools
Unsupervised learning algorithms (e.g., self-supervised learning, auto-encoder, contrastive learning) allow deep learning models to learn effective image representations from large-scale unlabeled data. In medical image analysis, even…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in…
We present the Open Supernova Catalog, an online collection of observations and metadata for presently 36,000+ supernovae and related candidates. The catalog is freely available on the web (https://sne.space), with its main interface having…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…
Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Current-generation Large Language Models (LLMs) have stirred enormous interest in recent months, yielding great potential for accessibility and automation, while simultaneously posing significant challenges and risk of misuse. To facilitate…
Fault-tolerant quantum computation promises to solve outstanding problems in quantum chemistry within the next decade. Realizing this promise requires scalable tools that allow users to translate descriptions of electronic structure…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
This work introduces a new software package `Sesame' for the numerical computation of classical semiconductor equations. It supports 1 and 2-dimensional systems and provides tools to easily implement extended defects such as grain…
SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging…
In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance.…
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…
The ability to cite software and give credit to its authors and contributors is increasingly important. While the number of online open-source software repositories has grown rapidly over the past few years, few are being properly cited…
Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…