Related papers: Twelve years of SAMtools and BCFtools
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
We describe the current state and future plans for a set of tools for scientific data management (SDM) designed to support scientific transparency and reproducible research. SDM has been in active use at our MRI Center for more than two…
C programs can use compiler builtins to provide functionality that the C language lacks. On Linux, GCC provides several thousands of builtins that are also supported by other mature compilers, such as Clang and ICC. Maintainers of other…
We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics,…
The availability of generative Artificial Intelligence (AI) tools such as ChatGPT or GitHub Copilot is reshaping the way in which software is developed, evolved, and maintained. Oftentimes, developers leave traces of such an usage in…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
In software engineering, it is not enough to simply write code that only works as intended, even if it is free from vulnerabilities and bugs. Every programming language has a style guide and a set of best practices defined by its community,…
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…
We are living in an information era from Twitter to Fitocracy every episode of peoples life is converted to numbers. That abundance of data is also available in information technologies. From Stackoverflow to GitHub many big data sources…
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…
Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…
The supercomputing platforms available for high performance computing based research evolve at a great rate. However, this rapid development of novel technologies requires constant adaptations and optimizations of the existing codes for…
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…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
LAMDA-SSL is open-sourced on GitHub and its detailed usage documentation is available at https://ygzwqzd.github.io/LAMDA-SSL/. This documentation introduces LAMDA-SSL in detail from various aspects and can be divided into four parts. The…
Organ transplantation, which is the utilization of codes directly related to some specific functionalities to complete ones own program, provides more convenience for developers than traditional component reuse. However, recent techniques…
To address intricate real-world tasks, there has been a rising interest in tool utilization in applications of large language models (LLMs). To develop LLM-based agents, it usually requires LLMs to understand many tool functions from…
Developing and training deep learning models is expensive, so software engineers have begun to reuse pre-trained deep learning models (PTMs) and fine-tune them for downstream tasks. Despite the wide-spread use of PTMs, we know little about…