Related papers: An Open Framework for Extensible Multi-Stage Bioin…

Research software refers to software development tools that accelerate discovery and simplifies access to digital infrastructures. However, although research software platforms can be built increasingly more innovative and powerful than…

Neuromorphic systems open up opportunities to enlarge the explorative space for computational research. However, it is often challenging to unite efficiency and usability. This work presents the software aspects of this endeavor for the…

Reconfigurable computing refers to the use of processors, such as Field Programmable Gate Arrays (FPGAs), that can be modified at the hardware level to take on different processing tasks. A reconfigurable computing platform describes the…

A wide variety of large-scale data has been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs…

Implementing large software, as software analyzers which aim to be used in industrial settings, requires a well-engineered software architecture in order to ease its daily development and its maintenance process during its lifecycle. If the…

The complexity of biological systems, governed by molecular interactions across hierarchical scales, presents a challenge for computational modeling. While advances in multiomic profiling have enabled precise measurements of biological…

GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…

An extensible, component-based framework has been developed at Fermilab to promote software reuse and provide a common platform for developing a family of test and data analysis systems. The framework allows for configuring applications…

Profiling techniques are used extensively at different parts of the computing stack to achieve many goals. One major goal is to make a piece of software execute more efficiently on a specific hardware platform, where efficiency spans…

Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…

Bioprocesses are central to modern biotechnology, enabling sustainable production in pharmaceuticals, specialty chemicals, cosmetics, and food. However, developing high-performing processes is costly and complex, requiring iterative,…

Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…

We present a scalable, robust approach to creating quantum programs of arbitrary size and complexity. The approach is based on the true abstraction of the problem. The quantum program is expressed in terms of a high-level model together…

The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…

Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…

The end of Dennard scaling combined with stagnation in architectural and compiler optimizations makes it challenging to achieve significant performance deltas. Solutions based solely in hardware or software are no longer sufficient to…

Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…

Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are…

Quantum computing is advancing rapidly in hardware and algorithms, but broad accessibility demands a comprehensive, efficient, unified software stack. Such a stack must flexibly span diverse hardware and evolving algorithms, expose usable…

Pre-trained large language models (LLMs) have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular…