Related papers: An Open Framework for Extensible Multi-Stage Bioin…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
Evolving software is challenging, even more when it exists in many different variants. Such software evolves not only in time, but also in space--another dimension of complexity. While evolution in space is supported by a variety of…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Creating a highly parallel and flexible discrete element software requires an interdisciplinary approach, where expertise from different disciplines is combined. On the one hand domain specialists provide interaction models between…
Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
Microscopy, in particular scanning probe and electron microscopy, has been pivotal in improving our understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most research characterization labs and…
We describe the foundation of the metaprogramming language, Moebius, which supports the generation of polymorphic code and, more importantly the analysis of polymorphic code via pattern matching. Moebius has two main ingredients: 1) we…
While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI…
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…
Fast Fourier Transforms (FFTs) are exploited in a wide variety of fields ranging from computer science to natural sciences and engineering. With the rising data production bandwidths of modern FFT applications, judging best which…
Concurrent advances across fields such as organoid technology, Microelectrode Arrays (MEAs), neuromorphic computing, and machine learning have given rise to a groundbreaking research paradigm: Synthetic Biological Intelligence (SBI). SBI…
OLAF (Open Life Science Analysis Framework) is an open-source platform that enables researchers to perform bioinformatics analyses using natural language. By combining large language models (LLMs) with a modular agent-pipe-router…
For the development of new digital signal processing systems and services, the rapid, easy, and convenient prototyping of ideas and the rapid time-to-market of products are becoming important with advances in technology. Conventionally, for…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
To harness the potential of advanced computing technologies, efficient (real time) analysis of large amounts of data is as essential as are front-line simulations. In order to optimise this process, experts need to be supported by…