Related papers: Twelve years of SAMtools and BCFtools
We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection,…
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…
Ongoing progress in computational intelligence (CI) has led to an increased desire to apply CI techniques for the purpose of improving software engineering processes, particularly software testing. Existing state-of-the-art automated…
Software is an important tool for scholarly work, but software produced for research is in many cases not easily identifiable or discoverable. A potential first step in linking research and software is software identification. In this paper…
For researchers in electromyography (EMG), and similar biosginals, signal processing is naturally an essential topic. There are a number of excellent tools available. To these one may add the freely available open source statistical…
The advancement of machine learning and the availability of large-scale reaction datasets have accelerated the development of data-driven models for computer-aided synthesis planning (CASP) in the past decade. Here, we detail the newest…
Large language models (LLMs) are increasingly applied to materials science questions, including literature comprehension, property prediction, materials discovery and alloy design. At the same time, a wide range of physics-based…
Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by 671 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their…
Biotoxins, mainly produced by venomous animals, plants and microorganisms, exhibit high physiological activity and unique effects such as lowering blood pressure and analgesia. A number of venom-derived drugs are already available on the…
Prototyping is one of the core activities of User-Centered Design (UCD) processes and an integral component of Human-Computer Interaction (HCI) research. For many years, prototyping was synonym of paper-based mockups and only more recently…
Inference on time series data is a common requirement in many scientific disciplines and internet of things (IoT) applications, yet there are few resources available to domain scientists to easily, robustly, and repeatably build such…
The need for large text corpora has increased with the advent of pretrained language models and, in particular, the discovery of scaling laws for these models. Most available corpora have sufficient data only for languages with large…
Deep learning methods have shown extraordinary potential for analyzing very diverse biomedical data, but their dissemination beyond developers is hindered by important computational hurdles. We introduce ImJoy (https://imjoy.io/), a…
GitHub, renowned for facilitating collaborative code version control and software production in software teams, expanded its services in 2017 by introducing GitHub Marketplace. This online platform hosts automation tools to assist…
More than 20 years after the end of NASA's Compton Gamma-Ray Observatory mission, the data collected by its Imaging Compton Telescope (COMPTEL) still provide the most comprehensive and deepest view of our Universe in MeV gamma rays. While…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
We introduce F2LLM - Foundation to Feature Large Language Models, a suite of state-of-the-art embedding models in three sizes: 0.6B, 1.7B, and 4B. Unlike previous top-ranking embedding models that require massive contrastive pretraining,…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…
Biobanks are indispensable resources for medical research collecting biological material and associated data and making them available for research projects and medical studies. For that, the biobank data has to meet certain criteria which…
Today, artificial intelligence systems driven by machine learning algorithms can be in a position to take important, and sometimes legally binding, decisions about our everyday lives. In many cases, however, these systems and their actions…