Related papers: MolSSI and BioExcel Workflow Workshop 2018 Report
We present BoolSi, an open-source cross-platform command line tool for distributed simulations of deterministic Boolean networks with synchronous update. It uses MPI standard to support execution on computational clusters, as well as…
Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several…
This paper presents the results of the shared task on Lay Summarisation of Biomedical Research Articles (BioLaySumm), hosted at the BioNLP Workshop at ACL 2023. The goal of this shared task is to develop abstractive summarisation models…
Electrochemistry workflows utilize various instruments and computing systems to execute workflows consisting of electrocatalyst synthesis, testing and evaluation tasks. The heterogeneity of the software and hardware of these ecosystems…
The collaborative efforts of large communities in science experiments, often comprising thousands of global members, reflect a monumental commitment to exploration and discovery. Recently, advanced and complex data processing has gained…
Research touts universal participation through accessibility initiatives, yet blind and low-vision (BLV) researchers face systematic exclusion as visual representations dominate modern research workflows. To materialize inclusive processes,…
The integration of Large Language Models (LLMs) into scientific workflows presents exciting opportunities to accelerate biomedical discovery. However, the reactive nature of LLMs, which respond only when prompted, limits their effectiveness…
Incorporating Machine Learning (ML) into existing systems is a demand that has grown among several organizations. However, the development of ML-enabled systems encompasses several social and technical challenges, which must be addressed by…
Scientific workflows are critical to scientific data analysis and often involve computationally intensive processing of large datasets on compute clusters. As such, their execution tends to be long-running and resource-intensive, resulting…
This volume contains the proceedings of MARS 2022, the fifth workshop on Models for Formal Analysis of Real Systems, held as part of ETAPS 2022, the European Joint Conferences on Theory and Practice of Software. The MARS workshops bring…
Most education and workplace learning takes place in classroom contexts far removed from laboratories or field sites with special arrangements for scientific research. But digital online resources provide a novel opportunity for large scale…
Scientific workflows are widely used to automate scientific data analysis and often involve processing large quantities of data on compute clusters. As such, their execution tends to be long-running and resource intensive, leading to…
Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science…
This paper presents the setup and results of the second edition of the BioLaySumm shared task on the Lay Summarisation of Biomedical Research Articles, hosted at the BioNLP Workshop at ACL 2024. In this task edition, we aim to build on the…
Keeping up with the research literature plays an important role in the workflow of scientists - allowing them to understand a field, formulate the problems they focus on, and develop the solutions that they contribute, which in turn shape…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Workflow management systems (WMS) support the composition and deployment of workflow-oriented applications in distributed computing environments. They hide the complexity of managing large-scale applications, which includes the controlling…
The use of approximation is fundamental in computational science. Almost all computational methods adopt approximations in some form in order to obtain a favourable cost/accuracy trade-off and there are usually many approximations that…
Computer-based scientific experiments are becoming increasingly data-intensive, necessitating the use of High-Performance Computing (HPC) clusters to handle large scientific workflows. These workflows result in complex data and control…
Domain experts can play a crucial role in guiding data scientists to optimize machine learning models while ensuring contextual relevance for downstream use. However, in current workflows, such collaboration is challenging due to differing…