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We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a…

Data is a valuable asset, and sharing it as a product across organizations is key to building comprehensive and useful insights in fields such as science and industry. Before sharing, data often requires transformation to comply with…

Developing high quality machine translation systems is a labour intensive, challenging and confusing process for newcomers to the field. We present a pair of tools OpusCleaner and OpusTrainer that aim to simplify the process, reduce the…

Background: Data mining and analyzing of public Git software repositories is a growing research field. The tools used for studies that investigate a single project or a group of projects have been refined, but it is not clear whether the…

The field of digital pathology has seen a proliferation of deep learning models in recent years. Despite substantial progress, it remains rare for other researchers and pathologists to be able to access models published in the literature…

We present SciServer, a science platform built and supported by the Institute for Data Intensive Engineering and Science at the Johns Hopkins University. SciServer builds upon and extends the SkyServer system of server-side tools that…

Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…

We present SAINE, an Scientific Annotation and Inference ENgine based on a set of standard open-source software, such as Label Studio and MLflow. We show that our annotation engine can benefit the further development of a more accurate…

This is a position paper for Sharing, Re-Use and Circulation of Resources in Cooperative Scientific Work, a CSCW'14 workshop. It discusses the role of software in NSF's CIF21 vision and the SI2 program, which is intended to support that…

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools,…

Scientific applications produce a huge amount of data, which imposes serious management and analysis challenges. In particular, limitations in current database management systems prevent their adoption in simulation applications, in which…

In computational science and in computer science, research software is a central asset for research. Computational science is the application of computer science and software engineering principles to solving scientific problems, whereas…

In this paper we describe EasyInterface, an open-source toolkit for rapid development of web-based graphical user interfaces (GUIs). This toolkit addresses the need of researchers to make their research prototype tools available to the…

NLTK, the Natural Language Toolkit, is a suite of open source program modules, tutorials and problem sets, providing ready-to-use computational linguistics courseware. NLTK covers symbolic and statistical natural language processing, and is…

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation…

To help researchers conduct a systematic review or meta-analysis as efficiently and transparently as possible, we designed a tool (ASReview) to accelerate the step of screening titles and abstracts. For many tasks - including but not…

Scientific computing is increasingly incorporating the advancements in machine learning and the ability to work with large amounts of data. At the same time, machine learning models are becoming increasingly sophisticated and exhibit many…

Personalized medicine remains a major challenge for scientists. The rapid growth of Machine learning and Deep learning has made them a feasible al- ternative for predicting the most appropriate therapy for individual patients. However, the…

The general purpose of a scientific publication is the exchange and spread of knowledge. A publication usually reports a scientific result and tries to convince the reader that it is valid. With an ever-growing number of papers relying on…

Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based…