Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
The NSF-SI 2 -funded LAPPS Grid project is a collaborative effort among Brandeis University, Vassar College, Carnegie-Mellon University (CMU), and the Linguistic Data Consortium (LDC), which has developed an open, web-based infrastructure through which resources can be easily accessed and within which tailored language services can be efficiently composed, evaluated, disseminated and consumed by researchers, developers, and students across a wide variety of disciplines. The LAPPS Grid project recently adopted Galaxy (Giardine et al., 2005), a robust, well-developed, and well-supported front end for workflow configuration, management, and persistence. Galaxy allows data inputs and processing steps to be selected from graphical menus, and results are displayed in intuitive plots and summaries that encourage interactive workflows and the exploration of hypotheses. The Galaxy workflow engine provides significant advantages for deploying pipelines of LAPPS Grid web services, including not only means to create and deploy locally-run and even customized versions of the LAPPS Grid as well as running the LAPPS Grid in the cloud, but also access to a huge array of statistical and visualization tools that have been developed for use in genomics research.
This paper explores interoperability for data represented using the Graph Annotation Framework (GrAF) (Ide and Suderman, 2007) and the data formats utilized by two general-purpose annotation systems: the General Architecture for Text Engineering (GATE) (Cunningham et al., 2002) and the Unstructured Information Management Architecture (UIMA) (Ferrucci and Lally in Nat Lang Eng 10(3-4): 2004). GrAF is intended to serve as a ''pivot'' to enable interoperability among different formats, and both GATE and UIMA are at least implicitly designed with an eye toward interoperability with other formats and tools. We describe the steps required to perform a round-trip rendering from GrAF to GATE and GrAF to UIMA CAS and back again, and outline the commonalities as well as the differences and gaps that came to light in the process.
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