A5007050739- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
Pennsylvania State University
2009-2022
European Molecular Biology Organization
2022
University of California, Santa Cruz
2007-2010
Howard Hughes Medical Institute
2009
Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started 2005, continues focus on three key challenges data-driven science: making analyses accessible all researchers, ensuring are completely reproducible, it simple communicate so that they can be...
High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical computational methods, as well substantial power. This has led an acute crisis life sciences, researchers without informatics training attempt perform computation-dependent analyses. Since 2005, Galaxy project worked address...
The University of California, Santa Cruz Genome Browser ( http://genome.ucsc.edu ) offers online access to a database genomic sequence and annotation data for wide variety organisms. also has many tools visualizing, comparing analyzing both publicly available user-generated sets, aligning sequences uploading user data. Among the features released this year are gene search tool track drag-reorder functionality as well support BAM BigWig/BigBed file formats. New display enhancements include...
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes about a dozen vertebrate species several major model organisms. annotations typically include assembly data, composition, genes gene predictions, mRNA expressed tag evidence, comparative genomics, regulation, expression variation data. database is optimized to support fast interactive performance with web tools that provide powerful visualization querying capabilities...
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 use, maintain contribute the project, support from multiple national infrastructure providers that enable freely analysis training services. The Training Network supports free, self-directed, virtual >230 integrated tutorials. Project engagement metrics have continued grow...
The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database publicly available sequence and annotation data along with an integrated tool set for examining comparing the genomes organisms, aligning to genomes, displaying sharing users' own data. As September 2009, genomic basic 'tracks' are provided 47 including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms yeast. New highlights this...
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in human genome. pilot phase for comparison existing methods and development new rigorously analyze a defined 1% genome sequence. Experimental datasets are focused on origin replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed multiple sequence alignment evolutionarily constrained elements....
Abstract Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic high‐throughput data resources be analyzed. As creating obtaining has become easier, the key decision faced by many researchers is a practical one: where how should an analysis performed? Datasets are tool set‐up use riddled complexities outside of scope core activities. The authors believe that Galaxy provides powerful solution simplifies acquisition...
Abstract Background Hands-on training, whether in bioinformatics or other domains, often requires significant technical resources and knowledge to set up run. Instructors must have access powerful compute infrastructure that can support resource-intensive jobs running efficiently. Often this is achieved using a private server where there no contention for the queue. However, places prerequisite labor barrier instructors, who spend time coordinating deployment management of resources....
Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and abundant. The computational savviness necessary analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access tools in a web-based interface. It also major public biological repositories, allowing private be combined with datasets. is hosted on high-capacity servers worldwide accessible free, option installed...
Abstract Summary Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie a asset management system that allows to easily organize, retrieve, share such datasets. Here, we describe the integration of refgenie into Galaxy platform. Server administrators are able configure make use made available on instance. Additionally, Data Manager tool has been developed provide graphical interface refgenie’s remote retrieval functionality. A...
Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie a asset management system that allows users to easily organize, retrieve share such datasets. Here, we describe the integration of refgenie into Galaxy platform. Server administrators are able configure make use made available on instance. In addition, Data Manager tool has been developed provide graphical interface refgenie's remote retrieval functionality. A large collection...