Galaxy Community Update
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1 Galaxy Community Update PAG XXVI January 17, 2018 San Diego, California, United States Dave Clements Johns Hopkins University Galaxy Team / Galaxy Community bit.ly/gxy-pag2018-upd
2 This talk complements yesterday's talks Today's talk focuses on what's happened since last year, and what's coming
3 Some New Features from the past year Switched to a 4 month release cycle 17.01, 16.05, is in the pipe Singularity Support (17.09) HPC-friendly containers Collection improvements (all releases) Continue to improve support for large, multi-sample analysis Propagating Dataset Tags (17.05) Tags make it easy to track dataset (and collection) relationships.
4 New Features in past year Drag & Drop Datasets into tool inputs (17.05) Drag datasets from history panel into tool forms. Conda package management (17.01) Became the default for tools and dependencies Plus hundreds more features large and small
5 New Releases of lots of Software BioBlend galaxy-lib Planemo StarForge sequence_utils Pulsar a Python library for interacting with CloudMan and Galaxy s API a subset of the Galaxy core code base designed to be used as a library. set of command-line utilities to assist in building tools for the Galaxy project. help build Galaxy things in virtualization set of Python modules for reading, analyzing, and converting sequence formats. Python server application that allows a Galaxy server to run jobs on remote systems (including Windows)
6 New Releases of lots of Software ephemeris CloudLaunch nebulizer CloudBridge Galaksio Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows. New platform for launching multiple appliances on multiple cloud platforms Command-line utilities for managing users, data libraries and tools in a Galaxy instance provides a simple layer of abstraction over different cloud providers New Galaxy user interface that emphasizes workflows over tools
7 Plans for the near future usegalaxy.org Better use of Jetstream (IU & TACC) Bridges (PSC), and Stampede (TACC) Interactive Environment support: RStudio, Jupyter Dataset Collections & Semantic Scalability More, more, more Workflows CWL support Running time feedback to users
8 Conversion from Wiki to Hub
9 Converted from Wiki to Hub From MoinMoin based to GitHub, Markdown, Metalsmith based First edits became an order of magnitude (or two) harder Subsequent small edits only slightly harder Big edits became an order of magnitude easier. github.com/galaxyproject/galaxy-hub
10 Relaunched Blog in October galaxyproject.org/blog
11 New Public Galaxy servers General Purpose / Genomics ABiMS Galaxy@GenOuest GVL Melbourne Domain BIPAA (BioInformatics Platform for Agroecosystem Arthropods) EuPathDB GrAPPA (Graph Algorithms Pipeline for Pathway Analysis) Tool Publishing Servers Antigen Receptor (ARGalaxy) BF2I-Map ChimeRScope Codon Harmonizer Langille Lab PICRUSt server USMI Galaxy 12 new servers in past year. Now 99 public servers
12 Publications: Hit 5,000 pubs in October
13 Publications: Some trends
14 Publications: Some trends In , there are 2.5x as many UseMain pubs as UsePublic pubs. In there are nearly 2x as many UsePublic pubs as there are UseMain pubs.
15 Move from CiteULike to Zotero In general, a big win.
16 Galaxy Training Network
17 Galaxy Training Network
18 Galaxy Training Network
19 Galaxy Admin Training At this time last year, there had been one week long Galaxy Admin training. We've now had 3 of these. Most recent one ended last Friday in Oslo. Safe to say they are probably here to stay.
20 Cool upcoming events
21 Just announced yesterday galaxyafrica.sanbi.ac.za
22 GCCBOSC 2018 Galaxy's Community Conference & OBF's Bioinformatics Open Source Conference are colocating in 2018 Please join us in Portland, Oregon, United States June 25-30,
23 The Galaxy Team Enis Afgan Dannon Baker Dan Blankenberg Dave Bouvier Marten Cech John Chilton Dave Clements Nate Coraor Jeremy Goecks Sam Guerler Jen Jackson Vahid Jalili Delphine Lariviere Anton Nekrutenko Nick Stoler James Taylor
24 Acknowledgements You Scott Cain The Galaxy Community NIH NSF Johns Hopkins University* Penn State University Oregon Health Sciences University Cleveland Clinic*
25 Dave Clements Thanks Galaxy Project Johns Hopkins University
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