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# A 5 minute introduction to the Galaxy project
Galaxy Global Steering Committee
Ross Lazarus
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??? Presenter notes contain extra information which might be useful if you intend to use these slides for teaching. Press `P` again to switch presenter notes off Press `C` to create a new window where the same presentation will be displayed. This window is linked to the main window. Changing slides on one will cause the slide to change on the other. Useful when presenting. --- # Work in Progress! Contributions and fixes welcomed. ## Introduction: Purpose of this Topic - Galaxy is the product of a global open science collaboration. - Not only source code, but pluggable tools, and analysis and training services. - The Hub provides detail about project components and current activities. - This is a user manual, for the ecosystem that generates the Hub. - A field guide to a project embedded in the open science ecosystem. - Maps of the major components, and their interactions - Stories about how collaborations and activities came about. - Many opinions and personal perspectives are needed. - Seeing the bigger picture makes it easier to navigate. ??? - Galaxy is a complicated project, delivering highly valued open science resources. - It has many interacting components. - The Hub can be confusing, because there is so much activity. - This video introduces a field guide to the project ecosystem. - There are descriptive maps, and stories about how new initiatives began. - No single perspective can cover all the complexities. - For individuals who want to understand the project better. --- ## Origins: The context in which Galaxy was created - 2005 saw a growing flood of raw sequence data. - Commodity sequencing data disrupted biology and biology research budgets. - Experienced bioinformaticians were in short supply. - Unreliable analyses were run under pressure to publish expensive data quickly. - Independent scrutiny, or computational replication of a result was usually infeasible - All data rich disciplines faced the same critical shortage of reliable analytic capacity - An open, generic solution would help avoid redundant technical effort for every analysis. ??? - The context in which Galaxy originated helps explain a lot. - Sequencing was expensive, but provided valuable scientific insights. - Technical skills needed to analyse raw data reliably, were in very short supply - Investigators were impatient for results to publish from expensive data. - If an analysis cannot be scrutinised, the results cannot gain scientific trust. - Galaxy was our response to this growing shortfall in reliable analysis capacity. - A scalable solution for transparent analysis in any field. --- ## Solution: An application for accessible transparent analysis. - Galaxy was designed as a solution to the growing need for reliable, shareable analysis. - Integrate sharing and computational reproducibility into a generic analysis framework. - XML "wrapper" turns any Linux command line package into an installable tool - Wrapped packages gain framework benefits, such as workflow interoperability and form interface. - ToolShed repository automates tool wrapper installation for server administrators. - Varied specific "Flavours" are available, to make a framework installation match user interests. - Adaptable to any kind of open science data where packages are available to wrap. ??? - Galaxy was created to put the Open into open analysis, by making it transparent. - Solve all those really hard challenges once, in a scientific workflow application. - Accommodate any command line analysis package, making it an accessible and interoperable tool. - Make it easy to wrap analysis packages as tools, into the generic framework. - Automate tool installation from the ToolShed repository for server administrators. - Installed tools provide a flavour for the framework, such as Public Health, or Muon Science. - The analysis needs of any field, can be satisfied, by creating a suitable set of tools. --- ## Free analysis services drive software quality improvement and scientific value - Galaxy source code has been running on real hardware since 2005, as part of the solution. - Providing free, reliable analysis services and storage for anyone, anywhere. - Increasingly heavy use provides realistic, non-stop software stress testing - Users contribute insight and experience to improve functionality - Independent developers contribute improvements and help fix bugs - Reliable software engineering practices are encouraged by heavy use at scale ??? - Galaxy's free analysis services have been available since two thousand and five. - It was highly innovative, and quickly attracted users, collaborators, and research grant support. - Running a free, and heavily used service, provides thorough field testing, for the project source code. - Tens of thousands of scientists generate bug reports, user feedback, and ideas for improvement. - Community contributors provide bug fixes, ideas, and code improvements. - This maintains robust code, and provides increasing value to users over time. --- ## Success driven by collaborations that increase value to scientists - Reliable code powering free analysis services provides many opportunities for open science. - Newcomers joining the collaboration, extend and enhance the whole project. - Open collaborations grow organically, as opportunities arise, rather than by design. - Shared open source values make it easier for large collaborations to function efficiently. - Scientists benefit from easy access to reliable complex analyses and training - Hundreds of community participants regularly contribute their skills and ideas. ??? - Galaxy continues to grow rapidly, because scientists value it highly - Encouraging new collaborations, brings new capabilities, and new user communities - Organic, self governed growth, produces increasing complexity and diversity - Shared open source community values help maintain engagement, coherence, and stability - Scientists gain free access to resources that they value highly in their work. - Contributor engagement drives growth and sustainability, in open projects --- ## The Galaxy project is much more than an open source code repository - Galaxy maintains public code repositories like all other open source projects. - It also runs that code 24x7, at scale, providing high availability services for researchers. - These "free" services depend on resources and effort provided by a global, self-governing community. - Participant contributions greatly increase the resulting value to open science practice. ??? - An open source repository on Github can be maintained without direct costs. - High reliability analysis services need dedicated staff and costly computational infrastructure, provided by collaborators. - Sustaining a global self-governing community and collaboration requires dedicated resources. - Support from the community multiplies the impact of core grant resources, providing additional benefit to scientists. --- ## Communities help sustain the project. - Open source works because users take responsibility for bug fixes and improvements, where they can. - Community engagement and participation are the main drivers of project improvement and success. - Project activities add value to code, by supporting diverse kinds of science. - Open communities govern themselves, and ensure that engagement a rewarding experience. - Encouraging many different kinds of skills, experience and ideas to be contributed. - Other Lessons in this Topic describe project components, processes and structures. - Designed to help participants navigate and engage with the project. - Open projects succeed when they offer sufficient value to attract real support from communities. - Please let us know of anything that would make this material more useful. ??? - Improving an open project like Galaxy, serves the interests of all who rely on it. - Engagement, participation and collaboration are core open project values. - Tools to suit specific disciplines are supported by their own communities of specialists - Shared values keep project work environments safe and welcoming. - Project complexity offers a multitude of opportunities for participation. - Lessons with more detail on structures and processes are part of this Topic. - You are invited to explore to find your own way to engage and contribute. - Support reproducible and trustworthy analyses for all open science researchers. - For example, community feedback improves these open training resources for everyone. --- --- ### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points - To summarise, Galaxy is a global open science collaboration - Providing accessible, shareable and reproducible analyses for researchers - Embedded in the much bigger open source and open science ecosystems - New contributors and investigators are highly valued and welcomed - Related lessons in this topic describe details of major project structures and stories of community development activities - To guide participants finding ways to join in our work --- ## Thank You! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!
Author(s)
Galaxy Global Steering Committee
Ross Lazarus
This material is licensed under the Creative Commons Attribution 4.0 International License
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