The Refinery Platform is a web-based data visualization and analysis system powered by an ISA-Tab-compatible data repository for public and private data sets. Analyses are implemented as Galaxy workflows and executed through the Galaxy API.
12 January 2016 | The Gehlenborg Lab at Harvard Medical School is looking for a data visualization software developer who will also be contributing to the Refinery Platform project. Our goal is to build groundbreaking open-source data visualization software that are employed in cutting-edge biomedical research and drive scientific progress. We are looking for a highly motivated and creative individual with a passion for code, data, design, and biomedical science.
20 November 2015 | We are thrilled to have been selected for an AWS in Education Research Grant award to support the development of a cloud-based version of the Refinery Platform!
2 September 2015 | The Refinery Team welcomes Scott Ouellette (@scottx611x) who joins us as a Software Developer. Welcome Scott!
10 July 2015 | We are presenting a poster about our provenance visualization approach at the BioVis 2015 conference at ISMB/ECCB 2015 in Dublin, Ireland.
5 January 2015 | The Refinery Team is hiring! As part of an initiative with the Harvard Stem Cell Institute, the Park Lab is looking for an experienced and enthusiastic software developer to participate in extending Refinery Platform for the Harvard Stem Cell Commons. The software developer should be comfortable with and be experienced in working on both server-side components (including compute clusters and/or clouds) and client-side (web UI) components, as well as modern software engineering practices such as automated testing and continuous integration/deployment. Our ideal candidate has experience in full stack web software development with a focus on designing, developing and maintaining production software systems in data-intensive settings, ideally for scientific applications. The detailed job ad is on the Harvard HR website.
9 October 2014 | We are thrilled that the Mozilla Science Lab has included the Refinery Platform project in the 1st round of their new collaboration program. If you are an open source developer interested in contributing to a scientific software project you can check out a list of tasks at collaborate.mozillascience.org/projects/refinery.
7 October 2014 | Guess what? Refinery is now on Twitter: @_refinery. Follow us for project updates and other important announcements.
29 June 2014 | Ilya Sytchev (@hackdna) participated in the Galaxy Community Conference Hackathon and contributed code to the Galaxy project that will allow us to cancel analyses running in Galaxy directly from Refinery. He also presented a poster on our experience in interacting with the Galaxy API.
8 June 2014 | Jeremy Liu (@jeremyjliu) from Yale will spend the summer with the Refinery team as an intern through the MIT HST and i2b2 Bioinformatics and Integrative Genomics (BIG) summer institute.
1 May 2014 | Anton Xue (@AntonXue) from Boston Latin School joins the project as an intern. Welcome Anton!
1 January 2014 | The Refinery project will be receiving additional funding through an NIH/NHGRI Pathway Independence Award to Nils Gehlenborg (@ngehlenborg).
10 December 2013 | In collaboration with Stefan Luger (@sluger) and Marc Streit (@mstreit) we have added a novel workflow visualization to Refinery that allows users to view and explore workflows imported into Refinery from a Galaxy instance.
28 August 2013 | Thanks to the efforts of Ilya Sytchev (@hackdna) from the Harvard School of Public Health team, we are now able to provide a painless deployment strategy using Vagrant, Puppet and Virtualbox for developers and others who would like to test the system on their own machine. The setup is almost completely automated and details can be found in the README in our GitHub repository.
Talks and Presentations
- Stem Cell Commons: a data management, analysis, and visualization platform for high-throughput sequencing experiments, International Society for Stem Cell Research 2017, Boston, USA, June 2017 | 12th Annual HSCI Malkin Retreat, Cambridge, USA, May 2017. [Poster]
- Interactive Visualization of Provenance Graphs for Reproducible Biomedical Research, BioVis 2015, Dublin, Ireland, July 2015. [Poster] [Short Talk]
- Transparent Layering for Visualizing Dynamic Graphs Using The Flip Book Metaphor, IEEE Information Visualization Conference (InfoVis) 2014, Paris, France, November 2014. [Poster]
- Refinery Platform: A Foundation for Integrative Data Visualization Tools, Symposium on Biological Data Visualization (BioVis) 2014, Boston, USA, July 2014. [Poster]
- Advantages and Challenges of Using the Galaxy API within an Integrated Data Analysis and Visualization Platform, Galaxy Community Conference 2014, Baltimore, USA, June 2014. [Poster]
- The Stem Cell Commons: An HSCI Resource for Stem Cell Genomics Data and Reproducible Analyses, Harvard Stem Cell Institute at 10: The Future is Now, Cambridge, USA, May 2014. [Poster] [Abstract]
- ￼￼Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform, Bio-IT World Expo 2014, Boston, USA, May 2014. [Slides]
- Reproducible Analyses of Large and Complex Epigenomics and Genomics Data: A Foundation for Visual Exploration, Keystone Symposium on Big Data in Biology 2014, San Francisco, USA, March 2014. [Poster]
- Refinery Platform - Integrating Visualization and Analysis of Large-Scale Biological Data, Bioinformatics Open Source Conference 2013, Berlin, Germany, July 2013. [Slides]
- An exemplar for data integration in the biomedical domain driven by the ISA framework, AMIA Joint Summits on Translational Science 2013, San Francisco, USA, March 2013. [Slides]
- Visualization and Analysis of Large (Epi)Genomics Data Sets with Refinery, Understanding Cancer Genomics Through Information Visualization Symposium, Tokyo, Japan, February 2013. [Slides]
- Connecting Galaxy to a Data Repository, Galaxy Community Conference 2012, Chicago, IL, USA, July 2012. [Slides]
- The Refinery Platform for Analysis and Visualization of Biomedical Genomics Data, Center for Biomedical Informatics & Countway Library Symposium, Boston, MA, USA, May 2012. [Video]
- July 2013 - GenomeWeb Bioinform, At ISMB '13, BOSC Talks Underscore Value of Open Source Infrastructure, Data for Scientific Research. [Link]
- July 2013 - Nature Methods, Data visualization: ambiguity as a fellow traveler. [Link]
- March 2013 - GenomeWeb Bioinform, Informatics Applications for Pharmacogenomics, Text Mining Among Trends Highlighted at TBI 2013. [Link]
Projects using the Refinery Platform
- The Stem Cell Commons | The Refinery Platform will provide data manipulation, analysis and visualization capabilities for the Harvard Stem Cell Institute (under development).
- The Genome Translation Commons | Integrates genomics resources to facilitate drug discovery.
- http://encode-x.med.harvard.edu | This is a site running the Refinery Platform in "repository mode". In repository mode workflows cannot be accessed (note that this is running an early version of Refinery).
Our documentation for Refinery Platform users, administrators and developers is available at http://refinery-platform.readthedocs.org. This is work in progress.
The Refinery Platform is a project of the Park and Gehlenborg Labs at Harvard Medical School in collaboration with the Hide Lab at Harvard School of Public Health.
Department of Biomedical Informatics at Harvard Medical School
- Nils Gehlenborg (@ngehlenborg)
- Fritz Lekschas (@flekschas)
- Jennifer K Marx (@jkmarx)
- Scott Ouellette (@scottx611x)
- Peter J Park
Department of Biostatistics at Harvard TH Chan School of Public Health
Sheffield Institute for Translational Neuroscience at The University of Sheffield
- David R Jones (@drj11)
- Winston Hide
Johannes Kepler University Linz (Austria)
The project is funded in part by an NIH/NHGRI Pathway to Independence Award to Nils Gehlenborg, an Agilent Technologies Emerging Insights Grant to Peter Park, by the Harvard Stem Cell Institute and supported by an AWS in Education Research Grant award.
Contact and Support
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