Provenance in Data Exploration for Reproducibility and Beyond Juliana Freire [email protected] VisTrails Group & Web and Databases Lab NYU Poly Science Today: Data Intensive Simulations Sensors User studies Particle colliders Obtain Analyze/ Publish/ Data Visualize Share Web Sequencing machines Databases CATT Research Review 2011 Juliana Freire 2 Science and Business Today: Data Intensive Simulations Sensors User studies Particle colliders Obtain Analyze/ Publish/ Data Visualize Share Web Sequencing machines Databases CATT Research Review 2011 Juliana Freire 3 Science Today: Data + Computing Intensive Simulations Sensors AVS User studies Particle colliders Obtain Analyze/ Publish/ Data Visualize Share Web Sequencing VisTrails machines Databases Taverna CATT Research Review 2011 Juliana Freire 4 Science Today: Data + Computing Intensive Simulations Sensors User studies Particle colliders Obtain Analyze/ Publish/ Data Visualize Share Web Sequencing machines Databases CATT Research Review 2011 Juliana Freire 5 Science Today: Data + Computing Intensive Simulations Sensors User studies Particle colliders Obtain Analyze/ Publish/ Data Visualize Share Web Sequencing machines Databases CATT Research Review 2011 Juliana Freire 6 Science Today: Incomplete Publications ◆ Publications are just the tip of the iceberg - Scientific record is incomplete--- to large to fit in a paper - Large volumes of data - Complex processes ◆ Others can’t (easily) reproduce results ◆ Authors can’t remember all the steps led to a result… CATT Research Review 2011 Juliana Freire 7 Science Today: Incomplete Publications ◆ Publications are just the tip of the iceberg “It’s impossible to verify most of the results that - Scientificcomputational record scientistsis incomplete--- present at conference to large to fit in a paper and in papers.” [Donoho et al., 2009] - Large“Scientific volumes and of mathematical data journals are filled - Complexwith pretty processes pictures of computational experiments ◆ Can’t that(easily) the reader reproduce has no resultshope of repeating.” [LeVeque, 2009] “Published documents are merely the advertisement of scholarship whereas the computer programs, input data, parameter values, etc. embody the scholarship itself.” [Schwab et al., 2007] CATT Research Review 2011 Juliana Freire 8 Science Today: Incomplete Publications ◆ Publications are just the tip of the iceberg “It’s impossible to verify most of the results that - Scientificcomputational record scientistsis incomplete--- present at conference to large to fit in a paper and in papers.” [Donoho et al., 2009] - Large“Scientific volumes and of mathematical data journals are filled - Complexwith pretty processes pictures of computational experiments ◆ Can’t that(easily) the reader reproduce has no resultshope of repeating.” [LeVeque, 2009] “Published documents are merely the advertisement of scholarship whereas the computer programs, input data, parameter values, etc. embody the scholarship itself.” http://[Schwaben.wikipedia.org/wiki/Scientific_misconduct et al., 2007] http://ori.dhhs.gov/misconduct/cases/ CATT Research Review 2011 Juliana Freire 9 Science and Reproducibility CATT Research Review 2011 Juliana Freire 10 Provenance in Science When ◆ Not a new issue! ◆ Lab notebooks have been used for a long time ◆ What is new? Annotation – Large volumes of data – Complex analyses— computational processes ◆ Writing notes is no longer an option Observed data DNA recombination By Lederberg CATT Research Review 2011 Juliana Freire 11 The VisTrails System ◆ Workflow-based system for data analysis and visualization – Allows multiple tools to be combined into pipelines ◆ Comprehensive provenance infrastructure ◆ Transparently tracks provenance of the discovery process---from data acquisition to visualization – The trail followed as users generate and test hypotheses ◆ Leverage provenance to streamline exploration – Support for reflective reasoning and collaboration – Query and mine provenance ◆ Focus on usability ◆ The system is open source: http://www.vistrails.org – Multi-platform: Linux, Mac, Windows – Written in Python + Qt CATT Research Review 2011 Juliana Freire 12 The VisTrails System ◆ Workflow-based system for data analysis and visualization – Allows multiple tools to be combined into pipelines ◆ Comprehensive provenance infrastructure ◆ Transparently tracks provenance of the discovery process---from data acquisition to visualization – The trail followed as users generate and test hypotheses ◆ Leverage provenance to streamline exploration – Support for reflective reasoning and collaboration • Study on the use of tms for improving memory • Visualizing environmental simulations (CMOP STC) – Query and mine provenance (Pyschiatry, U. Utah) • Simulation for solid, fluid and structural mechanics • eBird (Cornell, NSF DataONE) (Galileo◆ Network, UFRJ Brazil) Focus on usability • Astrophysical Systems (Tohline, LSU) • Quantum physics simulations (ALPS, ETH Switzerland) • NIH NBCR (UCSD) • Climate◆ The analysis system (CDAT) is open source: http://www.vistrails.org • Pervasive Technology Labs (Heiland, Indiana • Habitat modeling (USGS) – Multi-platform: Linux, Mac, WindowsUniversity) • Open Wildland Fire Modeling (U. Colorado, NCAR) • Linköping University (Sweden) • High-energy physics (LEPP, Cornell) – Written in Python + Qt • University of North Carolina, Chapel Hill • Cosmology simulations (LANL) • UTEP CATT Research Review 2011 Juliana Freire 13 Demo Provenance Beyond Reproducibility ◆ Support for reflective reasoning ◆ Ability to compare data products [Freire et al., IPAW 2006] CATT Research Review 2011 Juliana Freire 15 Provenance Beyond Reproducibility ◆ Support for reflective reasoning ◆ Ability to compare data products ◆ Explore parameter spaces and compare results [Freire et al., IPAW 2006] CATT Research Review 2011 Juliana Freire 16 Provenance Beyond Reproducibility ◆ Support for reflective reasoning ◆ Ability to compare data products ◆ Explore parameter spaces and compare results ◆ Support for collaboration [Ellkvist et al., IPAW 2008] CATT Research Review 2011 Juliana Freire 17 Provenance Enabling 3rd-Party Tools Autodesk Maya ParaView VisIt ImageVis3d [Callahan et al., IPAW 2008] CATT Research Review 2011 Juliana Freire 18 Provenance Plugin for ParaView http://www.cs.utah.edu/~juliana/videos/paraview_plugin.avi CATT Research Review 2011 Juliana Freire 19 Provenance Plugin for Autodesk Maya http://www.cs.utah.edu/~juliana/videos/paraview_plugin.avi CATT Research Review 2011 Juliana Freire 20 Provenance-Rich Publications http://www.crowdlabs.org/vistrails/medleys/details/2/ CATT Research Review 2011 Juliana Freire 21 Reproducible Publications: Benefits ◆ Produce more re-usable knowledge---not just text ◆ Allow scientists to stand on the shoulders of giants and on their own shoulders! ◆ Science can move faster – http://www.nytimes.com/2011/06/26/opinion/sunday/26ideas.html?_r=1 ◆ Higher-quality publications – Authors will be more careful – Many eyes to check results ◆ Describe more of the discovery process: learn from successes and mistakes ◆ Expose scientific community to different techniques and tools: expedite their training, reduce time to insight ◆ More impact, more citations (?) CATT Research Review 2011 Juliana Freire 22 !"#!"#$%&'&(%)*+(,-$%&'()#!*$+,-.# A Reproducible Paper: ALPS2.0 The ALPS project release 2.0: .#"/0#1# Open source software for strongly correlated systems B. Bauer1 L. D. Carr2 H.G. Evertz3 A. Feiguin4 J. Freire5 S. Fuchs6 L. Gamper1 J. Gukelberger1 E. Gull7 S. Guertler8 A. Hehn1 R. Igarashi9,10 S.V. Isakov1 D. Koop5 P.N. Ma 1 P. Mates 1,5 H. Matsuo11 O. Parcollet12 G. Pawlowski13 J.D. Picon14 L. Pollet1,15 E. Santos5 V.W. Scarola16 U. Schollw¨ock17 C. Silva5 B. Surer1 S. Todo10,11 S. Trebst18 M. Troyer1 M. L. Wall2 P. Werner1 S. Wessel19,20 ‡ 1Theoretische Physik, ETH Zurich, 8093 Zurich, Switzerland 2Department of Physics, Colorado School of Mines, Golden, CO 80401, USA 3Institut f¨ur Theoretische Physik, Technische Universit¨atGraz, A-8010 Graz, Austria 4Department of Physics and Astronomy, University of Wyoming, Laramie, Wyoming 82071, USA 5Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah 84112, USA 6Institut f¨ur Theoretische Physik, Georg-August-Universit¨atG¨ottingen, G¨ottingen, Germany 7Columbia University, New York, NY 10027, USA 2+3"'"+%4# 8Bethe Center for Theoretical Physics, Universit¨atBonn, Nussallee 12, 53115 Bonn, The ALPS projectGermany release 2.0: Open source software for strongly correlated systems 15 9Center for Computational Science & e-Systems, Japan Atomic Energy Agency, 110-0015 Tokyo, Japan !*$+#,-.# 10Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 332-0012 Kawaguchi, Japan 11Department of Applied Physics, University of Tokyo, 113-8656 Tokyo, Japan 12Institut de Physique Th´eorique, CEA/DSM/IPhT-CNRS/URA 2306, CEA-Saclay, F-91191 Gif-sur-Yvette, France 13Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Pozna´n, arXiv:1101.2646v4 [cond-mat.str-el] 23 May 2011 Poland /%0&120134# 14Institute of Theoretical Physics, EPF Lausanne, CH-1015 Lausanne, Switzerland 15Physics Department, Harvard University, Cambridge 02138, Massachusetts, USA 16Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA 17Department for Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, University of Munich, 80333 Munich, Germany 5'6'# 18Microsoft Research, Station Q, University of California, Santa