Oscon 2011 Practicing Open Science


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Oscon 2011 Practicing Open Science

  1. 1. PracticingOpen ScienceWilliam J Schroeder, Kitware, Inc.Brian Wylie, Sandia National LabsMarcus Hanwell, Kitware, Inc.
  2. 2. Speakers & Topics§  William Schroeder, President & CEO, Kitware, Inc. -  The whys and hows of Open Science§  Dr. Marcus Hanwell, R&D Engineer, Kitware, Inc. -  Building an open-source research program (in Chemistry)§  Brian Wylie, Sandia National Labs -  Research collaborations from a government perspective
  3. 3. The Scientific Method •  Document     •  Share   •  Data   •  Methodology   •  Archive   Galileo Galilei 1613
  4. 4. Open Science Ensuring reproducibility §  Open Documents -  Hypothesis -  Descriptions REPRODUCIBILITY -  Results Positive Evidence Negative Evidence§  Open Data Accumulate Disproof Support Hypothesis§  Open Methodology -  Experimental apparatus -  Software If it isn’t reproducible, it -  Workflow isn’t science -  Parameter Sets
  5. 5. Example: OSA Interactive Science Publishing (ISP)§  Augmented PDF§  Contains links to executable viewer§  Downloads data and viewer as necessary to reproduce paper images (results)
  6. 6. Example: Insight Journal§  Timely publishing of publications, data, and software§  Evaluated automatically; further reviewed by community PDF doc Journal Git Repository Code Input Author Data Results Web Build Data Site Machines
  7. 7. Benefits of Open Science§  Collaboration “…much of our intelligence and creativity results from interactions with tools and -  Leveraging international communities artifacts and from collaborating with other and expertize individuals.” -- Shneiderman§  Agile Innovation -  Facilitate technology mashups -  Move science to application faster -  More focus on technology; less on protection§  Business Models -  Growing the pie, creating new opportunities -  Customization, software integration
  8. 8. Example: Collaboration§  NIH National Center of Biomedical Computing NA-MIC§  Developing the OS NA-MIC Kit; 3D Slicer application
  9. 9. Example: Agile Innovation (Open Source for Medical Imaging)Creating VTK (VisualizationToolkit) Led to the creation of: -  ITK -  VolView and finally… -  BioImageXD -  Osirix -  MedINRIA -  VisTrails -  NIH / NCI caBIG – XIP -  VR-Renderer -  IGSTK -  ParaView -  Etc….
  10. 10. Example: Business Models§  Kitware: Building open source collaboration platforms -  The usual support and training -  Consulting -  Engaging in collaborative R&D CMake -  Providing technology integration services, aka creating custom solutions CDash
  11. 11. The Open Technology Highway§  Provide an open infrastructure -  Support research, teaching, non-profit and commercial activities -  Any (legal) activity can hang off of the highway -  Spur innovation, create opportunities -  Get from idea to product faster -  Do not have to replicate technology -  Too many toll gates (i.e., closed systems, unreasonable IP) slows everything down -  Prefer non-reciprocal licenses
  12. 12. Next Up§  Marcus: Building a research program for chemistry§  Brian: open science and research collaboration from a government perspective
  13. 13. Open ChemistryGrowing a Research Program Through OpenSourceDr. Marcus Hanwell, Kitware, Inc.
  14. 14. Grass Roots Effort§  Bootstrapped several efforts without funding -  Spare time -  Parts of other projects when possible§  Formed an “unorganization” – Blue Obelisk -  Published first article in 2005 -  Open data, open standards and open source -  Meet at ACS and other conferences when possible -  Follow-up article currently in press§  Quixote collaboration more recently -  Provide meaningful data storage and exchange -  Principally targeting computational chemistry
  15. 15. The Early Years§  Avogadro projected started in 2006§  First funded work in 2007 by Marcus Hanwell -  Google Summer of Code student -  Final year of Ph.D. spent the summer coding -  Funded as part of KDE project – Kalzium editor§  Built on several other open source projects -  Qt, Eigen, Open Babel, Blue Obelisk Data Repository§  Also uses open standards, such as OpenGL for rendering§  Cross platform, open source stack
  16. 16. Community Tools, Standards and Resources§  Make extensive use of Qt for standard GUI elements -  Much more than just GUI – multithreading, web resources -  Avogadro chosen as an outstanding example of “Qt in Use” -  Marcus Hanwell recently chosen as a “Qt Ambassador”§  OpenGL for cross platform 3D rendering -  Accelerated rendering of 3D molecular geometry -  Facilitates interacting with the scene -  Use of GLSL for impressive, fast rendering§  Open Babel for chemical input/output and more -  There are a lot of chemical file formats… -  Has a lot of chemical knowledge, e.g. bond perception§  Git for distributed version control -  We work across multiple sites, time zones and institutions -  Gerrit for code review more recently – improving code quality
  17. 17. Evangelizing: Getting the Message Out§  Traditional social media used to communicate -  Blogs, Planets, Twitter, Identi.ca, Friendfeed, Google+§  Talks and posters at conferences -  Open source conferences talking about chemistry -  Chemistry conferences talking about open source chemistry§  Several meetings and workshops about open chemistry -  Daresbury Laboratory: Chemical Visualization and Quixote -  NIH National Cancer Institute – Databases and Open Chemistry§  Publications in the traditional journals§  Screencasts showing off what the software can do§  In person workshops and training sessions
  18. 18. Bringing About Real Change§  2011 is the ”International Year of Chemistry”§  Chemistry has been quite closed traditionally§  We are working hard to change this§  Recently led a Phase I SBIR to develop “open chemistry tools” -  GUI acting as the center of the chemical workflow -  Database application using MongoDB, chemically aware -  Cluster integration on the desktop – submit, monitor and retrieve§  Chemical simulation/calculation now biggest HPC user in military§  Open tools can use both open and closed computational codes -  Largely written in Fortran to run on clusters -  NWChem recently open sourced – PNNL quantum code -  Already work with GAMESS, GAMESS-UK, Q-Chem, Gaussian…§  The time is right for change in chemistry -  Opportunity to accelerate the rate of research
  19. 19. Funding Open Chemistry Tools§  Kitware’s core business is based on “open collaboration platforms”§  Led a Phase I Small Business Innovation Research project (US Army) -  Invited to apply for Phase II funding, currently pending§  Make use of Apache and BSD licenses -  Allow for participation of a wider cross-section of the community -  Reduced licensing complications -  Important for industry and government collaboration§  Successfully taken part in Google Summer of Code – funded students -  Student in 2007 working on Avogadro and Kalzium -  Mentor for KDE in 2008-2010 -  VTK organization administrator and mentor in 2011§  Looking to other funding agencies and collaborations in future
  20. 20. Developing in Niche Areas§  The population of active researchers in chemistry is relatively small -  The number of those researchers who code is even smaller -  Of those, the number that wish to contribute to open source is tiny§  Developing and nurturing these communities can be challenging§  Some students develop a feature in a summer and disappear§  Other professors might develop code over the summers§  Have to lower the barrier to entry as much as possible§  Often need to help with tools, build systems, etc
  21. 21. Enabling Technologies in Chemistry§  Large number of computational chemistry codes -  Many do not have dedicated user interfaces -  Forming a new area enabling chemical workflows -  Some of the open source codes that can benefit -  NWChem – quantum chemistry code -  Quantum Espresso – plane wave code -  Free for use codes such as GAMESS -  Commercial codes such as Molpro, Q-Chem, others -  These codes are executed in a separate process§  Libraries that can be used in the GUI: -  The Visualization Toolkit (VTK) provides advanced rendering -  ParaView library provides client-server technology for large data
  22. 22. Working With Academia, Industry and Government§  In the past licensing has not been ideal -  Some form of GPL or non-commercial only license fine for most academics -  Industry and government need more liberal licenses in general, e.g. BSD, Apache 2§  Can be challenging to ensure everyone gets something out of the deal§  Avoiding the trap of dual-licensing – often kills community and shared ownership§  Funders can find it harder to understand commercialization§  We normally employ a services/consulting role
  23. 23. Government  Open  Source                Collaboraons  Brian WylieSandia National Laboratories Sandia  Na7onal  Laboratories  is  a  mul7-­‐program  laboratory  managed  and  operated  by  Sandia   Corpora7on,  a  wholly  owned  subsidiary  of  Lockheed  Mar7n  Corpora7on,  for  the  U.S.  Department  of   Energy’s  Na7onal  Nuclear  Security  Administra7on  under  contract  DE-­‐AC04-­‐94AL85000.  
  24. 24. Government Open Source Resources  •  GOSCON  Government  Open  Source  Conference  (goscon.org)  •  Open  Source  Center:  Foreign  open  source  intelligence  data  (opensource.gov)  •  Open  Source  SoQware  Ins7tute:  Non-­‐profit  corp/govt/acad  (oss-­‐ins7tute.org)  •  Government  Open  Source  SoQware  Resource  Centre  (gossrc.org)    •  Center  for  Strategic  and  Interna7onal  Studies  (tracks  open  source  legisla7on  csis.org)    
  25. 25. Government Open Source Around  the  World   180   Open  Source  Iniaves  by  Region  (2000-­‐2009)   160   140   120   100   Failed   80   Proposed   60   Approved   40   20   0   Europe   Asia   La7n   North   Africa   Middle   America   America   East   Data  Courtesy  of  the  Center  for  Strategic  and  Internaonal  Studies  
  26. 26. Government Open Source Example  Projects   Sandia     Los  Alamos   Kitware   University  of   Utah   Open  source  data  analysis  and  visualiza7on  pla[orm  
  27. 27. Government Open Source Example  Projects   Sandia   Kitware   Indiana   University   Stanford  
  28. 28. Government Open Source Collaboraon  Benefits   No  specific  vendor  “lock-­‐in/out”   Allows  a  diversified  development  team   Government   Known  code  base  (strengths  and  weaknesses)   Typically  easier  to  integra7on  with  other  OS  tools   Improvement  of  the  OS  project     Money   Commercial   Leveraging  project  for  other/future  work   Improvement  of  the  OS  project       Student/Professor  support   Academic   Publishing/Sharing   Improvement  of  the  OS  project      
  29. 29. Government Open Source Collaboraon  Issues   Need  to  relax  into  exis7ng  OS  license*   Government   New  projects  should  pick  a  liberal  OS  license   Funding  source  may  hesitate  on  Open  Source   Proprietary  projects  /  Intellectual  Property     Government  bureaucracy   Commercial   Mixed  soQware  skill  set   Deliverables  can  get  distorted   *  No  gov’t  sell  back  clause       Academic   Work  may  not  be  publica7on  material   If  you  do  publish,  it  may  be  a  joint  publica7on  
  30. 30. Government Open Source Quesons  Secon  
  31. 31. Contact Information§  Will Schroeder will.schroeder@kitware.com§  Brian Wylie bnwylie@sandia.gov§  Marcus Hanwell marcus.hanwell@kitware.com
  32. 32. (view included video)