Oscon 2011 Practicing Open Science

PracticingOpen ScienceWilliam J Schroeder, Kitware, Inc.Brian Wylie, Sandia National LabsMarcus Hanwell, Kitware, Inc.

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

The Scientific Method •  Document •  Share •  Data •  Methodology •  Archive Galileo Galilei 1613

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

Example: OSA Interactive Science Publishing (ISP)§  Augmented PDF§  Contains links to executable viewer§  Downloads data and viewer as necessary to reproduce paper images (results)

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

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

Example: Collaboration§  NIH National Center of Biomedical Computing NA-MIC§  Developing the OS NA-MIC Kit; 3D Slicer application

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….

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

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

Next Up§  Marcus: Building a research program for chemistry§  Brian: open science and research collaboration from a government perspective

Open ChemistryGrowing a Research Program Through OpenSourceDr. Marcus Hanwell, Kitware, Inc.

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

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

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

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

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

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

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

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

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

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.

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)

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

Government Open Source Example Projects Sandia Los Alamos Kitware University of Utah Open source data analysis and visualiza7on pla[orm

Government Open Source Example Projects Sandia Kitware Indiana University Stanford

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

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

Government Open Source Quesons Secon

Contact Information§  Will Schroeder will.schroeder@kitware.com§  Brian Wylie bnwylie@sandia.gov§  Marcus Hanwell marcus.hanwell@kitware.com

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Oscon 2011 Practicing Open Science

by Marcus Hanwell on Aug 11, 2011

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