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Oscon 2011 chemistry_hanwell


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OSCON 2011 presentation: Growing a

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Oscon 2011 chemistry_hanwell

  1. 1. Open ChemistryGrowing a Research Program Through OpenSource
  2. 2. 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
  3. 3. 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
  4. 4. 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
  5. 5. Evangelizing: Getting the Message Out Traditional social media used to communicate - Blogs, Planets, Twitter,, 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
  6. 6. 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
  7. 7. 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
  8. 8. 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
  9. 9. 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
  10. 10. 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