Open ChemistryGrowing a Research Program Through OpenSource
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
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