OSCON 2011 presentation: Growing a

1. Open Chemistry
Growing a Research Program Through Open
Source

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. 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. 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. 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

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. 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. 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. 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. 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