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Empowering Computational Research Through Trustworthy Communication

Join Neil Chue Hong at Columbia University on April 4, 2013, to discuss enabling criticism in communicating computational research. Learn how to build better software for enhanced research outcomes by negotiating boundaries in development cycles. Discover tools, expertise, and policies for the research software community. Trust the code with a water-swap reaction coordinate for accurate protein-ligand binding free energies. Elevate software quality with openness, review, tests, and automation. Explore the 5 Stars of Research Software criteria for community-driven, open, defined, extensible, and runnable software. Engage with the Software Sustainability Institute for community events, consultancy, training, and software carpentry to enhance your research capabilities.

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Empowering Computational Research Through Trustworthy Communication

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  1. Communicating trust, enabling criticismCommunicating Computational Research4 April 2013, Columbia University, New YorkNeil Chue Hong (@npch) ORCID: 0000-0002-8876-7606N.ChueHong@software.ac.uk Where indicatedslides licensed under

  2. The Software Sustainability Institute A national facility for cultivating world-class research through software • Better software enables better research • Software reaches boundaries in its development cycle that prevent improvement, growth and adoption • Providing the expertise and services needed to negotiate to the next stage • Developing the policy and tools tosupport the community developing andusing research software Better software Better research Supported by EPSRC Grant EP/H043160/1

  3. “Episodis Critics” Photo by Camilay el Arte CC-BY-NC-SA If we cannot be critical, we cannot be researchers www.software.ac.uk

  4. But systems are complex www.software.ac.uk “Paint by Particle – aerosol movement” Photo by NASA Goddard Photo and Video CC-BY

  5. … and software is always growing Function Algorithm Program Library / Suite / Package …

  6. Water Swap Reaction Coordinate A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies Woods CJ, Malaisree M, Hannongbua S, Mulholland AJ J. Chem. Phys. (2011) vol. 134, pp. 054114 http://dx.doi.org/10.1063/1.3519057

  7. How can I trust this code? lam = Symbol("lambda") S_sym = Symbol("S") S_scl = S_sym - 4*(S_sym-1)*(lam-0.5)**2 ligand_bound_nrg_sym = Symbol("E_{ligand:bound}") ligand_bound_nrg = ligand_intraclj.components().total() + \ ligand_intraff.components().total() + \ bound_ligand_mobile.components().total(0) + \ bound_ligand_fixed_nrg swap_bound_nrg_sym = Symbol("E_{swap:bound}") swap_bound_nrg = ((S_scl) * swap_interclj.components().coulomb()) + \ swap_interclj.components().lj() + \ bound_swap_mobile.components().total(0) + \ bound_swap_fixed_nrg bound_nrg_sym = Symbol("E_{bound}") bound_nrg = bound_bound_nrg_sym + ((1-lam) * ligand_bound_nrg_sym) + (lam * swap_bound_nrg_sym) free_nrg_sym = Symbol("E_{free}") free_nrg = free_free_nrg_sym + (lam * ligand_free_nrg_sym) + ((1-lam) * swap_free_nrg_sym) total_nrg_sym = system.totalComponent() total_nrg = bound_nrg_sym + free_nrg_sym system.setComponent(total_nrg_sym, total_nrg) Openness Review Tests Automation

  8. “Social Media Information Overload” Photo by Joe Intersection Consulting CC-BY-NC Increase the amount of information on the software(without drowning in it)increase the trust

  9. Academic Software Should Not Suck Courtesy of C. Titus Brown http://ivory.idyll.org/blog/ladder-of-academic-software-notsuck.html

  10. 5 Stars of Research Software • Community • There is a community infrastructure • Open • Software has permissive license • Defined • Accurate metadata for the software • Extensible • Usable, modifiable for my purpose • Runnable • I can access and run software C R O E D • c.f. • 5 Stars of Linked Data (Berners-Lee) • 5 Stars of Online Journals (Shotton) “Golden Star” Originally bySsolbergj CC-BY

  11. “Scared” Photo by Capture Queen CC-BY Isn’t sharingscary? www.software.ac.uk

  12. There is only one thing in life worse than beingtalked about, andthat is not beingtalked about. – Oscar Wilde www.software.ac.uk

  13. Journal of Open Research Software http://openresearchsoftware.metajnl.com

  14. “Lady and the Tramp” Photo by Joe Shlabotnik CC-BY-NC-SA The stigma of sharing will disappear www.software.ac.uk

  15. Communicationisn’t just questions + answers… it’s about sharing knowledge http://bit.ly/datasharingpanda

  16. SSI Organisation • Community Engagement (Lead: Shoaib Sufi) • Fellowship Programme • Events and Roadshows • Consultancy (Lead: Steve Crouch) • Open Call for Projects / Funded Collaborations • Software Evaluation • Policy and Publicity (Lead: Simon Hettrick) • Guides and Case Studies • Best Practice and Policy • Training (Lead: Mike Jackson) • Software Carpentry (500+ students/year) • Software Surgeries • Collaboration between universities of Edinburgh, Manchester, Oxford and Southampton. 9.5 FTEs for 5 yrs supplemented by additional project funding.

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