communicating trust, enabling criticism
TRANSCRIPT
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Communicating trust, enabling criticismCommunicating Computational Research4 April 2013, Columbia University, New YorkNeil Chue Hong (@npch) ORCID: [email protected] Where indicated
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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
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If we cannot be critical, we cannot be researchers
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But systems are complex
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Algorithm
Function
Pro
gram
Library / Su
ite / Package
…
… and software is always growing
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Water Swap Reaction Coordinate
A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energiesWoods CJ, Malaisree M, Hannongbua S, Mulholland AJJ. Chem. Phys. (2011) vol. 134, pp. 054114http://dx.doi.org/10.1063/1.3519057
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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
TestsReview
Automation
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Increase the amount
of information on the software
(without drowning in it)
increase the trust
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Academic Software Should Not Suck
Courtesy of C. Titus Brownhttp://ivory.idyll.org/blog/ladder-of-academic-software-notsuck.html
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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
O
DE
R
c.f.5 Stars of Linked Data (Berners-Lee)5 Stars of Online Journals (Shotton)
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Isn’t sharingscary?
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There is only one thing in life worse than beingtalked about, andthat is not beingtalked about.– Oscar Wilde
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Journal of Open Research Software
http://openresearchsoftware.metajnl.com
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The stigma
of sharing will disappear
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Software Sustainability Institute
www.software.ac.ukCommunicationisn’t just questions + answers
… it’s about sharing knowledge
http://bit.ly/datasharingpanda
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SSI Organisation
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