where indicated slides licensed under
DESCRIPTION
Communicating trust, enabling criticism Communicating Computational Research 4 April 2013, Columbia University, New York Neil Chue Hong (@ npch ) ORCID: 0000-0002-8876-7606 [email protected]. Where indicated slides licensed under. The Software Sustainability Institute. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/1.jpg)
Software Sustainability Institute
www.software.ac.uk
Communicating trust, enabling criticismCommunicating Computational Research4 April 2013, Columbia University, New YorkNeil Chue Hong (@npch) ORCID: [email protected]
Where indicatedslides licensed under
![Page 2: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/2.jpg)
Software Sustainability Institute
www.software.ac.uk
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 Supported by EPSRC
Grant EP/H043160/1
Better software
Better research
![Page 3: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/3.jpg)
Software Sustainability Institute
www.software.ac.uk
If we cannot be critical, we cannot be researchers
“Episodis Critics”Photo by Camila y el ArteCC-BY-NC-SA
www.software.ac.uk
![Page 4: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/4.jpg)
Software Sustainability Institute
www.software.ac.uk
But systems are complex
“Paint by Particle – aerosol movement”Photo by NASA Goddard Photo and VideoCC-BY
www.software.ac.uk
![Page 5: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/5.jpg)
Software Sustainability Institute
www.software.ac.uk
Algorithm
Function
Prog
ram
Library / Suite / Package
…
… and software is always growing
![Page 6: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/6.jpg)
Software Sustainability Institute
www.software.ac.uk
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
![Page 7: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/7.jpg)
Software Sustainability Institute
www.software.ac.uk
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
![Page 8: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/8.jpg)
Software Sustainability Institute
www.software.ac.uk
Increase the amount
of information on the software
(without drowning in it)
increase the trust
“Social Media Information Overload”Photo by Joe Intersection ConsultingCC-BY-NC
![Page 9: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/9.jpg)
Software Sustainability Institute
www.software.ac.uk
Academic Software Should Not Suck
Courtesy of C. Titus Brownhttp://ivory.idyll.org/blog/ladder-of-academic-software-notsuck.html
![Page 10: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/10.jpg)
Software Sustainability Institute
www.software.ac.uk
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)
“Golden Star”Originally by SsolbergjCC-BY
![Page 11: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/11.jpg)
Software Sustainability Institute
www.software.ac.uk
Isn’t sharingscary?
“Scared”Photo by Capture QueenCC-BY
www.software.ac.uk
![Page 12: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/12.jpg)
Software Sustainability Institute
www.software.ac.uk
There is only one thing in life worse than being talked about, and that is not being talked about. – Oscar Wilde
www.software.ac.uk
![Page 13: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/13.jpg)
Software Sustainability Institute
www.software.ac.uk
Journal of Open Research Software
http://openresearchsoftware.metajnl.com
![Page 14: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/14.jpg)
Software Sustainability Institute
www.software.ac.uk
The stigma
of sharing will disappear
“Lady and the Tramp”Photo by Joe ShlabotnikCC-BY-NC-SA
www.software.ac.uk
![Page 15: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/15.jpg)
Software Sustainability Institute
www.software.ac.uk
Communication isn’t just questions + answers
… it’s about sharing knowledge
http://bit.ly/datasharingpanda
![Page 16: Where indicated slides licensed under](https://reader035.vdocument.in/reader035/viewer/2022070501/56816934550346895de08b81/html5/thumbnails/16.jpg)
Software Sustainability Institute
www.software.ac.uk
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.