Talk given at the National Science Foundation on the UK e-Science programme, the UK Software Sustainability Institute, and some of the challenges faced in ensuring long term development and maintenance of scientific software

1. Software Sustainabilitypreserving the future of research software 22 November 2010 NSF Neil Chue Hong N.ChueHong@software.ac.uk

2. Overview e-Science software in the UK A brief history OMII-UK Commissioned Software Programme ENGAGE Programme Software Sustainability Institute Approaches Software Preservation Challenges

3. UK e-Science Programme: Preparing the Ground “e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it” John Taylor, D-G RCUK e-Science Centres e-Science Pilot Projects

4. UK e-Science Budget (2001-2006) EPSRC Breakdown + Industrial Contributions £25M + £100M via JISC Total: £213M Staff costs - Grid Resources Computers & Network funded separately Source: Science Budget 2003/4 – 2005/6, DTI(OST) Slide from Steve Newhouse

5. OMII: Sowing the first seeds 11 initial projects funded by Managed Programme Many projects flourished But some wilted and decayed OMII setup to harvest and maintain software output of UK e-Science Core Programme

6. OMII-UK: Cultivating and Nurturing Emphasis on helping existing software grow Extra gardeners brought in (Edinburgh and Manchester) with their own plant stock Making the garden public through initiatives like Google Summer of Code and ENGAGE Inviting specialists through the PALs scheme Cultivate and sustain community software important to research

7. Software Sustainability Institute: pruning, staking, grafting Working with research softwareusers and developers Helping review and refactor Providing support and skills Identifying areas of convergence Producing strong, capablesoftware able to live longand be successfully built on

8. OMII-UK: Cultivating software for all kinds of users

9. Software Services for eResearch Software Maturation Cycle Documentation and Training Research Users Requirements Gathering Information Provision Software Support Software Improvement Community Development Governance Software Deployment Infrastr Providers Deployment Analysis Promotion + Exploitation Integration Packaging/porting Design /Code Evaluation Software Innovators Testing / Dev Infrastructure Software Contributions

11. Abcam

12. AstroGrid

13. BioDA

14. BioSimGrid

15. BRIDGES

16. CancerGrid

17. Cancer Research UK

18. CARMEN

19. Chimactica

20. CISBAN

21. CISBIC

22. Cobra-CT

23. ConvertGrid

24. CPIB

25. CSBE

26. DAASI

27. DynamO

28. Eagle Genomics

29. EaSTCHEM

30. eDiaMonD

31. e-Family

32. e-Fungi

33. e-Protein

34. EDINA

35. EMBL-EBI

36. EMBOSS

37. First Group plc

38. Fujitsu Labs Europe

39. GEDDM

40. GEESE

41. GeneGrid

42. Genomic Technology and Informatics

43. GEODE

44. GOLD

45. Healthcare@Home

46. Integrative Biology

47. ISPIDER

48. John Innes Centre

49. LaQuAT

50. MAISGrid

51. MCISB

52. MESSAGE

53. MRC Harwell

54. MRC Human Genetics Unit

56. NeRC CEH

58. ONDEX-SABR

59. Qurator

60. Roslin Institute

61. Rothamsted Research

62. Shared Genomics

63. SINAPSE

64. Unilever Centre for Chemistry

65. Utopia

66. VOTES

68. BioMart

69. BioTeam

70. caBIG

71. BIRN

72. ePCRN

73. FLOSS

74. Globus Alliance

75. iCapture

76. Indiana University

77. iPlant

78. J Craig Venter Institute

79. GEON

80. LEAD

81. Lexicon Genetics

82. MCS

83. MEDICUS

84. NASA JPL

85. NCSA

86. Partners Healthcare

87. PlexLogic

88. RENCI

89. Secure Data Grid

91. ADMIRE

92. @NeurIST

93. AstroGrid-D

94. BEinGrid

95. BioSapien

96. BioSeeds

97. Casimir

98. CERN

99. Ciemat

100. C-INB

101. Cnio

102. CSC Finland

103. DataMiningGrid

104. DEISA

105. D-GRID

106. eChase

107. EMBRACE

108. ENFIN

109. eSysBio

110. ESO

111. GeneSilico

112. Genomining

113. GridMiner

114. GridSphere

115. HELIO

116. IBIS

117. IPB – Halle

118. INB

119. Inteligrid

120. IST

121. KeyGene

122. KnowArc

123. MOTEUR

124. N2Grid

125. NBIC

126. OntoGrid

127. Orfeus Data Center

128. PLANET

129. Provenance

130. RUPAGATION

131. Scana

132. Sigenae

133. SIMDAT

134. SPIDR/ESSE

135. SysMO

136. UnIDART

137. ViroLab

138. VLe-S

139. VPH

140. Woonstichting De Key

142. ChinaGrid

143. EADDG

144. cnGrid

145. SAIC

147. BioGrid

148. GeoGrid

149. NAREGI

151. IRRI

152. KooPrime

153. TCELS

155. BASF

156. Bayer

157. BristolMyersSquibb

158. Hewlett=Packard

159. IBM

160. Microsoft

161. Novartis

162. Oracle

163. Pfizer

164. Philips

165. Philip Morris

166. Roche

168. INWA

170. PCB ChileTutorials to over 2000 researchers: Antwerp, Bangkok, Basel, Boston, Cambridge, Catania, CERN, Chicago, Edinburgh, Hanoi, Hawaii, Helsinki, Leeds, London, Manchester, Newcastle, Nijmegen, Nottingham, Oxford, San Francisco, Seattle, Seoul, Sheffield, Southampton, Tenerife, Tokyo, Toronto, ISSGC 03 to 09

171. Developing the role of standards in the community OMII-UK is instrumental in the development and use of standards Enabling interoperation over continental scale AHE across TeraGrid, DEISA, EGEE DataMINX across SRB, GridFTP Reference implementations SAGA enabling legacy applications WS-DAI for data access JSDL/BES/HPC BP for computational job submission

172. Impact on UK Research The top 75% of “Quality of Research” funding is allocated to 49 UK research institutions out of a total of 159 HEIs

173. Impact on UK Research OMII-UK has worked with all 7 of the top research intensive institutions in each region: Oxford, Cambridge, UCL, Imperial Edinburgh Cardiff QUB

174. Commissioned Software Programme Commissioning Supporting Developing GridSAM Condor WS Geodise Lab AHE BPEL Designer Compute Grimoires Open Grid Manager Info / Registry MANGO Visual/ Collab WSRF:: Lite FINS/ FIRMS Infra / Security WSeSSH £3.4m initial funding for Managed Programme 2006: Q1 – Initial projects commissioned; open call to community Deprecated:

175. Commissioned Software Programme Commissioning Supporting Developing GridSAM Geodise Lab AHE BPEL Designer Compute Grimoires Open Grid Manager Info / Registry KNOOGLE MANGO Visual/ Collab WSRF:: Lite FINS/ FIRMS Infra / Security OMII-AuthZ 2006: Q3 – trials complete; new specific commissions Deprecated: Condor WS WSeSSH

176. Commissioned Software Programme Commissioning Supporting Developing GridSAM Geodise Lab AHE BPEL Designer Compute Grimoires Open Grid Manager Info / Registry KNOOGLE MANGO Visual/ Collab RAVE WSRF:: Lite FINS/ FIRMS Infra / Security OMII-AuthZ 2007: Q1 – Application focussed projects complete Deprecated: Condor WS WSeSSH

177. Commissioned Software Programme Commissioning Supporting Developing GridSAM Geodise Lab GridBSBroker RAPID AHE BPEL Designer Compute OGRSH SAGA Grimoires Open Grid Manager Info / Registry KNOOGLE Visual/ Collab RAVE NGS JSDL App Rep PAG WSRF:: Lite Infra / Security OMII-AuthZ SCAMP NDG Security WHIP £1.4m additional funding for Commissioned Software Programme 2007: Q3 – Software integrated; new portal and simplified access calls Deprecated: MANGO Condor WS WSeSSH FINS/ FIRMS

178. Commissioned Software Programme Commissioning Supporting Developing GridSAM GridBSBroker RAPID AHE BPEL Designer Compute OGRSH SAGA Grimoires Open Grid Manager Info / Registry Visual/ Collab KNOOGLE RAVE NGS JSDL App Rep VIC + RAT PAG WSRF:: Lite Infra / Security OMII-AuthZ SCAMP NDG Security WHIP 2008: Q1 – significant support for implementations of standards Deprecated: MANGO Condor WS WSeSSH FINS/ FIRMS Geodise Lab

179. Commissioned Software Programme Commissioning Supporting Developing GridSAM GridBSBroker RAPID AHE BPEL Designer Compute OGRSH SAGA Grimoires Open Grid Manager Info / Registry Visual/ Collab RAVE NGS JSDL App Rep VIC + RAT PAG WSRF:: Lite Infra / Security OMII-AuthZ SCAMP NDG Security WHIP 2008: Q3 – start of investment in community development Deprecated: MANGO Condor WS WSeSSH FINS/ FIRMS Geodise Lab KNOOGLE

180. Commissioned Software Programme Commissioning Supporting Developing GridSAM GridBSBroker RAPID AHE BPEL Designer Compute SAGA Grimoires Open Grid Manager Info / Registry Visual/ Collab RAVE NGS JSDL App Rep VIC + RAT PAG WSRF:: Lite Infra / Security OMII-AuthZ WHIP SCAMP NDG Security 2009: Q1 – many projects complete, in use by community Deprecated: MANGO Condor WS WSeSSH FINS/ FIRMS Geodise Lab KNOOGLE OGRSH

181. Commissioned Software Programme Commissioning Supporting Developing GridSAM GridBSBroker RAPID AHE BPEL Designer Compute SAGA 8 projects with multiple international contributors through SF/CPAN/PyPl 75+ evaluations of 40+ components Grimoires Info / Registry Visual/ Collab RAVE NGS JSDL App Rep VIC + RAT PAG WSRF:: Lite Infra / Security WHIP SCAMP NDG Security Data DiGS CIAS Data MINX OSCAR 2009: Q3 – Data call commissioned; focus on community need Deprecated: Open Grid Manager MANGO Condor WS WSeSSH FINS/ FIRMS Geodise Lab OMII-AuthZ KNOOGLE OGRSH

182. Case Study: TavernaWorkbench Initially funded through e-Science myGrid project (2001-2005) Directly funded through OMII-UK (2006-2010) Plus marketing, outreach, legal and networking Platform funding (2009-2014) caBIG subcontract Eli Lilly development 40,000+ downloads of Taverna 1.x Take up in other domains,e.g. astronomy

183. Case Study: NERC Data Grid Security Provides single sign-on to federated data infrastructure NDGS software now installed at major NERC data centres in the UK Now used across multiple projects Filter based approach and OpenID work used by US Earth System Grid for access to CMIP5 archive METAFOR QUESTIONNAIRE COWS/NCEO Contributions back to Python community ndg_saml, ndg_xacml, MyproxyClient

184. Case Study: VIC + RAT Media backbone tools for audio and video maintained by UCL since early 90s Used as the basis for Access Grid, VRVS OMII-UK funding when other sources cut Allowed continued maintenance and bug fixes Enabled projects from Australia, Korea to contribute However difficulties in sustaining Rapid changes in hardware / software Too low profile Other projects not contributing back

185. Engaging Research with e-Infrastructure 53 direct interviews 200+ interviews total Interviews 30 month programme 14 projects 3-6 months duration £650,000 funding Wider deployment 17 papers 10 posters 50 presentations £1.36m further funding Projects Dissemination Adoption New requirements

186. First Phase ENGAGE Development Projects High Throughput Humanities for e-Research Exposing bioinformatic programs as Web Services Protein Molecule Simulation on the Grid Enable workflows in a Shared Genomics causality workbench Linking and Querying Ancient Texts SWARMCloud Rapid Chemistry Portals by Engaging Users

187. Second Phase ENGAGE Development Projects Monte Carlo Treatment Planning Crystal Energy Landscape Application Epigraphy and papyrology image processing Strengthening and support for eMinerals RMCS system Configuration parameters for the GENIE simulator Lab Blog Book Strengthening and supporting the text and data analysis toolkit OSCAR

188. ENGAGE Findings Significant findings include the most challenging aspects of e-Science application development is the communication between development and research teams there are differing time constraints on researchers and developers having good facilitators improves the success of a project centralisation of IT services means that it is harder to do exploratory development adherence to standards can reduce the barriers for the deployment of technology removing complexity can allow researchers to become developers there are still issues when trying to migrate from local to national resources issues which appear trivial to computer scientists can cause researchers to consider the software unusable.

189. ENGAGE Outputs Significant outputs of the development projects include: publicly available workflows in daily use by students to do analyses of 15,000 protein sequences a protein molecule simulation portal available to any user with a valid UK e-Science certificate a live portal being used teach over 140 students how to optimise molecule structures new data exploration techniques being enabled a number of follow-on projects funded to take the work pioneered in ENGAGE to a larger or different community; many improvements to commonly used software being released back to the community

190. Case Study: Crystal Energy Landscapes Understanding polymorphism in drugs E.g. Dosage profile Chemists Computational Experimental Developers Domain S/W Engineers Integrators Research Computing Services Facilitator http://www.youtube.com/watch?v=bkbRwOWmiwo

191. The Software Sustainability Institute A national facility for research software Providing services for research software users and developers Developing research community interactions and capacity Promoting research software best practice and capability Sustaining software by helping to negotiate the stages of the software maturity cycle

193. consultative advice (software evaluation , development process, community engagement, dissemination, workshops+surgeries)

197. Funded by EPSRC for 5 years, 9.5 FTE

199. How are you going to choose the right approach? Preservation (techno-centric) Emulation (data-centric) Migration (functionality-centric) Transition (process-centric) Hibernation (knowledge-centric) Approach SSI effort focused here

200. Current SSI Guides Software development Software development: general best practice Developing maintainable software Testing your software Repositories Choosing a repository for your software project Migrating project resources: what to remember Creating and managing SourceForge projects Retrieving project resources from NeSCForge Open source Adopting an open-source licence Supporting open-source software Community building Recruiting champions for your project Recruiting student developers

201. SSI Evaluation Criteria Importance: the alignment of the research domain to the UK’s strategic research roadmap. Enthusiasm: the impact which the work will have on the community, engagement of software authors with process and the likely additional contribution that would be gained from the community. Value: the impact on the research outputs. Would the science enabled be significantly improved by the work? This is a measure of the User Demand for improvement. Availability: the likelihood that the work would enable the software to reach a new stage of availability e.g. taking it from within one collaboration to make it fit for the whole research community or a new community Tractability: the impact on the software. Will it be possible to improve easily the quality or performance of the software? Opportunity: will the work lead to new opportunities for sustainability, e.g. collaboration with other groups, commercialisation, alternative funding or new effort?

203. Climate Policy

204. GeospatialLinked Data

205. CrystalStructure

206. Brain Imaging

208. Case Study: NeISS 40

209. Case Study: NeISS 41

210. Exploiting software for sustainability Models Grant Mosaic Institutional support Fully Costed Service External Enterprise / Consultancy Royalties and Fees Donations Advertising T-shirt (spinoff merchandising) Vehicles University based Spin out company Consultancy and Customisation Industrial knowledge transfer Contracts Licensing Certification Support services / training Software as a Service Software Foundation Most common but what happens when PI retires?

211. Sustainability in Context Support / Contributions Software Sustainability Community Engagement Software Engineering Product Management Market Development Funding/ Effort

212. Software sustainability is part of the process Comparable to risk management No one right “solution” but many examples of best practice and process Plan from before the start if possible But must be reviewed regularly No longer considering timescales bounded by a project, but considering the product

213. Software development comes in stages Bridging criteria: strength of team; strength of market; proximity of software to market Idea Prototype Research Idea Prototype Idea Idea Prototype Research Supported Product Idea Prototype Research Supported An idea to solve a problem Understand the functionality Scaling to work for others Allow othersto participate

215. Giant Magnetoresistance (1988 – 1999)

216. Frequency Hopping (1903/1942 – 1976)

217. Bayesian statistics (1763 – 1996)Applied Research

218. Case Study: Signal Processing Slide from Jim Austin

219. Case Study: CASTEP Building intellectual access ramps to support incremental engagement – building capacity and capability Individual Group Consortium W/ industry Community Active 48

220. Case Study: R-Project Basics: Website, mailing list, code repository, issue resolution Remove barriers to participation, increase efficiency 1993: First public release; 2 devs 1995: Code open sourced; 3 devs 1996: r-testers list set up 1997: lists split: r-announce, r-help,r-devel; public CVS; 11 devs 2000: CRAN split and mirror 2001: BioConductor 2003: Namespaces 2005: I8n, L8n 2007: R-Forge Today: BioConductor (33 core devs), R-Forge (532 projects, 1562 devs), CRAN (1400+ packages) 49 http://cran.r-project.org/doc/html/interface98-paper/paper_2.html

221. The Software Maturity Curve Portals Quantum chemistry Cloud Computing RDBMS Social Simulation Workflows Spatio- Temporal viz Molecular Dynamics Geospatial viz Digitised Doc Analysis Digital repositories Software proliferation Innovation Consolidation Customisation Time

222. Enabling Innovation Supporting emergent disciplines Needs recognition of innovative software development as part of funding Breaking down barriers We cannot assume that the way people interact with resources will conform to expectations e.g. researchers will use/store files outside of universities Researchers will do whatever they can to get an edge – they will not always conform

223. Supporting Consolidation “e-Science is an organic, emergent process requiring ongoing, coordinated investment from multiple funders and coordinated action by multiple research and infrastructure communities. It is both an enabler of research and an object of research” – RCUK Review of e-Science Bridging the expectation gaps between participants Maintenance vs. research Different timescales for “exciting” work Well supported open platforms are the key in the age of the research mashup Platforms to enable bottom-up innovation Platforms to enable citizen participation Competition/innovation built on top c.f. industry

224. Sustaining Customisation “The time constants for real transformative impact and significant competitive advantage is decades” – RCUK Review of e-Science Sustain software infrastructure in the long term Differing models: through centres; within institutions; distributed Need to change perceptions so that software is seen as valuable! (and not just invaluable) Lower barriers to community growth and participation Increase value of providing services Virtually merge + map small amounts of effort / funding

225. Invest in people People are the most important investment Adaptability, ability to recognise transferable skills, not strict career paths Software developers come from many backgrounds If e-Science is multi-disciplinary, multi-institution, multi-scale then make it easier to recognise peoples efforts as they move University structures do not make it easy These people are key to effective e-Science as they bridge the gap between other participants

226. The credit question How do we get credit for reusing, extending and sustaining software? Research credit is based on publication output Data citations and credit for reuse are still not commonplace Software credit is the next stage Otherwise how can we persuade people to contribute back?

228. Climate Policy

229. GeospatialLinked Data

230. CrystalStructure

231. Brain Imaging

232. Scholarly JournalsBecome our next collaborators! Email: info@software.ac.uk Blog: http://www.software.ac.uk/blog Twitter: twitter.com/SoftwareSaved SlideShare: slideshare.net/SoftwareSaved YouTube: youtube.com/user/SoftwareSaved Telephone: +44 (0) 131 650 5030