Doing Science Properly in the Digital Age: Software Skills for Free-Range Researchers

Software Sustainability Institute

www.software.ac.uk

Doing Science Properly in the Digital Age10 September 2012, Digital Research 2012, OxfordNeil Chue Hong (@npch) [email protected]


www.software.ac.uk

Four Paradigms of Research

Empirical

Theoretical

Computational

Data Exploration


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Software is pervasive in research


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Just the Nature of the problem?

Maintenance is not funHacking new stuff is fun

Statistics courtesy of Jo Hannay et al, “How Do Scientists Develop and Use Scientific Software?

Published online 13 October 2010 | Nature 467, 775-777 (2010) doi:10.1038/467775a


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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


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SSI Drivers and Themes

• Two key drivers which cause people to seek the SSI’s advice: They want to be more productive in their research They don’t want to be embarrassed by appearing worse than

their peers

• Broadly, our work falls into a few key themes: The role and reward of software in research Recognition of software career paths Developing the scientific computing / software development

skill base


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The Foundations of Digital Research


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Software Skills for Free-Range Researchers


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Seven recommendations to improve learning

1. Space learning over time2. Interleave worked example solutions with problem-solving

exercises3. Combine graphics with verbal descriptions4. Connect and integrate abstract and concrete representations of

concepts 5. Use quizzing to promote learning6. Help students allocate study time efficiently7. Ask deep explanatory questions

Organizing Instruction and Study to Improve Student Learninghttp://ies.ed.gov/ncee/wwc/practiceguide.aspx?sid=1


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Traditional teaching

• Traditional software teaching is aimed at “caged” students Full-time Able to allocate study-time Able to space learning over

time Teach in groups

• But still focussed on how and not why

Picture by Farm Sanctuary


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The free-range researcher

• The free range researcher has different requirements Already working at 200% No common “baseline”

knowledge Often just one or two

researchers• Why do they care about

software engineering?

Picture by Brookford Farm


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No common baseline

Bhargen Basepair

Bioinformatics RANovice coding in Javaand Perl to test groupspattern algorithms

Helen Helmet

Mech Eng internExploratory codingbased on tinkeringwith legacy code

Fan Fullerene

Chemistry PhDRunning analyseson behalf of hissupervisor

Mehrdad Mapping

Forestry studentField data collectioncurrently correlatingusing Matlab

Courtesy of Greg Wilson


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Case Study: Ligand Binding

• Centre for Computational Chemistry, Bristol New methods for rapid MC sampling of

biomolecular systems modelled using QM/MM Developed two codes ProtoMS (F77) + Sire (C++) Water-Swap Reaction Coordinate method to

calculate absolute protein-ligand binding free energies

• SSI’s work is helping to scale development ProtoMS and Sire both single developer codes ASPIRE/ACQUIRE framework has multiple devs

• Split architecture between ASPIRE (adaptive multiresolution hybrid MD simulation) and ACQUIRE (WorkPacket scheduling system with optimisation for time to result vs “green-ness”

• http://www.siremol.org/adaptive_dynamics


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Case Study: Climate Policy Modelling

• CIAS team at Tyndall Centre for Climate Change Research, University of East Anglia Develop linked climate and economic models for detailed

analysis Their software was not ready to be used by other groups

• One researcher/developer at UEA, several users

• SSI’s work means the software is robust enough that it can be installed and used by others Enabled use of the software by the WWFN’s Climascope

project and James Cook University• Documented software to allow extensions by contributors• Made it easier to maintain and backup• Added job scheduling to improve modeling throughput• New modelling framework enables new models i.e. new

science

• http://www.tyndall.ac.uk/research/cias

http://www.tyndall.ac.uk/research/cias


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Case Study: textual studies

• TextVRE team at CeRCH, Kings College London Developed an environment which is used to integrate

various tools used in the e-Humanities textual studies lifecycle

Builds on the German TextGrid project, and many other existing tools

• SSI’s work means the software is can be run “out of the box” – an important requirement for the researchers Developed a VM image containing the TextVRE installation

• Improve installation instructions• Develop tests to check each installed component• Improve modularisation to allow others to contribute and

maintain Feeding back work to TextGrid

• http://textvre.cerch.kcl.ac.uk

http://textvre.cerch.kcl.ac.uk/


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The modern researcher…

• … worries about: Data management

and analysis Reproducible

research Scalable simulations Integration of

models and workflows

CollaborationPicture of Otto Stern courtesy of Emilio Segre Visual Archives

Where do they learn how to do this?


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Software Skills Training

Basic Advanced

ProgrammingFocussed

ResearchFocussed Software

Carpentry

Programming 101

SummerSchools

Advanced HPC Training

HPC Short CoursesDoctoral Training

MSc in HPC / scientific

computing

Programming 201

Who fills this gap?


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A part of the process

• Foundations of scientific computing in undergraduate courses Like presentation skills

• Methods of scientific computing in postgraduate courses Like statistics and ethics

• Show the benefits from the knowledge and methods of digital research Not just programming 101


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Supporting the system

Picture by mira66

• Centres for Doctoral Training• Institutional support• Professional bodies• Career paths for software

specialists• Recognition for software reuse• Case studies to change practice


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Methods and mechanisms

• Train and support the trainers• Open source materials• Common structure• Enable online participation• Encourage local delivery• Support local follow-up• Shared spaces for discussion

• Spacing learning over time, asking deep questions

• Teaching software skills for the free-range researcher

Picture by fallsroad


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Skills allow us to show off

• Software is a key part of the life of a researcher

• A broad base of software skills is required and must be supported by the institutions

• What skills do we teach now to provide the computational scientists of the future?

• Reward the application of these skills


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More Information / Collaborate

• Today 2pm – 4.30pm: Drop-In Software Surgery

• SSI Resources http://www.software.ac.uk/resources

• SSI Fellowship Programme: £3000 to support your work, deadline 20th Sep http://www.software.ac.uk/fellowship-programme

• SSI Open Call for Projects: Collaborate with us, next deadline 30th Sep http://www.software.ac.uk/open-call

• Journal of Open Research Software A metajournal of record for your software and its metadata http://openresearchsoftware.metajnl.com

http://www.software.ac.uk/resources

http://www.software.ac.uk/fellowship-programme

http://www.software.ac.uk/open-call

http://www.software.ac.uk/open-call

http://openresearchsoftware.metajnl.com/

Doing Science Properly in the Digital Age: Software Skills for Free-Range Researchers

Education

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