Software Sustainability Institute The Software Sustainability Institute 20 January 2015, HEP Software Foundation workshop Neil Chue Hong Software Sustainability Institute ORCID: | Where indicated slides licensed under Supported by Project funding from

Software Sustainability Institute Of course, we don’t deliberately set out to create code that can’t be used by others Right?

Software isn’t special, it’s mainstream Survey of researchers from 15 Russell Group unis conducted by SSI between Aug- Oct respondents covering representative range of funders, discipline and seniority. 69% 92%

This isn’t just about the “traditional” computational sciences Survey of researchers from 15 Russell Group unis conducted by SSI between Aug- Oct respondents covering representative range of funders, discipline and seniority.

And it isn’t just using software, it’s researchers developing software too Survey of researchers from 15 Russell Group unis conducted by SSI between Aug- Oct respondents covering representative range of funders, discipline and seniority. 56% 21%

So what’s the issue? Survey of researchers from 15 Russell Group unis conducted by SSI between Aug - Oct respondents covering representative range of funders, discipline and seniority. Analysis of data from 49,650 grant titles and abstracts published on Gateway to Research covering Analysis of job adverts posted to jobs.ac.uk in 1H % 4% Of UK researchers have had no formal software development training Of jobs advertised in UK universities were software related 77% Of PIs had not included costs for software development in bids 30% Of UK research investment has been spent on research which relies on software … and then there are gender related issues

Career Paths in UK Careers outside academic sector Non-university Research (industry, government etc.) ProfessorPermanent Research Staff Early Career Research PhD students Source: The Scientific Century, Royal Society, 2010 (revised to reflect first stage clarification from “What Do PhD’s Do?” study) UK STEM graduate career paths

Software Sustainability Institute Software is pervasive in research

Software Sustainability Institute Pleiotropic loci – diabetes and Parkinson’s disease Selection at pleiotropic loci underlies disease co-occurrence in human populations. Navarro, Haley, Karosas et al. Submitted to Nature Genetics

Software Sustainability Institute Behind every great piece of science… #go through each SNP of interest for(my $x = 0; $x < $x++) { #and then each downstream SNP of interest for(my $y = $x+1; $y < $y++) { #if SNPs within our chosen distance (500kb) and both present in the haplotypes file if((!($trait[$x] eq $trait[$y])) && (abs($pos[$x] - $pos[$y]) <= ) && (exists($legArrayPos{$pos[$x]})) && (exists($legArrayPos{$pos[$y]}))) { my $snp1ArrayPos = "”; my $snp2ArrayPos = "”; my $snp1All = "”; my $snp2All = "”; #create output file for this SNP pair my $filename = "ConditionedResults2/$chr[$x].$pos[$x]-$pos[$y].EHH.GBR.2.txt”; print "$filename\n”; unless (-e $filename) { open(OUT, ">$filename"); #####################CHANGE THESE IF NOT FOCUSING ON SECOND SNP######################### my $start = $pos[$y] ; if ($start < 1) { $start = 1; } my $end = $pos[$y] ; if ($end > $chrLengths{$chr[$x]}) { $end = $chrLengths{$chr[$x]}; }

Software Sustainability Institute Just the Nature of the problem? Maintenance is not fun Producing new code is fun Statistics courtesy of Jo Hannay et al, “How Do Scientists Develop and Use Scientific Software? Published online 13 October 2010 | Nature 467, (2010) doi: /467775a

Software Sustainability Institute The modern researcher… … worries about:  Data management and analysis  Reproducible research  Scalable simulations  Integration of models and workflows  Collaboration Picture of Otto Stern courtesy of Emilio Segre Visual Archives

Software Sustainability Institute reuse reproduce repeatreplicate same experiment same lab same experiment different lab same experiment different set up different experiment some of same test Figure by Carole Goble adapted from Drummond C, Replicability is not Reproducibility: Nor is it Good Science, online and Peng RD, Reproducible Research in Computational Science Science 2 Dec 2011:

Software Sustainability Institute SIGMOD Reproducibility SIGMOD conference offered to attempt to repeat/reproduce papers accepted at conference  “High burden on reviewers when setting up experiments”  Use of VMs advocated Bonnet et al, SIGMOD Record, June 2011 (Vol. 40, No. 2) doi: /

Software Sustainability Institute People UK Research Computing Ecosystem Network/Collaboration Instruments Software Computing Data Communities … Communities …

Software Sustainability Institute 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:  Developing the scientific computing / software development skill base  The role and reward of software in research  Recognition of software career paths  Re[peatable|producible|computable] research

Software Sustainability Institute The Foundations of Digital Research Re- search Careers Recognition / Reward Skills and Capability

Software Sustainability Institute 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 to support the community developing and using research software Supported by EPSRC Grant EP/H043160/1

Software Sustainability Institute SSI Objectives 1.Getting software on the research agenda 2.Supporting communities that want change 3.Increasing skills 4.Improving software Building a platform Engaging the community Being an authoritative voice

Communication Website & blog Campaigns Advice Guides Courses Workshops Fellowship Research Software Policy Training Community Consultancy 41 projects 92 evaluations 4 surgeries 33 UK SWC workshops learners 50,000 readers 41 domain ambassadors 20+ workshops organised 740 researchers 50,000 grants analysed 150+ contributed articles 19,000 unique visitors per month 272 RSEs engaged1700 signatures 13 issues highlighted

Architectural Dominance Image courtesy PDES Inc Slide from Sean Barker, BAE SYSTEMS, DPC Designed to Last

Software Sustainability Institute SSI Organisation Community Engagement (Lead: Shoaib Sufi)  Fellowship Programme Fellowship Programme  Events and Roadshows Research Software (Lead: Steve Crouch)  Open Call for Consultancy Projects / Funded Collaborations Open Call for Consultancy Projects  Software Evaluation Software Evaluation Policy (Lead: Simon Hettrick)  Guides and Case Studies Guides and Case Studies  Best Practice and Policy Training (Lead: Aleksandra Pawlik)  Software Carpentry Software Carpentry  Software Surgeries Collaboration between universities of Edinburgh, Manchester, Oxford and Southampton.

Software Sustainability Institute 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

Software Sustainability Institute 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”

Software Sustainability Institute Case Study: ICAT ICAT metadata catalogue, STFC  Support experimental data linking at Large Facilities  RAL UK (ISIS, DIAMOND, CLF), SNS US, ELLETRA Italy  ICAT operationally critical at sites, other projects looking to use  Undertook interview-based organisational review 92 observations, 32 recommendations SSI’s work means the project has move forward  Taking forward: steering group, induction process, expanded roadmapping activity, technical workshops via Skype, involved with deployment  1 year post-project 25 (75%) recommendations implemented Used by other major projects (PandataODI, CRISP) behind-some-worlds-large-experimental-facilities behind-some-worlds-large-experimental-facilities

Software Sustainability Institute Case Study: Fusion Plasma Culham Centre for Fusion Energy  GS-2 used to study low-frequency turbulence in magnetized plasma  No common visualisation across different groups  Deliver mutually agreeable framework that can be extended easily and can be maintained by the small fusion community SSI’s work means the software can be used between groups  Simplified & enhanced plasma visualisation tool Based on ParaView o/s tool For simulations using GS-2 o/s package  Aim to allow CCFE to contribute back to GS-2 community  “I am very confident the tool will be invaluable” Colin Roach, CCFE

Software Sustainability Institute Preservation vs sustainability Image courtesy of RGB Kew – not for reuse Image courtesy of London Permaculture under CC-by-nc-sa license Preservation? Sustainability?

Software Sustainability Institute Sustainable Communities Cohesion and Identity: Creating a community Tolerance and Diversity: Smart growth through collaboration Efficient use of resources: Leveraging infrastructure Adaptability to change: Governing sustainably

Software Sustainability Institute 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

Software Sustainability Institute Case Study: Tinkering with APES NSF/EPSRC Funded  Polarisable empirical force fields (AMOEBA)  AMBER, Tinker, DL_POLY, ONETEP, Q-Chem SSI’s work is helping to coordinate development across many packages and many people  Different languages, licenses, styles, teams

Software Sustainability Institute Case Study: Brain Imaging Brain Research Imaging Centre, Edinburgh  Develop PrivacyGuard software, a DICOM image deidentification toolkit  Created software to support new multispectral colouring modulation and variance identification technique (“MCMxxxVI”) to identify white matter lesions that are indicative of declining cognitive ability  BRIC are not principally software developers, but do provide software to other researchers SSI’s work means the software has been reviewed and refactored  Looked at exploitation Usability review, Naming/trademark review  Made it easier for BRIC staff to maintain and develop Move to standard repositories, testing and documentation processes Examination of licencing for MCMxxxVI Extraction and refactoring to create standalone tools

Software Sustainability Institute SSI Fellows : 16 fellows 2013: 15 fellows 2012: 10 fellows Range of subjects, career stages software.ac.uk/fellows

Software Sustainability Institute Journal of Open Research Software

Software Sustainability Institute SSI Website Disseminating best practice, gathering information 19,000+ unique visits/month

Software Sustainability Institute SSI Guides and Top Tips Guides provide in depth information  Licences  Software development  Project management  Repositories and project infrastructure  Open source  Community building  Publicising software  Policy Top Tips provide quick overviews  Software development  Repositories and project infrastructure  Software carpentry  Citing software  Data handling  Promoting and communicating your project  Community building and project management

Software Sustainability Institute SSI Briefing Papers

Software Sustainability Institute SSI Blog Articles on research software and related issues  Ask the Institute  A Day in the Software Life  Heroes of Software Engineering  Top Tips  Women in Software 150+ posts written by external contributors  10,000+ unique pageviews/month

Software Sustainability Institute SSI Training Software Carpentry   International initiative to teach basics of software engineering to computational researchers The “why” more than the “how”  Phenomenally successful – 2x oversubscription  Cheap to run but budget for 3x the coffee!  SSI are UK Coordinators for SWC  We ran 13 workshops in 2013 to 600+ learners Software Sustainability Surgeries  “Bring your own code”  “What makes Good Code good?”  Run at existing conferences, and for software funding programmes  Offering bespoke advice as well as training

Software Sustainability Institute Creating a training community Bringing together 39+ organisations with interest in e- Infrastructure training Raising issues and enablers with RCUK, BIS software.ac.uk/policy

Software Sustainability Institute Research Software Engineer Join the RSE community at

Software Sustainability Institute No-one sets out to write unsustainable software People need the skills and incentives to maintain software through its lifetime The Institute helps UK researchers benefit from more sustainable software

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