This document discusses the importance of software sustainability. It notes that software is everywhere, long-lived, and hard to define, which makes sustainability challenging. It emphasizes that software sustainability requires cultivating skills in developers and researchers, providing proper incentives, and recognizing that people are a key part of maintaining software over long periods of time.
The document discusses various challenges around tracking contributions and attributing authorship to software. It notes that while version control systems make it easy to track changes to software, they do not uniquely attribute the work to individuals. There are open questions around what level of a software project deserves attribution (e.g. functions vs. whole packages). Micro-attribution of individual contributions is also discussed. The document proposes that following the "Five Stars of Research Software" can help make software more identifiable, reusable and accessible to others.
The document discusses the foundations of digital research and software sustainability. It promotes practices like developing reusable, reproducible software and careers in software. It also addresses issues like skills and training, recognition for software, and ensuring software is accessible, open, and its "correctness" can be assured. The document proposes a 5-star rating system for software quality and sustainability.
The document discusses an iterative and user-centered approach to developing administrative systems at the University of Washington. It involves collaborating closely with end users to design prototypes and conduct user testing in an agile manner. This evolutionary approach aims to develop systems that meet user needs by engaging stakeholders from across the university throughout the entire development process. In contrast to traditional top-down IT projects, these user-driven projects have vague scopes but produce flexible systems through open communication and feedback.
The document discusses the creation of a wiki catalogue to catalog open source toolkits and testbeds related to software defined networking (SDN), network function virtualization (NFV), mobile edge computing (MEC) and 5G technologies. It notes that there are many toolkits and testbeds but a lack of visibility among researchers. A wiki is proposed to provide a centralized place for researchers, students and developers to discover relevant tools and testbeds. The wiki is being developed in phases, beginning with data collection and developing the initial structure, then opening it for community contributions and updates.
An Open and Improved VISIR System Through PILAR Federation for Electrical/Ele...Manuel Castro
Worksho of PILAR Federated VISIR systems celebrated in the TALE 2018 conference (Teaching, Assessment and Learning for Engineering) in December 2018, in Wollongong (Australia). Here you have the PILAR project link >>> http://www.ieec.uned.es/pilar-project/index.html?lng=en
Software Maintenance Support by Extracting Links and Models (revised)Hironori Washizaki
This Friday (November 13, 2015) we are honored to have Dr. Hironori Washizaki from Waseda University (Japan) as speaker.
The similar will start at 13:30 in room M-2109 pavillons Claudette-MacKay-Lassonde et Pierre-Lassonde.
Please find bellow, title, abstract of talk, and biography of Dr. Washizaki.
Title:
Software Maintenance Support by Extracting Links and Models
Abstract:
Extracting missing important links and models from software is the
key to success of its maintenance such as specifying locations that
need correction. This talk firstly introduces two novel techniques
for recovering traceability links precisely between requirements and
program source code: log-based interactive recovery (CAiSE'15) and
transitive recovery (ICSME'15 ERA). Secondly the talk introduces two
novel preventive maintenance techniques employing behavioral model
extraction and model checking targeting Ajax applications: design
pattern based invariants verification (ASE'13) and delay-based
mutation (ASE'14).
Bio:
Hironori Washizaki is head and associate professor at Global
Software Engineering Laboratory, Waseda University, Japan. He is also
visiting associate professor at National Institute of Informatics,
and, visiting professor at Ecole Polytechnique de Montreal during his
sabbatical stay till Dec 2015. He received PhD in Information and
Computer Science from Waseda University in 2003. His research interests
include software and systems requirements, architecture, reuse,
maintenance, quality assurance, and education. He has served on the
organizing committees of many international conferences (such as ASE,
ICST, SPLC, CSEE&T, SEKE, BICT and APSEC) as well as editorial boards
of several international journals (such as Int. J. Soft. Eng. Know.
Eng. and IEICE Trans). He also has served at various professional
societies such as IEEE Computer Society Japan Chapter Chair, SEMAT
Japan Chapter Chair, IPSJ SamurAI Coding Director, and ISO/IEC/
JTC1/SC7/WG20 Convenor. http://www.washi.cs.waseda.ac.jp/?page_id=2
The document discusses various challenges around tracking contributions and attributing authorship to software. It notes that while version control systems make it easy to track changes to software, they do not uniquely attribute the work to individuals. There are open questions around what level of a software project deserves attribution (e.g. functions vs. whole packages). Micro-attribution of individual contributions is also discussed. The document proposes that following the "Five Stars of Research Software" can help make software more identifiable, reusable and accessible to others.
The document discusses the foundations of digital research and software sustainability. It promotes practices like developing reusable, reproducible software and careers in software. It also addresses issues like skills and training, recognition for software, and ensuring software is accessible, open, and its "correctness" can be assured. The document proposes a 5-star rating system for software quality and sustainability.
The document discusses an iterative and user-centered approach to developing administrative systems at the University of Washington. It involves collaborating closely with end users to design prototypes and conduct user testing in an agile manner. This evolutionary approach aims to develop systems that meet user needs by engaging stakeholders from across the university throughout the entire development process. In contrast to traditional top-down IT projects, these user-driven projects have vague scopes but produce flexible systems through open communication and feedback.
The document discusses the creation of a wiki catalogue to catalog open source toolkits and testbeds related to software defined networking (SDN), network function virtualization (NFV), mobile edge computing (MEC) and 5G technologies. It notes that there are many toolkits and testbeds but a lack of visibility among researchers. A wiki is proposed to provide a centralized place for researchers, students and developers to discover relevant tools and testbeds. The wiki is being developed in phases, beginning with data collection and developing the initial structure, then opening it for community contributions and updates.
An Open and Improved VISIR System Through PILAR Federation for Electrical/Ele...Manuel Castro
Worksho of PILAR Federated VISIR systems celebrated in the TALE 2018 conference (Teaching, Assessment and Learning for Engineering) in December 2018, in Wollongong (Australia). Here you have the PILAR project link >>> http://www.ieec.uned.es/pilar-project/index.html?lng=en
Software Maintenance Support by Extracting Links and Models (revised)Hironori Washizaki
This Friday (November 13, 2015) we are honored to have Dr. Hironori Washizaki from Waseda University (Japan) as speaker.
The similar will start at 13:30 in room M-2109 pavillons Claudette-MacKay-Lassonde et Pierre-Lassonde.
Please find bellow, title, abstract of talk, and biography of Dr. Washizaki.
Title:
Software Maintenance Support by Extracting Links and Models
Abstract:
Extracting missing important links and models from software is the
key to success of its maintenance such as specifying locations that
need correction. This talk firstly introduces two novel techniques
for recovering traceability links precisely between requirements and
program source code: log-based interactive recovery (CAiSE'15) and
transitive recovery (ICSME'15 ERA). Secondly the talk introduces two
novel preventive maintenance techniques employing behavioral model
extraction and model checking targeting Ajax applications: design
pattern based invariants verification (ASE'13) and delay-based
mutation (ASE'14).
Bio:
Hironori Washizaki is head and associate professor at Global
Software Engineering Laboratory, Waseda University, Japan. He is also
visiting associate professor at National Institute of Informatics,
and, visiting professor at Ecole Polytechnique de Montreal during his
sabbatical stay till Dec 2015. He received PhD in Information and
Computer Science from Waseda University in 2003. His research interests
include software and systems requirements, architecture, reuse,
maintenance, quality assurance, and education. He has served on the
organizing committees of many international conferences (such as ASE,
ICST, SPLC, CSEE&T, SEKE, BICT and APSEC) as well as editorial boards
of several international journals (such as Int. J. Soft. Eng. Know.
Eng. and IEICE Trans). He also has served at various professional
societies such as IEEE Computer Society Japan Chapter Chair, SEMAT
Japan Chapter Chair, IPSJ SamurAI Coding Director, and ISO/IEC/
JTC1/SC7/WG20 Convenor. http://www.washi.cs.waseda.ac.jp/?page_id=2
Software Sustainability in e-Research: Dying for a ChangeNeil Chue Hong
The document discusses challenges with sustaining software developed for research purposes. It describes how early UK e-science projects led to the establishment of organizations like OMII and the Software Sustainability Institute to help maintain software over the long term. However, software sustainability remains a challenge, as researchers are often more interested in developing new software than maintaining existing tools. The document advocates developing communities around research software and viewing software sustainability as an ongoing process rather than a single solution. It also argues that researchers should receive proper credit for their work sustaining software over time.
Doing Science Properly In The Digital Age - Rutgers SeminarNeil Chue Hong
The document discusses the role of software in research and the Software Sustainability Institute's (SSI) work to address challenges. SSI helps researchers make their software more sustainable and reusable through consulting, training, and community engagement. Case studies show how SSI has helped research groups improve software to enable new science and broader adoption. The document observes that software is now pervasive in research but culture does not widely support reuse or recognize software contributions. SSI aims to address gaps in skills, recognition, and sustainable practices to support digital research foundations.
Keynote on software sustainability given at the 2nd Annual Netherlands eScience Symposium, November 2014.
Based on the article
Carole Goble ,
Better Software, Better Research
Issue No.05 - Sept.-Oct. (2014 vol.18)
pp: 4-8
IEEE Computer Society
http://www.computer.org/csdl/mags/ic/2014/05/mic2014050004.pdf
http://doi.ieeecomputersociety.org/10.1109/MIC.2014.88
http://www.software.ac.uk/resources/publications/better-software-better-research
Six Principles of Software Design to Empower ScientistsDavid De Roure
Keynote talk for Workshop on Managing for Usability:
Challenges and Opportunities for E-Science Project Management, 10-11 April 2008,
OeRC, University of Oxford, UK
Cloud Standards in the Real World: Cloud Standards Testing for DevelopersAlan Sill
Learn about standards studied in the US National Science Foundation Cloud and Autonomic Computing Industry/University Cooperative Research Center Cloud Standards Testing Lab and how you can get involved to extend the successes from these results in your own cloud software settings. Presented at the O'Reilly OSCON 2014 Open Cloud Day.
Video available at https://www.youtube.com/watch?v=eD2h0SqC7tY
Socio-technical evolution and migration in the Ruby ecosystemTom Mens
Presentation by Eleni Constantinou (joint work with Tom Mens, Software Engineering Lab, UMONS) at the BENEVOL 2016 Software Evolution Research Seminar, Utrecht University, The Netherlands
Rodney McDonell is a problem solver currently employed at Lockheed Martin Australia as a software and systems verification and validation engineer. He is completing his Master of Science in Computer Science with a focus on machine learning and statistics. His career goal is to work in data analysis, machine learning, or a related field. He has over 15 years of experience in software engineering roles, specializing in C/C++, Java, databases, machine learning tools and techniques, and Agile methodologies. He also has a history of volunteering in science education and outreach.
The Software Sustainability Institute and engagement with the Digital HumanitiesShoaib Sufi
The Software Sustainability Institute supports digital humanities research through several programs:
1) It runs a fellowship program that has funded over 100 fellows since 2012, including several digital humanities fellows, to support events and activities around research software.
2) It provides training in software skills through programs like Software Carpentry and Data Carpentry, and supports instructor training and curriculum development for digital humanities topics.
3) It develops sustainable research software, such as tools for analyzing cultural heritage artifacts, and supports open source projects like the Programming Historian library.
4) It engages with research councils and stakeholders to advocate for software and develop policies that support reproducible and reusable research software in the digital humanities.
OMII-UK is an open-source organization established by the EPSRC to provide software and services to help the UK research community adopt e-Research practices and technology. It is currently funded by EPSRC, JISC and others. OMII-UK's mission is to cultivate and sustain important community software through various channels of support like requirements gathering, software development expertise, and community development. It has undertaken initiatives like the ENGAGE Initiative to better understand researchers' computational needs and develop focused projects to address these needs.
The document describes the VETworking project which aims to help veterans find permanent work. It will develop the project using an agile methodology. Design artifacts that will be produced include user stories, class diagrams, sequence diagrams, and state diagrams. These artifacts will provide sufficient information for programmers to develop an initial prototype. The document also discusses establishing roles for participants in the program, developing a class diagram, and analyzing user stories to identify classes and their attributes and methods.
- Keiichiro Ono presented on his experience developing and maintaining bioinformatics visualization applications over 15 years, including Cytoscape.
- Expanding applications to support new technologies like web, Python, and JavaScript is important to attract developers and connect to popular tools, but breaking API changes are difficult.
- A loosely coupled approach integrating existing applications, Jupyter notebooks, and new web apps may be better than rewriting applications from scratch.
Software Analytics: Data Analytics for Software EngineeringTao Xie
This document summarizes a presentation on software analytics and its achievements and opportunities. It begins by noting how both how software and how it is built and operated are changing, with data becoming more pervasive and development more distributed. It then defines software analytics as enabling analysis of software data to obtain insights and make informed decisions. It outlines research topics covering different areas of the software domain throughout the development cycle. It describes target audiences of software practitioners and outputs of insightful and actionable information. Selected projects demonstrating software analytics are then summarized, including StackMine for performance debugging at scale, XIAO for scalable code clone analysis, and others.
Cultivating Sustainable Software For ResearchNeil Chue Hong
Keynote given at the NSF Cyberinfrastructure Software and Sustainability Workshop, March 26th-27th 2009, Indianapolis.
Exploration of software sustainability based on experiences from UK.
The Software Sustainability Institute (SSI) provides services to help research groups sustain their software over the long term. It collaborates with groups in various fields to improve key software through advice, training, and partnerships. Case studies describe projects in fields like fusion energy, climate modeling, geospatial data, and computational chemistry. The SSI aims to promote best practices and change perceptions so software is recognized as a valuable long-term asset, not just for initial research. Sustaining software requires support for both technical aspects and community engagement over decades.
Why developing research software is like a startup (and why this matters)Neil Chue Hong
When we think about the software used in research and science, we might think of the commercial packages with thousands of users, or the millions of lines of code that support experiments such as the Large Hadron Collider, or indeed the millions of scripts written every day by researchers across the world to undertake simple tasks. What is clear is that modern research relies on software: a recent survey of UK researchers conducted by the Software Sustainability Institute reported that 92% of researchers used software, and 69% could not conduct their work without it. Millions of dollars are invested each year in supporting a quasi-industry of software production, with the equivalent of the full-spectrum from large multinationals and tiny cottage industries, but little is known about whether this is efficient or indeed appropriate. This talk will examine the similarities between the development of software in the research environment and the lifecycle of technology startup companies. It will also consider the driving factors behind adoption of software and the impact of software sustainability on the ability to conduct research.
UK Funder Policy - the results of the Academic Spring?Neil Chue Hong
The document discusses recent UK funder policies that emphasize open access and reproducibility in computational research. Two influential reports in 2012 addressed improving access to published research findings. In response, the Research Councils UK implemented new open access and data policies starting in 2013. These policies require publicly sharing research publications and data, with exceptions for legal or commercial reasons. The policies aim to make publicly funded research outputs openly available and reusable. Assessment of research is expanding to include software and datasets as valid research outputs.
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Keynote on software sustainability given at the 2nd Annual Netherlands eScience Symposium, November 2014.
Based on the article
Carole Goble ,
Better Software, Better Research
Issue No.05 - Sept.-Oct. (2014 vol.18)
pp: 4-8
IEEE Computer Society
http://www.computer.org/csdl/mags/ic/2014/05/mic2014050004.pdf
http://doi.ieeecomputersociety.org/10.1109/MIC.2014.88
http://www.software.ac.uk/resources/publications/better-software-better-research
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Keynote talk for Workshop on Managing for Usability:
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The Software Sustainability Institute supports digital humanities research through several programs:
1) It runs a fellowship program that has funded over 100 fellows since 2012, including several digital humanities fellows, to support events and activities around research software.
2) It provides training in software skills through programs like Software Carpentry and Data Carpentry, and supports instructor training and curriculum development for digital humanities topics.
3) It develops sustainable research software, such as tools for analyzing cultural heritage artifacts, and supports open source projects like the Programming Historian library.
4) It engages with research councils and stakeholders to advocate for software and develop policies that support reproducible and reusable research software in the digital humanities.
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1. Scientific Software:
sustainability, skills & sociology
Neil Chue Hong, N.ChueHong@software.ac.uk
Director, Software Sustainability Institute
US/IAEA Workshop on Software Sustainability
for Safeguards Instrumentation, Vienna
Institute
Software
Sustainability
www.software.ac.uk
2. 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
Institute
Software
Sustainability
www.software.ac.uk
3. Anatomy of my talk
Institute
Software
Sustainability
www.software.ac.uk
SOFTWAREis…
…areIMPORTANT
everywhere
hard to define
long-lived
context
reasons
people
7. Tamiflu binding to mutant influenza
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. 054114
http://dx.doi.org/10.1063/1.3519057
8. Favouring of disease risk alleles
Selection at pleiotropic loci underlies disease
co-occurrence in human populations.
Navarro, Haley, Karosas et al.
Submitted to Nature Genetics
9. Behind every great piece of science…
#go through each SNP of interest
for(my $x = 0; $x < scalar @pos; $x++)
{
#and then each downstream SNP of interest
for(my $y = $x+1; $y < scalar @pos; $y++)
{
#if SNPs within our chosen distance (500kb) and both present in the haplotypes file
if((!($trait[$x] eq $trait[$y])) && (abs($pos[$x] - $pos[$y]) <= 500000) && (exists($legArr
{
my $snp1ArrayPos = "”;
my $snp2ArrayPos = "”;
my $snp1All = "”;
my $snp2All = "”;
#create output file for this SNP pair
my $filename = "ConditionedResults2/$chr[$x].$pos[$x]-$pos[$y].EHH.GBR.2.txt”;
print "$filenamen”;
unless (-e $filename) {
open(OUT, ">$filename");
#####################CHANGE THESE IF NOT FOCUSING ON SECOND SNP####################
my $start = $pos[$y]-500000;
if ($start < 1) {
$start = 1;
}
my $end = $pos[$y]+500000;
if ($end > $chrLengths{$chr[$x]}) {
$end = $chrLengths{$chr[$x]};
}
10. Software is long-lived
(and outlasts computational hardware)
Institute
Software
Sustainability
www.software.ac.uk
12. Computational Chemistry - CASTEP
From the first implementation of a DFT algorithm to a
completely new code to community supported software
• Individual
• Group
• Consortium
• W/ industry
• Community
• Active
Software advances
< hardware speedup
13http://www.castep.org/
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13. LOTAR: storing aeronautical models
Life of CAD System: 10 years
Time between CAD Versions: 6 months
Life of Product: 70 years +
time
Production
CAD Obsolete
CAD Forgotten
Services
Legal Liability
Modifications
10 years 20 30 40 50 60
Spares
Image courtesy PDES Inc
Slide from Sean Barker, BAE SYSTEMS, DPC Designed to Last
Institute
Software
Sustainability
www.software.ac.uk
14. So we have to maintain it…
• “The modification of a software product after
delivery to correct faults, to improve
performance or other attributes, or to adapt the
product to a modified environment” – IEEE defn.
– Corrective maintenance: fixing faults
– Adaptive maintenance: adapting to changes in
environment
– Perfective maintenance: meeting new/different user
requirements
– Preventative maintenance: increasing maintainability
Institute
Software
Sustainability
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15. … because we cannot change this
with process and practice alone …
• “Many of us have tried to discover
ways to prevent code from
becoming legacy. But …
prevention is imperfect. Even the
most disciplined development
team, knowing the best principles,
using the best patterns, and
following the best practices will
create messes from time to time.
The rot still accumulates. It’s not
enough to prevent the rot – you
have to be able to reverse it.”
Institute
Software
Sustainability
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16. … so we work with what we have
• Identify change points
• Find test points
• Break dependencies
• Write tests
• Make changes and refactor
Testing, infrastructure, documentation are key
Institute
Software
Sustainability
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17. Software is hard to define
(and thus hard to sustain)
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Software
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18. What do we sustain:
- Workflow?
- Software that runs workflow?
- Software referenced by workflow?
19. Novel reuse of public sector data
http://www.mysociety.org
What do we sustain:
- Map?
- Software that creates map?
22. Comb badge, Museum of London
• Without context, objects have no meaning
What’s this item?
32x28mm, lead alloy, late Medieval 14-15th century
23. What about repositories?
re⋅pos⋅i⋅tor⋅y
/noun/ [ri-poz-i-tawr-ee]
• 1. a receptacle or place where things are
deposited, stored, or offered for sale.
• 2. a burial place; sepulchre.
Institute
Software
Sustainability
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24. The Zombie Effect
• Software not always fully alive
when you reanimate it!
• Complex set of dependencies
– Significant Properties of Software
– Purposes and benefits of
software preservation
http://www.jisc.ac.uk/media/documents/
programmes/preservation/significantprop
ertiesofsoftware-final.doc
http://softwarepreservation.jiscinvolve.org/wp/
25. Reasons are important
(so you take the right approach)
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26. Why are you considering
software sustainability?
Achieve legal compliance
Create heritage value
Enable continued access
to data and services
Encourage software reuse
Purpose
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27. 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
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28. Preservation vs sustainability
Image courtesy of RGB Kew – not for reuse
Image courtesy of London Permaculture under CC-by-nc-sa license
Preservation?
Sustainability?
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30. 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
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Software
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31. Cultivate Contributors – 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)
34
http://cran.r-project.org/doc/html/interface98-paper/paper_2.html
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32. We under-appreciate training
• Basic training for
kitchen chef: 3-4 years
• Head chef: 10 years
• Basic training for s/w
engineer: 3-4 years
• Architect: 10 years
PhotobyZagatBuzz
• Training in S/W Dev in UG Physics: 140 hours
• Training in S/W Dev in UG Geography: 0 hours
Institute
Software
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33. Software Carpentry
• Lab skills for scientific
computing
– http://software-carpentry.org
– International initiative to
teach basics of software
engineering to
researchers
• The “why” more than
the “how”
– We ran 13 workshops
in 2013 to 600+ learners
34. Incentives are important
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Software
Sustainability
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Courtesy of James Howison and James Herbsleb
Incentives and Integration In Scientific Software Production
Rewrite by original team:
address fragility
Fork to add specific functionality
Maintained separately
Optimised for
hardware
Facilitate hardware
sales
Exploit new techniques /
architectures
35. And money isn’t everything
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Software
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Funding/Staffing
Time
Next expt.
running
Experiment
Running
Analysis of
Data
New experiment
design starts
Maintenance of software
to process data from
physics experiment
36. So beware your bus factor
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Software
Sustainability
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37. Summary of my talk
Institute
Software
Sustainability
www.software.ac.uk
SOFTWAREis…
…areIMPORTANT
everywhere
hard to define
long-lived
context
reasons
people