1. How an RSE can benefit your projects:
Good (enough) practice in Research Computing
Dr James Grant
Plant Lab Seminar
24th November 2017
Hi, I’m me

2. What is an RSE? Expertise in research and software engineering
(Should) understand the needs of researchers and practices that can benefit research
Central
Supports training, research software development and …
Local
Primarily work on software development for a single project
Isambard

3. Computational Chemistry focus Validating/Benchmarking VASP:
Isambard – GW4 Tier 2 HPC:
Computational Chemistry focus
Validating/Benchmarking VASP:
Phase 1 - x86/GPU/Phi
Phase 1 – Arm prototype
Phase 2 – arriving 2018
Your favourite codes?
Isambard

4. Co-ordinate group training Assist development/code review
Within Bath:
Co-ordinate group training
Assist development/code review
One-to-one training
Collaborate on grant applications and projects
Other

5. Co-ordinate group training Assist development/code review
Within Bath:
Co-ordinate group training
Assist development/code review
One-to-one training
Collaborate on grant applications and projects
Other

6. Good (enough) practice in Research Computing1
What constitutes good practice in research computing?
Why should we do it? (Carrot shaped sticks)
‘Okay, let’s say I believe it, how can you help?’
[1] Wilson G, et al (2017) Good enough practices in scientific computing. PLoS Comput Biol13(6): e

7. What constitutes good practice in research computing?
Data management
Software
Collaboration
Project Organisation
Track Changes
Manuscripts
[1] Wilson G, et al (2017) Good enough practices in scientific computing. PLoS Comput Biol13(6): e

8. What constitutes good practice in research computing?
Data management:
Back-up
Friendly data, readable
Easy to analyse
Record workflows
Publish data
Software:
What is it? Document
How to use it? Tutorials
Modularise; don’t repeat yourself
Use libraries; don’t reinvent the wheel
Test/validate
[1] Wilson G, et al (2017) Good enough practices in scientific computing. PLoS Comput Biol13(6): e

9. Why should we do it? Availability of computer code
Authors must make available upon request, to editors and reviewers, any previously unreported custom computer code used to generate results that are reported in the paper and central to its main claims. Any practical issues preventing code sharing will be evaluated by the editors who reserve the right to decline the paper if important code is unavailable.
Upon publication, Nature Journals consider it best practice to release custom computer code in a way that allows readers to repeat the published results.
For all studies using custom code that is deemed central to the conclusions, a statement must be included in the Methods section, under the heading "Code availability", indicating whether and how the code can be accessed, including any restrictions to access.
[2]

10. There are also some carrots
Reproducibility
Use scripts, for data analysis workflows
Automate == efficiencies
Data processing and plotting
Re-use
Submit with/alongside data
Testable, reviewers can follow your analysis
Usable/Citable by others

11. How can RSEs help your research?
Attribution: By Jsslee - Own work, CC BY-SA 4.0,
Original:

12. How can RSEs help your research?
Share Skills and Knowledge
Group/individual training
Work with you on your code
Identify opportunity for collaborations, from proposal onwards
Attribution: By Jsslee - Own work, CC BY-SA 4.0,
Original:

13. How can RSEs help your research?
Consultancy:
Review code
Advise on practice
Port codes/analysis to HPC
Suggest training
Work with you
Attribution: By Jsslee - Own work, CC BY-SA 4.0,
Original:

14. How can RSEs help your research?
Collaboration:
Identify opportunity for joint RA/PDRAs
Develop proposals with you
CI invested in the project
Time split between RSE team learning and research group developing and training
Attribution: By Jsslee - Own work, CC BY-SA 4.0,
Original:

15. How can RSEs help your research?
Sustainability:
Usable codes for the community
Must be maintainable after project
Software must be understandable by domain researchers
Researchers must acquire skills to maintain software
Attribution: By Jsslee - Own work, CC BY-SA 4.0,
Original:

16. Useful Links & References
Best practises for scientific computing:
Good enough practises in scientific computing:
The book: Effective Computation in Physics: Field Guide to Research with Python
(Don’t be put off the title, for physics read research)
[1] Wilson G, et al (2017) Good enough practices in scientific computing. PLoS Comput Biol13(6): e
[2]