Greetings, Imperial RSEs!
It’s May, rough winds, darling buds and another community newsletter. If there’s more than a whiff of antiseptic coming from this month’s selections, it’s because the guest editor has lingered too long in the Faculty of Medicine; normal service will resume next month (maybe).
In this newsletter:
The first Imperial College Research Software in Physics event took place on Friday 17th of May, and if you weren’t there you missed a treat. This event, organised by the Imperial Research Software Community and supported by the College’s ICT department, aimed to help researchers to meet others writing or using research software in Physics and learn about resources available to help them do so. And there were chocolate biscuits. Read the full event report for more.
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30 May: Peter Lindsay Memorial Lecture, The AI Revolution: Hype vs Reality
31 May: The 4th conference of Research Software Engineers isn’t until September, but you only have until this Friday if you want to get free entry by signing up as a volunteer. It’s in Birmingham.
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10-12 June: Free 2-topic passes are available for one-day entry to The Festival of AI and Emerging Technology at Kings Cross London:
Listen to, learn from, and engage in debates with the brightest minds on the planet from industry, government and academia. 12 stages of great content will cover topics like: Web 3.0, research & science, health, infrastructure, culture, finance & economy, planet, future or work, ethics, lab to live, cutting edge, the impact of AI and emerging technology
To get the free pass, register here, scroll down and enter the discount code CX19Professors.
15-16 June: Tickets are still available for PyLondinium at Bloomberg’s office in the City of London. You might also like to get your name down for the lunchtime Mithraeum tour they’re running, or just nip out and see it while you’re there!
19 June: Spend a day at the UK Biobank’s annual jamboree at the QE2 Conference Centre in London. UK Biobank holds sets of phenotypic, genomic and imaging data from 500,000 volunteers which are available to health researchers on application; come and find out the latest on how this resource is being used. £20 a ticket, which includes lunch and post-event reception. Last year the lunch was fantastic.
Or you could skip the reception and head over to UCL instead, to catch their RSE event at 5pm. (There’s actually quite a lot of fun summer activity going on in the so-called Knowledge Quarter, if you fancy a break from research software engineering)
A couple of Imperial symposia are coming up in June, which while being quite domain specific may also appeal to research software specialists:
25-27 June: the Software Sustainability Institute present the first European CarpentryConnect event, in Manchester, of particular interest to those delivering and developing research software curricula. Our very own Katerina Michalickova will be leading a session.
8-12 July: Statistics in Medicine Data Dive at Imperial:
Medicine is a source of great challenges to statistics, machine learning and data science. The 2019 Data Dive is a week-long hackathon, looking at data from real medical problems. These problems are provided by medical researchers, and represent topical and pressing challenges. We aim to deploy novel methodology to move toward effective solutions, and to initiate longer-term collaborations. The event is open to all researchers with experience of data analysis, including PhD students, postdoctoral researchers and academics.
More details here.
12 July: PyData London 2019. Mainly about Python tools but also R & Julia.
15-19 July: registration is open for the ARCHER Summer School 2019. This includes a Hands-on Introduction to HPC and Message-passing Programming with MPI. Info and registration.
22-26 July: in Warsaw, Poland: 3rd International Summer School on Deep Learning
2-6 September: 12th European Conference on Python in Science in Bilbao, Spain.
17-19 September: RSE 2019 will be held at the University of Birmingham.
28 September: The Festival of Maintenance in Liverpool. A celebration of those who maintain different parts of our world, and how they do it, recognising the often hidden work done in repair, custodianship, stewardship, tending and caring for the things that matter. And that includes code maintainers everywhere…
17 November: Supercomputing 2019, Denver, Colorado, includes the International Workshop on Software Engineering for HPC-Enabled Research
This month’s pick is 3D Slicer, an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. Use the existing modules (plentiful) or write your own (C++, Python). It’s well supported and constantly updated.
I came across Slicer when trying to do a spot of 3D trachea segmentation using this extension module. The algorithm grows a model of the patient’s airway from a single seed point placed in the trachea, using a chest scan in DICOM or NiFTI format. It’s implemented in C++ wrapped in Python, and can be scripted to run in batch mode using the built-in Python interactor window. Models can be exported in a variety of formats including for 3D printing.
Download at slicer.org or DIY via github.com/Slicer.
If you have a suggestion for software that you’d like to see us feature in this section, please email rse-committee at imperial.ac.uk.
The Crick Networking Fund will support networking activities for collaborations, up to £3K: the next deadline is 3 June.
The Chan-Zuckerberg Initiative is offering $50-$250K for biomedical research open source tools in one year grants to organisations (not individuals). The mystic portal opens 18 June.
Imperial’s Maths for Machine Learning on Coursera is theoretically free to Imperial peeps, although how to access it without charge remains mysterious to the editor. Do write in if you know how! But in the meantime don’t let that put you off; Part One particularly is accessible even for the mathematically rusty, and will have you impressing your friends with terms like eigenbasis before you know it.
As always, keep an eye on this page for in-house up-coming training events. If you have any questions about Software Carpentry or any of the other listed training courses please email Katerina Michalickova.
The Imperial College Advanced Hackspace may be of interest too.
Want to find out about other software development related topics not listed? Contact Jeremy Cohen to discuss.
How to begin data science projects from Research Engineering at the Turing:
Part of the joy of being a data scientist is that we get to mess around in new domains.
Some JupyterHub and Binder excitement from CSVConf held on the 8-9 May
And now, Fortran users can GOTO Jupyter too! <sigh/>
That’s all for this month, and thanks to everyone who suggested links for this edition. If you’d like anything included in the newsletter, have ideas about how it could be improved, or would even like to guest-edit a future edition then just drop us a line at rse-committee at imperial.ac.uk. And if you’re reading this on the web and would like to receive the next newsletter directly to your inbox then please subscribe here.
This edition of the Research Software Community Newsletter was edited by Jazz Mack Smith