9190581261_7cefddac29_z.jpgBy Gillian Law.

New Research Software Engineer (RSE) fellow Leila Mureşan will be using her microscopy image analysis skills to develop software for biologists, physicists and mathematicians as part of her RSE fellowship.

As a scientific software engineer at the University of Cambridge’s Cambridge Advanced Imaging Centre (CAIC) Mureşan designs and implements software to analyse imaging data. Computational microscopy uses software and computation to get around the limitations of optical systems, she says. Mureşan trained as a computer scientist in Romania, and went on to study the analysis of single molecule microscopy images with application to ultra-sensitive microarrays for her PhD at the Johannes Kepler University in Linz, Austria.  After doing post-doctoral research at the École Normale Supérieure in Paris and the Centre de Génétique Moléculaire at CNRS in Gif-sur-Yvette France she joined CAIC as it launched in 2014.

Mureşan has developed a particular interest in lightsheet microscopy imaging, which allows developmental biology scientists to follow the development of an embryo in a “fast and gentle” way over several days, she says. This process naturally produces an enormous amount of data, which requires software that can handle the analysis. Mureşan also works on super resolution microscopy, which increases resolution by an order of magnitude.

“I like this area a lot. The…

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5148710483_a9c0c77da4_z.jpgBy Gillian Law.

Joanna Leng is a computational scientist and visualisation expert who will focus her Research Software Engineer (RSE) fellowship on bringing research computing to imaging. She believes that some areas of the imaging community are failing to fully pick up on the potential of computing, and Leng hopes to transform the use of technology in the field to accelerate scientific discovery.  

Leng will develop software on campus at the University of Leeds for three new imaging techniques, collaborating with Sven Schroeder for spectral X-ray imaging, Rik Drummond-Brydson for spectral electron microscopy imaging and Michelle Peckham for super-resolution light microscopy, in partnership with Diamond Light Source, SuperSTEM and the SCI Institute in Utah, USA.

With 20 years of experience in imaging, visualisation and High Performance Computing (HPC), Leng brings a broad network of contacts to her fellowship, having been interested in imaging and visualisation since her undergraduate degree in biophysics at the University of Leeds. After university, she retrained in computer science, looking for a better paid career, only to “realise at the last minute that I couldn’t face working for one of the banks!” That moment of clarity “brought her to her senses”, and she moved to work in visualisation at the University of Manchester at the Computer Graphics Unit that shortly afterwards hosted an academic…

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8897696003_c549d5e58e_z.jpgBy Gillian Law.

Physicist and new RSE fellow Phil Hasnip specialises in software to predict materials properties, and in making that software accessible to all researchers.

Hasnip believes that most physics problems end up being materials problems. “You want a better battery? You need a better battery material. A better turbine? You need a stronger material for the blades. Wherever you look, materials are key.” says Hasnip. Running experiments on these potential new materials is expensive and difficult, so using computational methods to either predict what a material might do, or to explain what is going in on experiments, is incredibly useful.

Having completed his PhD at the University of Cambridge followed by several post doc positions, Hasnip is now at the University of York where he is developing tools including the CASTEP program which uses quantum mechanics to compute the properties of materials and chemicals.

There is a constant tension in research between taking the time to improve the tools used and getting research results, Hasnip says, and he hopes to use his fellowship as an opportunity to focus on improving the tools available and making them more accessible to all researchers, rather than just those with computational skills. “Many of the tools being used aren’t really high enough quality. They’ve been developed by researchers who are good scientists…

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8523276256_b32bcc2df2_z.jpgBy Gillian Law

Research software ought to be easier to use, says newly appointed 2018 RSE Fellow Jeremy Cohen.

A computer scientist by background, Cohen has spent the bulk of his career to date in the Department of Computing at Imperial College London, supporting scientists in their research. “I’ve worked in a lot of domains, offering applied computing research to support scientists in various areas” he says. This has included using high-performance computing platforms and cloud-computing infrastructure.

“Of course, in general scientists tend to have some computing knowledge, but they often have very much a domain-focused view,” Cohen says. He aims to make their codes easier to access and use. Even if the scientist could do it themselves, they may end up doing it in a more complicated or inefficient way if they’re learning as they go along, “so I aim to make life simpler and let them focus on the science, not the computing.” Good code can also help scientists to make their modelling and simulation work more accessible to their broader team. “There’s often a lot of post processing needed on a model or simulation and so what I’m trying to do is bridge the gaps, or glue together different processes, and simplify complex things. Again, we’re working with people who are very experienced and they can do this work themselves, but we can help them to do it much more effectively.” That opens up the code to…

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Regular Institute collaborator Dr. Jeffrey Carver of the University of Alabama is conducting a couple of studies relating to the way that people develop research software. These will help provide the community with a better understanding of how different practices, including code review and software metrics are being used in the development of research software.

If you'd like to provide input into these studies, please participate in the following web surveys (each of which will take approximately 15 minutes to complete): 

Code review survey (in conjunction with Nasir Eisty of the University of Alabama) : https://universityofalabama.az1.qualtrics.com/jfe/form/SV_bBdeMr08ix8YbXL

Software metrics survey (in conjunction with Dr. George Thiruvathukal from Loyola University-Chicago): https://universityofalabama.az1.qualtrics.com/jfe/form/SV_darjzw2JlY3OXY1

 

Your participation is completely anonymous and voluntary.  You are free not to participate or stop participating any time before you submit your answers. Both research studies have been approved by the University of Alabama Institutional Review Board.

By Simon Hettrick 

Next week, we will be hearing from the successful applicants to last year’s RSE Fellowship, funded by the EPSRC. The Fellows are exceptional individuals in the software field who demonstrate leadership and have combined expertise in programming and a solid knowledge of the research environment.

We’ll first hear from Jeremy Cohen who believes that “research software ought to be easier to use” and will describe his plans to help build communities of RSEs. We’ll hear why Phil Hasnip believes that most physics problems end up being materials problems. Joanna Leng will describe her desire to bring research computing techniques into the imaging community. Finally, we’ll hear from Leila Mureşan who will focus on the field of microscopy imaging.

The EPSRC has recognised the importance of investing in software development and the development of skills and career development for those engaged in software engineering. It is these aspects that this RSE Fellowship addresses. The Software Sustainability Institute and the RSE community campaigned for the development of this Fellowship so, and we are very happy to welcome the new RSE Fellows!

cardforfellows(hols2018).jpgEveryone at the Software Sustainability Institute wishes our friends and colleagues all the best for the holiday season.

In a nutshell, this year has seen the announcement of a wonderful new set of Fellows, a second edition of the RSE conference, even more events, Software and Data Carpentry workshops, and Open Call projects.

After a busy year, we need a little break to get ready for everything we plan to do in  2018, like our Collaborations Workshop 2018. So please excuse us while we switch off our email and social media from the 23rd December to the 3rd January.  

Enjoy the festivities!

We would like to invite everyone working on research software in the Netherlands to complete the RSE survey and spread the word.

The Netherlands Research Software Engineer community (NL-RSE) was started to gain insight into the various communities of RSEs in the Netherlands and increase the interaction between them. The RSE surveys in the UK in 2016 and 2017 [1, 2] have allowed to gain valuable insights and spread the word about the RSE movement. That is why the Netherlands eScience CenterePLAN (Platform of eScience/Data Research Centres in the Netherlands), NL-RSE, and the UK RSE Association are organising this survey for 2017 in the Netherlands.

The study is conducted by the University of Southampton on behalf of the Software Sustainability Institute and complies with University of Southampton ethics guidelines (reference no.: ERGO/FPSE/30610). The investigators are Simon Hettrick and Olivier Philippe. Contacts in the Netherlands are Ben van Werkhoven and Tom Bakker from the Netherlands eScience Center.

[1]: See RSE State of the Nation Report 2017, page 21.

[2]: See UK-…

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The Software Sustainability Institute and zaf-RSE invite anyone coding in and for academia in South Africa to complete this survey on research software. 

As of now there is not much knowledge about the community of those in research and science who develop software. This survey aims to gain valuable insights into this community in order to support research funders and other institutions to develop strategies and funding programs as well as policies.

Last and this years’ UK surveys [1, 2] allowed to gain valuable insights. We would like to build on the momentum gained in the UK RSE community and help to create a voice for the South African RSE community. Similar surveys will be conducted in Canada, Australia, Norway, the Netherlands, the USA and again in the UK. For reasons of comparability, this survey was closely coordinated with the others. We thank Prof Ilani Loubser from the North-West University's Space Physics programme for working with the NWU eResearch Initiative to provide South African context to the survey.

This survey gives South African researchers and scientist the opportunity to make their point of view and experiences be heard, and thus be part of the development of this community. It would be also very helpful if you could spread the word to others who develop software in the South African research landscape, or anyone who employs software experts in the South African academic landscape.

There are ca. 65 questions in this survey. It takes about 10 - 15 minutes to complete. Please note that this research is not compulsory and even if you decide to participate you can withdraw at any…

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As part of our on-going effort to collect information about RSEs in different countries, the SSI and de-RSE have created a specific version of the UK RSE survey for Germany (more information can be found here). 

Participants are needed for this survey on research software and people writing scientific software for Germany. If you are coding in and for academia in Germany then complete the survey and help us spread the word. You can also access a german version of the survey.

As of now there is not much knowledge about the community of those in research and science who develop software. This survey aims to gain valuable insights into this community in order to support research funders and other institutions to develop strategies and funding programs as well as policies.

Last and this years’ UK surveys [1, 2] allowed to gain valuable insights. To continue our success with this campaign, we need to track how the community evolves at other places. Simultaneously, similar surveys will be conducted in Canada, Australia, Norway, the Netherlands, the USA and South Africa. For reasons of comparability, this survey was closely coordinated with the others.

This survey gives German researchers and scientists the opportunity for their point of view and experiences to be heard and thus be part of the development of this community. It would be also very helpful if you could spread the word to others who develop…

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