Day in the software life

ArticDEM project

By Daniel S. Katz, Assistant Director for Scientific Software and Applications at the National Center for Supercomputing Applications, University of Illinois Urbana-Champaign.

This article is part of our series: A day in the software life, in which we will be asking researchers from all disciplines to discuss the tools that make their research possible.

A large amount of today’s computational and data science involves combining the execution of many tasks that each run a model or transform data, to build up a multi-component model or a multi-stage data transformation. Most researchers initially do this manually, and then (if they have any programming experience) eventually move to using shell scripts when the manual process gets too painful.  However, shell scripts tend to limit the work to single resources, as they don’t really work well with parallel computing.

An alternative method is to use a system that I’ve been involved in developing: the Swift Parallel Scripting Language. (Note that there’s no relation here to Apple’s Swift, other than that they reused our name.) Swift provides an implicitly parallel and deterministic programming model, which applies…

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Arab poetry, use of SolrBy Swithun Crowe, Research Computing, University Library, University of St Andrews

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their or someone else’s research possible.

Most of the data I work with is in XML format—Text Encoding Initiative (TEI)— either handwritten or edited using XForms: XML exported from other programs such as Zotero, or taken from third party web services, such as the Library of Congress authority files. To search these files, I use Apache's Solr document search engine, usually communicating with it via PHP's Solr extension. The source XML documents are transformed into a form which Solr can ingest using XSLT. 

The examples in this…

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TexGen: Modelling textilesBy Louise Brown, Senior Research Fellow at the University of Nottingham and EPSRC Research Software Engineer Fellow

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their or someone else’s research possible.

Composite materials are increasingly used in a wide range of applications, particularly in the aerospace and automotive industries. Here their low weight and high strength are a significant advantage, and they will contribute to achieve targets for reduction of greenhouse gas emissions by decreasing the weight of components and therefore energy used. They comprise a reinforcement embedded in a matrix and may be made up from many combinations of materials, typically glass or carbon fibre in a polymer matrix.  Often the reinforcements are produced in the form of textiles for ease of handling, either layering ‘2D’ weaves to give the required thickness or by creating complex ‘3D’ weaves which can enhance properties and reduce manufacturing time.

Given the many possible combinations of reinforcement textiles and matrix materials, it is beneficial to be able to model these systems so that simulations can be run to predict properties for both manufacturing processes and the final…

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Software and decision-making, oncologyBy Jakob Nikolas Kather, MD, MSc, National Center for Tumor Diseases (NCT), Heidelberg, Germany.

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

Diagnosis and treatments in oncology

Cancer is a common disease and one of the leading causes of death. If detected at an early stage, some types of cancer can be cured by surgery, but often a tumour is detected at an advanced stage, and its cells have already spread throughout the body. Although many of these patients cannot be completely healed, several different treatment options are available. These treatments make a difference for cancer patients: they can significantly prolong life and often reduce symptoms as well. For each patient, we face the question: which treatment option is optimal at the current point of the disease? Clinical trials in the last decades are providing us with guidance in many situations. Often, there is an established "state of the art" for a treatment that has been shown to be superior to other options. However, as the arsenal of treatment options keeps growing, it is increasingly difficult to compare all options under all circumstances. Also, on the other hand, novel and more…

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Grassroot mappingBy Karen Anderson, University of Exeter, and David Griffiths, FoAM Kernow

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

Smartphones have emerged as powerful research tools for collecting scientific data because they are equipped with a broad suite of sensors (e.g. cameras, microphones, light sensors, accelerometer, compass, gyroscope, and GPS) and on-board microcomputers and are widely used globally. Many smartphones are designed to service the information requirements of multinational developers—they are location-aware—, and applications downloaded by users can transmit information back to providers. This capability can be exploited through the programmable nature of smartphones: sensors developed to supply  location-based services to providers can now be hacked using readily available computing resources. One such opportunity that remains untapped is the smartphone as a remote sensing imaging device that can be deployed in conjunction with rapidly developing lightweight drone technology.

We undertook a short project to explore the…

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Gaia artist's impresion
Gaia artist's impression. Credits: ESA/ATG MEDIALAB;
Background Image: ESO/S. Brunier, June 2013

By Francesca De Angeli, in collaboration with Marco Riello, Gregory Holland, Patrick Burgess and Paul Osborne.

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

On 19 December 2013, at 09:12:19 UTC, a spacecraft containing the Gaia satellite was launched from Europe's Spaceport in French Guiana. The Gaia satellite reached its stable operational orbit around L2 (approximately 1.5 million km from the Earth) about one month later. Since then, a continuous stream of data has been downloaded for further processing on ground. This data includes broad-band photometry and low-resolution spectra for all sources brighter than magnitude 20 and high-resolution spectra for sources brighter than magnitude 16.

The Gaia focal-plane assembly is the largest ever developed for a space application, with…

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Figure 1: Inspect your raw mass spectra and run tools from within the OpenMS visualisation tool TOPPView
Figure 1: Inspect your raw mass spectra and run tools
from within the OpenMS visualisation tool TOPPView

By Timo Sachsenberg and Oliver Kohlbacher, University of Tübingen

This article is part of our series A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

High-throughput mass spectrometry has become a versatile technique to tackle a large range of questions in the life sciences. Being able to quantify diverse classes of biomolecules opens the way for improved disease diagnostics, elucidation of molecular structure and investigation of cellular pathways. In an interplay with other open-source software, OpenMS enables powerful workflows to transform biological data into meaningful knowledge.

In recent years, mass spectrometry has gained significant attention in the life sciences. The mass spectrometer determines the…

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By Christopher Hunt, Lead Developer at i-DAT, Plymouth University.

This article is part of our series: a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.

Organisations use a wide range of methods to measure how audiences engage with a cultural experience. These include audience surveys, focus groups, interviews, blog posts and a range of more experimental and creative methods. However, most of these methods are expensive, use a great deal of resources and lack a standardised set of metrics. Often they focus on evaluation data and lose sight of the users’s incentives for leaving this feedback in the first place.

Artory, part of i-DAT’s on-going open source research project, Qualia, attempts to tackle this through the use of data driven smartphone applications and open-source data analytics systems. It is developed as an incentivised “what’s on” app for cultural events in Plymouth, which enables users to leave feedback and cultural organisations to understand their audiences better.

Central to the development is the recognition of user motivation and the requirement for independent user driven evaluation data, or rather, automated data collection and analytics, which saves…

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By Alina Călin, Chief Research Officer at MIRA Rehab, and Dr. Emma Stanmore, Lecturer in Nursing at the University of Manchester.

This article is part of our series: a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.

Gamification is the next big innovation in the field of rehabilitation, and makes use of remote sensors and aspects of video game design to engage patients in their rehab and make it more accessible, which in turn encourages participation and so keeps costs down.

Exergames was our attempt to develop this possibility, and is a successful collaboration between The University of Manchester, Central Manchester University Hospitals NHS Foundation Trust and MIRA REHAB Ltd. It lead to the development of several exergames, designed to use the Microsoft Kinect sensor, and all of which use exercises known to help prevent falls and improve function in older people.

Falls are a common problem for the UK’s ever growing ageing population. Every year, around 10% of older people are treated by a doctor due to a fall and approximately 100,000 older people in Europe die from a fall related injury each year, according to 2013 data by the European Association for Injury Prevention and Safety Promotion (Eurosafe).

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One of the biggest problems facing researchers is the best way to share their research to as broad an audience as possible. In fact, it’s this important part of research impact, or how academic research makes a contribution to wider society, that is used as one of the yardsticks to judge the success of a research project.

The Software Sustainability Institute has been addressing this problem through its blog, which regularly features articles by researchers from across the disciplines, all of whom have used software to enhance and develop their work. The question, however, was how to make all this fascinating material and the researchers’ output even more accessible.

With this in mind, the Institute has launched its own Android phone app. This displays the latest content from the site in an easy to read mobile and tablet-friendly format and lets users access the site's complete blog archive. It also allows offline functionality and opens the content in its own streamlined interface rather than through a browser.

This includes blogs about making Dinosaurs and ancient spiders walk again, Google Glass in the operating theatre, tracking the…

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