September 17, 2014

The SSI Blog

Reducing the Distance between theory and practice

Polar bears

By Mike Jackson, Software Architect.

Clever theory about how to estimate the density or abundance of wildlife is of limited value unless this theory can be readily exploited and applied by biologists and conservationists. Distance sampling is a widely-used methodology for estimating animal density or abundance and the Distance project provides software, Distance, for the design and analysis of distance sampling surveys of wildlife populations. Distance is used by biologists, students, and decision makers to better understand animal populations without the need for these users to have degrees in statistics or computer science. Distance places statistical theory into the hands of practitioners.

Consultancy
Consultancy, open call, wildlife, statistics, population modelling, environment, biology, conservation
Consultancy

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by m.jackson at September 17, 2014 10:42

September 16, 2014

The SSI Blog

“Is this a good time?” – how ImprompDo can tell when you’re busy

By Liam Turner, PhD student at Cardiff School of Computer Science & Informatics.

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.

Growth in smartphone technology has led to the traditional trawl for information to be devolved down to an individual level. This presents a challenge as traditional methods of making information available depend on when it is ready available, rather than when it is most convenient for a busy user.

Currently users have to work out the best way to get information while still managing their other commitments at the same time, but it would be more useful if this could be managed proactively. This predictive estimation would analyse and arrange itself around its user’s behaviour before it sent them the new information. This forms the backbone of our project in using the technical capabilities of the smartphone to infer interruptibility and so make a decision as to whether to deliver or delay.

Community
author:Liam Turner, Day in the software life, DISL, Android, Artificial Intelligence, Cardiff

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by a.hay at September 16, 2014 09:00

September 15, 2014

The SSI Blog

What makes good code good at EMCSR 2014

By Steve Crouch.

On August 8th 2014, I attended the first Summer School in Experimental Methodology in Computational Research at the University of St. Andrews in Scotland. Run as a pilot for primarily computer scientists, it explored the latest methods and tools for enabling reproducible and recomputable research, and the aim is to build on this successful event and hold a bigger one next year.

The Institute already works with the Summer School organisers in a related project, recomputation.org. Led by Ian Gent, this project aims to allow the reproduction of scientific results generated using software by other researchers, by packaging up software and its dependencies into a virtual machine that others can easily download and run to reproduce those results.

Consultancy
Training
author:Steve Crouch, Consultancy, recomputation.org, recomputation, reproducibility, EMCSR

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by s.crouch at September 15, 2014 13:00

September 11, 2014

SouthGrid

Configuring CVMFS for smaller VOs

We have just configured cvmfs for t2k, hone, mice and ilc after sitting on the request for long time. The main reason for delay was the assumption that we need to change cvmfs puppet module to accommodate non lhc VOs.   It turns out to be quite straight forward with  little effort.
We are using cern cvmfs module and there was an update a month ago so it is better to keep it updated.
  https://github.com/cvmfs/puppet-cvmfs

 Using hiera to pass parameters to module, our hiera bit for cvmfs

   t2k.gridpp.ac.uk:
      cvmfs_server_url: 'http://cvmfs-egi.gridpp.rl.ac.uk:8000/cvmfs/@org@.gridpp.ac.uk;http://cvmfs01.nikhef.nl/cvmfs/@org@.gridpp.ac.uk'
    mice.gridpp.ac.uk:
      cvmfs_server_url: 'http://cvmfs-egi.gridpp.rl.ac.uk:8000/cvmfs/@org@.gridpp.ac.uk;http://cvmfs01.nikhef.nl/cvmfs/@org@.gridpp.ac.uk'
    hone.gridpp.ac.uk:
      cvmfs_server_url: 'http://cvmfs-egi.gridpp.rl.ac.uk:8000/cvmfs/@org@.gridpp.ac.uk;http://cvmfs01.nikhef.nl/cvmfs/@org@.gridpp.ac.uk'
    ilc.desy.de:
      cvmfs_server_url: 'http://grid-cvmfs-one.desy.de:8000/cvmfs/@fqrn@;http://cvmfs-stratum-one.cern.ch:8000/cvmfs/@fqrn@;http://cvmfs-egi.gridpp.rl.ac.uk:8000/cvmfs/@fqrn@'

One important bit is the name of cvmfs repository e.g  t2k.gridpp.ac.uk instead of t2k.org

Other slight hitch is public key distribution of various cvmfs repositories.  Installation of cvmfs also fetch cvmfs-keys-*.noarch rpm which put all the keys for cern based repository into /etc/cvmfs/keys/.

I have to copy publich key for gridpp.ac.uk and desy.de to /etc/cvmfs/keys. It can be fetched from  repository
wget http://grid.desy.de/etc/cvmfs/keys/desy.de.pub -O desy.de.pub
or copied from
https://www.gridpp.ac.uk/wiki/RALnonLHCCVMFS

we  distributed the keys through puppet but outside cvmfs module.
It would be great if some one can convince cern to include public keys of other repositories into cvmfs-keys-* rpm. I am sure that there is not going to be many cvmfs stratum 0s.

Last part of the configuration is to change SW_DIR in site-info.def or vo.d directory
 SW_DIR="/cvmfs/t2k.gridpp.ac.uk"

WNs requires re-yaim  to configure SW_DIR in /etc/profile.d/grid-env.sh.  You can also edit grid-env.sh file manually and distribute it through your favourite configuration management system.





by Kashif Mohammad (noreply@blogger.com) at September 11, 2014 14:09

The SSI Blog

Online psychological therapy for Bipolar Disorder

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.

By nicholas [dot] todd [at] nhs [dot] net (Nicholas Todd), Psychologist in Clinical Training at Leeds Teaching Hospitals NHS Trust.

People with Bipolar Disorder often have problems gaining access to psychological therapy. Online interventions are an innovative solution to this accessibility problem and are recommended in clinical guidelines for mild to moderate anxiety and depression. These interventions provide round-the-clock, evidence based, self-directed support for a large number of people at a reduced cost to the NHS. 

The Living with Bipolar project was funded by Mersey Care NHS Trust and led by myself under the supervision of Professor Fiona Lobban and Professor Steven Jones, from the Spectrum Centre for Mental Health Research, Lancaster University. It was the first randomised controlled trial of an online psychological intervention for Bipolar Disorder to find preliminary evidence that the web-based treatment approach is feasible and potentially effective.

Community
Day in the software life, DISL, author:Nicholas Todd, Lancaster, Leeds, Psychology

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by a.hay at September 11, 2014 09:00

September 09, 2014

The SSI Blog

The Wild Man Game - bringing historic places to life

By Gavin Wood and Simon Bowen, Digital Interaction Group, Newcastle 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.

Heritage organisations, such as museums, and managers of historic sites are increasingly interested in using mobile phones as a way of adding value to visits and directly connecting with the general public. App designers have responded by creating gamified digital experiences by borrowing game mechanics and game elements in an attempt to engage the user.

However, these experiences often fall short and we are given uninteresting treasure hunts that are often more about achieving goals and collecting rewards rather than thinking about and connecting with the heritage space itself. In response, we are exploring how digital play can bring our cherished cultural spaces to life, challenging the typical role for mobile phone apps in such contexts.

Community
author:Gavin Wood, author:Simon Bowen, Day in the software life, DISL, Newcastle, Wildman, Belsay Hall

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by a.hay at September 09, 2014 09:00

September 04, 2014

The SSI Blog

A map of many views - what Google Earth and a 1500 AD chart of Venice have in common

By Juraj Kittler, Assistant Professor of Communication at St. Lawrence University, and Deryck Holdsworth, Professor of Geography at Penn State 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.

Our recent study, published last month in New Media & Society, surveyed the technical approaches adopted by Renaissance artist Jacopo de’ Barbari when he drafted his iconic bird’s-eye view of Venice in the last decade of the fifteenth century. We pointed out some important parallels between this masterpiece of Renaissance mapmaking and the current computer-supported digital representations of urban spaces.

The historical sources that we analysed indicate that de’ Barbari’s map was a composite image stitched together from a multitude of partial views. These were produced by surveyors using a technical device, called the perspectival window, and in a fashion that may be seen as a proto-digital technology. When constructing his two-dimensional image, the artist was intentionally tricking the eye of the observer into seeing a three-dimensional panoply, evoking what has later became known as virtual reality.

Community
author:Juraj Kittler, author:Deryck Holdsworth, Day in the software life, DISL, Virtual Reality, Maps, Venice

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by a.hay at September 04, 2014 09:00

September 02, 2014

The SSI Blog

Super-computing, graphics cards, brains and bees

There's a bit of a buzz about brain simulation and GPUs.By Thomas Nowotny, Professor of Informatics at the University of Sussex.

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.

Computer simulators have transformed almost every aspect of science and technology. From Formula One cars to modern jet engine aircraft, from predicting the weather to the stock market, and to the inner workings of the brain itself, most research and development activities today depend heavily on numerical simulations.

This is thanks to rapid advances over the last decades that have seen computer speeds double every two years. For much of this time, computer speed was raised by both simply shrinking the size of components and doubling the frequency at which central processing units (CPUs) – the workhorse of every computer – would operate. Yet we are now near the limits set by quantum physics that prohibit further advances in this direction. This has lead to a trend to instead focus on parallel architectures, where CPUs still run at the same speed but there are more of them that share the work.

Community
author:Thomas Nowotny, Day in the software life, DISL, Sussex, Bees, Artificial Intelligence

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by a.hay at September 02, 2014 09:00

August 29, 2014

The SSI Blog

Desert Island Hard Disks: Daniel S. Katz

You find yourself stranded on a beautiful desert island. Fortunately, the island is equipped with the basics needed to sustain life: food, water, solar power, a computer and a network connection. Consummate professional that you are, you have brought the three software packages you need to continue your life and research. What software would you choose and - go on - what luxury item would you take to make life easier?

Today we hear from Daniel S. Katz, Senior Fellow at the Computation Institute, University of Chicago & Argonne National Laboratory, and currently Program Director, Division of Advanced Cyberinfrastructure, National Science Foundation.

Following the example of lots of fairy tales, I’ll bend the rules and say that I want a single tool that enables me to do lots of different things: a browser. Yes, this is the equivalent of using my first wish for an infinity of additional wishes. (I wonder how the fable authors will punish me for my conceit in trying to trick them?)

Community
Desert Island Hard Disks, author:Daniel Katz

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by s.hettrick at August 29, 2014 08:43

August 28, 2014

The SSI Blog

Going viral in social media - networks & intercepted misinformation

By Luke Sloan, Matthew Williams and Pete Burnap of the COSMOS Project, Cardiff 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.

It’s any organisations’ worst nightmare. Be it a faulty product or a food scare, the impact of rumour can be significant both for businesses and regulators. This has always been the case, but the advent of social media and proliferation of platforms such as Twitter have enabled faster and more extensive flows of information, thus greatly increasing the speed at which misinformation can spread.

So what happens when a food scare such as the 2013 horse meat scandal comes to the surface? How should industry stakeholders and regulators act? Indeed, is it even possible for them to respond to inaccuracies and properly address public concerns by communicating accurate information through social media?

Community
author:Luke Sloan, author:Matthew Williams, author:Pete Burnap, Day in the software life, DISL, Cardiff, Social Media, Analytics

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by a.hay at August 28, 2014 09:00

August 26, 2014

The SSI Blog

Game Developer - A Walk to Confidence

By Helana Santos, games programmer and developer for Modern Dream.

This article is part of our series Women in Software, in which we hear perspectives on a range of issues related to women who study and work with computers and software.

How does it feel to be a woman in the games industry, you ask? Great, I say! I love working in an industry filled with people passionate about what they do. It is always wonderful to meet game developers making innovative, creative and fun experiences, to meet people who give wings to those creations and make them known around the world, and to engage with those who play the games, provide feedback and build communities around them.

Community
author:Helana Santos, Women in software, Games, Comment, Career development, Modern Dream

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by a.hay at August 26, 2014 13:00

BioC 2014 - the right way to conduct Bioconductor

Last month saw the BioC 2014 conference take place at the Dana-Farber Cancer Institute, Boston, MA. Starting with a Developer Day on July 30th, it continued with a series of talks and workshops until August 1st.

Bioconductor is an R-based open-source, open-development software project. It  provides tools for the analysis and comprehension of high-throughput genomics data. First developed in 2001 by Robert Gentleman, who also co-founded R with Ross Ihaka, it is overseen by a core team based at the Fred Hutchinson Cancer Research Center, alongside several other American and international institutions.

Community
author:Aleksandra Pawlik, BioC, Bioconductor, Bioinformatics, R, Dana-Farber Cancer Institute

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by a.pawlik at August 26, 2014 09:00

August 22, 2014

The SSI Blog

The 20-line script that saves you hours of mind-numbing tedium

By Simon Hettrick, Deputy Director.

Apart from a brief liaison during my undergraduate years, I am cursed with a complete lack of training in programming. When I face problems that are easily solved with some basic coding, I experience the beginner’s dilemma (not unlike the problem with automation): do I choose the frustration entailed in working out how to write a short program to do the work automatically, or the monotony of performing the same simple task a thousand times by hand?

Once you’ve taken a first step into coding, and you see how quickly and efficiently it can change your work, it’s difficult to stop. My epiphany occurred when someone renamed a hundred images for me using a single command line instruction. I was going to make those changes by hand, so this little trick saved me something like an hour of tedious work. In addition to these tricks, I find short programs provide the most compelling reason for researchers to learn a bit about coding. The heavyweight software packages are, of course, very important to research, but the 20-line script that saves you hours of mind-numbing tedium is the real hero of research.

Community
Opinion, author:Simon Hettrick, R, Bash, Coding, Programming

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by s.hettrick at August 22, 2014 13:00

GridPP Storage

Lambda station

So what did CMS say at GridPP33?  Having looked ahead to the future, they came up with more speculative suggestions. Like FNAL's Lambda Station in the past, one suggestion was to look again at scheduling network for transfers, what we might nowadays call network-as-a-service (well, near enough): since we schedule transfers, it would indeed make sense to integrate networks more closely with the pre-allocation at the endpoints (where you'd bringOnline() at the source and schedule the transfer to avoid saturating the channel.) Phoebus is a related approach from Internet2. 

by Jens Jensen (noreply@blogger.com) at August 22, 2014 10:50

August 21, 2014

GridPP Storage

Updated data models from experiments

At the GridPP meeting in Ambleside ATLAS announced having lifetime on their files: not quite like the SRM implementation where a file could have a finite when created, but more like a timer which counts after each access. Unlike SRM, deletion when the file has been not accessed for the set length of time, the file will be automatically deleted. Also notable is that files can now belong to multiple datasets, and they are set with automatic replication policies (well, basically how many replicas at T1s are required.) Now with extra AOD visualisation goodness.

Also interesting updates from LHCb, they are continuing to use SRM to stage files from tape, but could be looking into FTS3 for this. Also discussed the DIRAC integrity checking with Sam over breakfast. In order to confuse the enemy they are not using their own GIT but code from various places: both LHCb and DIRAC have their own repositories, and some code is marked as "abandonware," so determining which code is being used in practice requires asking. This correspondent would have naïvely assumed that whatever comes out of git is being used... perhaps that just for high energy physics...

CMS to speak later.

by Jens Jensen (noreply@blogger.com) at August 21, 2014 11:31