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Yearly Archives: 2015

GAP 4.7.9 released

New release of GAP 4.7.9 was announced in the beginning of December 2015. In this guest post (reproduced from here), Alexander Konovalov tells about his work from research software engineering perspective.

This week I was mainly wearing my Research Software Engineer (RSE) hat. RSE support for the GAP system has three related strands: development of the core GAP system; support of package authors and other GAP users; training future users and contributors to the system. They are all important for the thriving community of users and developers, and this week I’ve done something to advance each of them.

First, I’ve prepared a new release of GAP 4.7.9. (more…)

CoDiMa training school: week in tweets

The First CoDiMa Training School in Computational Discrete Mathematics (Manchester, 16th-20th) November) was a success. We will publish a detailed blog post about it shortly. In the meantime, please have a look at this collection of #codima2015 tweets on Storify!

CoDiMa training school is ready to begin!

We are organising the First CoDiMa Training School in Computational Discrete Mathematics, which will take place on November 16th-20th at the University of Manchester. Please see the recently updated school’s page for the programme of the school and further information.

Rebecca Waldecker visited St Andrews

Prof. Rebecca Waldecker visited St Andrews on August 23rd-29th, 2015. From the report by Markus Pfeiffer, “… During her one-week visit to St Andrews, Rebecca Waldecker, Chris Jefferson, and I discussed many ideas around the notion of fixity, the partition backtrack algorithm first published by Leon and the canonical image algorithm. We found it to be a very productive week and agreed to apply to a further grant to make our work into a longer-term project.”

Open Research Funding

This is the fourth part part of Peter Cameron‘s trilogy on open science. For the other parts, see Open Publication, Open Data and Open Software. If you would like to leave comments for the author, please leave them here.

Douglas Adams wrote The Hitch-Hiker’s Guide to the Galaxy as a radio series. It was published in book form as a trilogy, but later he added two further parts. At the start of the first part, the Earth is destroyed. Later we learn that it hasn’t really been destroyed, but at the end of the last part it is destroyed again, and we are led to understand that this time is for real. Presumably he didn’t want to write any more.

More modestly, here is the fourth part of my trilogy on open science. It is devoted to the question How do we acknowledge the source of funding for our research?

At first it seems obvious that we should do this. But as ever I believe that things are not so clear-cut. (more…)

Open Software

This is the third part of Peter Cameron‘s post on Open Publication, Open Data and Open Software (the fourth part of the trilogy, called Open Research Funding, appeared later). If you would like to leave comments for the author, please leave them here.

My thoughts about this were sparked by reading the presidential address to the Royal Statistical Society by Peter Diggle. The title was “Data science and statistics”, and the address covered much more than open software. But one of the points he makes is particularly relevant:

Principally, we learn that a published article is no longer a complete solution to a practical problem. We need our solutions to be implemented in software, preferably open source so that others can not only use but also test and, if need be, improve our solutions. We also need to provide high quality documentation for the software. And in many cases we need to offer an accessible, bespoke user interface.

At a time when some research organisations (even high-status ones) are dispensing with statisticians on the grounds that every researcher has on her desk a computer running Excel, it is necessary to be very clear about what researchers can add. One area where expertise matters is experimental design. (more…)

Open Data

This is the second part of Peter Cameron‘s post on Open Publication, Open Data and Open Software (the fourth part of the trilogy, called Open Research Funding, appeared later). If you would like to leave comments for the author, please leave them here.

I recently wrote about open data on my own blog; some of the points I made there will be repeated.

Open data is an important issue. For example, drug companies invest huge sums of money in new drugs, and have traditionally been reluctant to advertise the failure of a drug in clinical trials. It can be worse; sometimes they can cherry-pick the results of the trials and claim that the drug is useful in some situations. Ben Goldacre and others are campaigning for more transparency in the publication of clinical trials.

More generally, scientific journals tend to have a publication bias towards positive results, so that an important study finding no connection between certain factors may be suppressed, leading to repetition and waste of resources. This has led to calls for all experimental data to be made freely available to all researchers, subject to various safeguards.

I began to think about this when I was asked to comment on a draft concordat proposed by the UK research councils on open data. Here is their definition of research data: (more…)

Open Publication

Peter Cameron is a half-time Professor in the School of Mathematics and Statistics at the University of St Andrews, and an Emeritus Professor of Mathematics at Queen Mary, University of London. His blog is cameroncounts.wordpress.com. Here we are publishing his new blog post which he kindly wrote for our website. It consists of three parts: Open Publication (below), Open Data and Open Software (the fourth part of the trilogy, called Open Research Funding, appeared later). If you would like to leave comments for the author, please leave them here.

The Internet has brought about big changes in the way we do science. Recently, a word very much favoured by science funders is “open”. I want to say a few things about this, under three headings (open publication, open data, open software) which raise different issues for the scientific community.

I write as a pure mathematician here. Some of the issues are not so relevant in mathematics; others are relevant, but perhaps with a twist. There are things which concern all scientific researchers.

Open publication

On the face of it, open publication (accessible to all readers without cost) sounds as harmless as apple pie. But all is not so simple … (more…)

Dima Pasechnik’s visit to Birmingham

Dima Pasechnik’s visit to Birmingham to collaborate with Sergey Shpectorov took place from 22/07/2015 to 24/07/2015. This is a quote from their report on this visit: “The focus of this collaboration is on the improvements to Sergey’s GAP package for computation of axial algebras. These are commutative non-associative algebras generated by idempotents satisfying certain fusion rules. The motivating example is the Griess-Norton algebra for the Monster sporadic simple group. The available programs for computations with axial algebras rely on the linear algebra functions available in GAP. This means that the program cannot handle partial algebras (intermediate stages) over the rationals whose dimension exceeds two-three thousand. At the same time, the algebras that we construct have significant groups of symmetries and, in particular, every partial algebra is a G-module for a certain group G. It is hoped that an efficient implementation of the basic module operations using the known character table of G will allow to increase the limit on the dimension by several orders. It is also hoped that, due to the fundamental nature of the module operations, the new routines will also find applications in many other places.”

Visiting St Andrews (feedback by Nick Loughlin)

Nick Loughlin (Newcastle) visited Alexander Konovalov in St Andrews on September 7th-9th, 2015. We acknowledge very much his feedback, which we are reproducing below:

“Two principal aims of my visit to St Andrews were to get familiar with package design and developing a parallel implementation of existing sequential code. Secondary objectives included discussing the upcoming software carpentry workshop and GAP days in Manchester in November, GAP’s built-in and user-contributed profiling features and creating new objects and methods for them.

We focused on the *philosophy* of the package design good-practice as is usually practiced in the GAP community, and Alexander said this will appear shortly as a blog post on his website; I’ve volunteered to help develop a hands-on tutorial in creating a package using the “example” package as a template. As far as parallel computing goes, we studied the shared-memory model implemented in HPC-GAP and the distributed model that SCSCP package is built around, and implemented some of my code in both so I have now a working example in each.

My secondary objectives were all happily satisfied at least in part. The one thing that we didn’t cover fully was profiling, and Alexander suggested that perhaps this was a sensible subject for a tutorial at the upcoming GAP days.”