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 Olexandr 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 Olexandr 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 Olexandr suggested that perhaps this was a sensible subject for a tutorial at the upcoming GAP days.”
First Joint GAP-SageMath Days
The First Joint GAP-SageMath Days will be held at the University of St Andrews on January 18th-22nd, 2016. The focus of this event will be on improving GAP-SageMath integration and interaction between our systems. Further details will be posted soon!
First CoDiMa Training School in Computational Discrete Mathematics
We have just finalised the date and location for the First CoDiMa Training School in Computational Discrete Mathematics which will take place at the University of Manchester on November 16th-20th, 2015. This school is intended for PhD students and researchers from UK institutions. It will start with the 2-days hands-on Software Carpentry workshop covering basic concepts and tools, including working with the command line, version control and task automation, continued with introductions to GAP and SageMath systems, and followed by the series of lectures and exercise classes on a selection of topics in computational discrete mathematics. The school will finish at Friday lunchtime, with an option to stay for the NBSAN (North British Semigroups and Applications Network) meeting on Friday afternoon.
Travel updates – Summer 2015
Our short research visits programme successfully continues. Since the beginning of the project, we have received 14 applications for travel support, and 12 visits already took place. This is an overview of summer travel activities which were fully or partially funded by CoDiMa after the publication of the previous travel update.
In June, (more…)
Release of Sage 6.8
Sage 6.8 was released on 26 July 2015 and is available for download from the SageMath website. This release closes 351 tickets and incorporates changes made by 95 contributors, including 13 first making their first contribution to Sage. Among other improvements and bugfixes, this Sage release includes also the latest GAP 4.7.8 (June 2015) and some fixes in Sage’s interface to GAP and its packages. Please see the release announcement for further details.
Average order of group elements: a demo of test-driven development in GAP
By Olexandr Konovalov, Research Fellow in the Centre for Interdisciplinary Research in Computational Algebra, University of St Andrews (reproduced from the original post here)
This blog post is based on an improvised demo that I gave at the Newcastle University on May 21st, 2015 during a short visit supported by the CoDiMa project.
Let’s consider the following exercise: for a finite group G, calculate the average order of its element (that is, the sum of orders of its elements divided by the order of the group). We begin with a very straightforward approach, iterating over all elements of the group in question:
gap> S:=SymmetricGroup(10);
Sym( [ 1 .. 10 ] )
gap> sum:=0;
0
gap> for g in S do
> sum := sum + Order(g);
> od;
gap> sum/Size(S);
39020911/3628800
Now assume that we would like to save this fragment of the GAP code and later repeat this calculation for some other groups. (more…)
Short research visits programme begins
We have already funded several trips under our short research visits programme.
Mark Kambites (Manchester) visited St Andrews on 21-23 April 2015 for the initial planning meeting and discussing further collaboration on implementing a tropical algebra/geometry package for GAP, based on his earlier work with Markus Pfeiffer (St Andrews).
Olexandr Konovalov visited Newcastle University on May 21st, 2015 to meet the members of the algebra research group in Newcastle: (more…)