This paper is open, executable and reproducible: the whole process of writing this paper is captu... more This paper is open, executable and reproducible: the whole process of writing this paper is captured in the source control repository hosting both the source of the paper, supplementary codes and data; we are providing setup for several experiments on which we were working; finally, we try to describe what we have achieved during the week of the school in a way that others may reproduce (and hopefully improve) our experiments.
This paper investigates the reproducibility of computational science research and identifies key ... more This paper investigates the reproducibility of computational science research and identifies key challenges facing the community today. It is the result of the First Summer School on Experimental Methodology in Computational Science Research. First, we consider how to reproduce experiments that involve human subjects, and in particular how to deal with different ethics requirements at different institutions. Second, we look at whether parallel and distributed computational experiments are more or less reproducible than serial ones. Third, we consider reproducible computational experiments from fields outside computer science. Our final case study looks at whether reproducibility for one researcher is the same as for another, by having an author attempt to have others reproduce their own, reproducible, paper. This paper is open, executable and reproducible: the whole process of writing this paper is captured in the source control repository hosting both the source of the paper, supplementary codes and data; we are providing setup for several experiments on which we were working; finally, we try to describe what we have achieved during the week of the school in a way that others may reproduce (and hopefully improve) our experiments.
Social network sites (SNSs) and other online social networks such as Facebook and Twitter represe... more Social network sites (SNSs) and other online social networks such as Facebook and Twitter represent a huge source of data for research in many fields, including sociology, medicine, anthropology, politics and computer science. Such sites may contain sensitive information and care needs to be taken when designing experiments or collecting SNS data. We outline some of the potential ethical concerns, describe our efforts to develop best practices, and solicit help with outstanding challenges.
Social Network Sites (SNSs) are used for sharing personal data and delivering personalised servic... more Social Network Sites (SNSs) are used for sharing personal data and delivering personalised services to hundreds of millions of users, and thus represent an important sector of the Digital Economy. Measuring and collecting data from SNSs is crucial for research and development of new services, but the sensitive and personal nature of these data means that great care must be taken by researchers when conducting SNS studies.
Mass spectrometry, in the past five years, has increased in speed, accuracy and use. With the abi... more Mass spectrometry, in the past five years, has increased in speed, accuracy and use. With the ability of the mass spectrometers to identify increasing numbers of proteins the identification of undesirable peptides (those not from the protein sample) has also increased. Most undesirable contaminants originate in the laboratory and come from either the user (e.g. keratin from hair and skin), or from reagents (e.g. trypsin), that are required to prepare samples for analysis. We found that a significant amount of MS instrument time was spent sequencing peptides from abundant contaminant proteins.
Facebook and other social network sites (SNSs) are used by hundreds of millions of people daily. ... more Facebook and other social network sites (SNSs) are used by hundreds of millions of people daily. 1 With such a large number of social interactions being made and recorded digitally, it is not surprising that researchers from many fields in the humanities and both physical and social sciences have exploited this rich source of data, with one recent survey listing 410 social science papers studying the Facebook SNS alone (W ilson et al. 2012). This includes HCI researchers, who have studied, for instance, mobile SNSs to understand location- ...
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Papers by Luke Hutton