Documenting numerical experiments in support of the Coupled Model Intercomparison Project Phase 6 (CMIP6)

Numerical simulation, and in particular simulation of the earth system, relies on contributions from diverse communities, from those who develop models to those involved in devising, executing, and analysing numerical experiments. Often these people work in different institutions and may be working with significant separation in time (particularly analysts, who may be working on data produced years earlier), and they typically communicate via published information (whether journal papers, technical notes, or websites). The complexity of the models, experiments, and methodologies, along with the diversity (and sometimes inexact nature) of information sources, can easily lead to misinterpretation of what was actually intended or done. In this paper we introduce a taxonomy of terms for more clearly defining numerical experiments, put it in the context of previous work on experimental ontologies, and describe how we have used it to document the experiments of the sixth phase for the Coupled Model Intercomparison Project (CMIP6). We describe how, through iteration with a range of CMIP6 stakeholders, we rationalized multiple sources of information and improved the clarity of experimental definitions. We demonstrate how this process has added value to CMIP6 itself by (a) helping those devising experiments to be clear about their goals and their implementation, (b) making it easier for those executing experiments to know what is intended, (c) exposing interrelationships between experiments, and (d) making it clearer for third parties (data users) to understand the CMIP6 experiments. We conclude with some lessons learnt and how these may be applied to future CMIP phases as well as other modelling campaigns

Do cognitive aids reduce error rates in resuscitation team performance? : trial of emergency medicine protocols in simulation training (TEMPIST) in Australia

Background: Resuscitation of patients with time-critical and life-threatening illness represents a cognitive challenge for emergency room (ER) clinicians. We designed a cognitive aid, the Emergency Protocols Handbook, to simplify clinical management and team processes. Resuscitation guidelines were reformatted into simple, single step-bystep pathways. This Australian randomised controlled trial tested the effectiveness of this cognitive aid in a simulated ER environment by observing team error rates when current resuscitation guidelines were followed, with and without the handbook. Methods: Resuscitation teams were randomised to manage two scenarios with the handbook and two without in a high-fidelity simulation centre. Each scenario was video-recorded. The primary outcome measure was error rates (the number of errors made out of 15 key tasks per scenario). Key tasks varied by scenario. Each team completed four scenarios and was measured on 60 key tasks. Participants were surveyed regarding their perception of the usefulness of the handbook. Results: Twenty-one groups performed 84 ER crisis simulations. The unadjusted error rate in the handbook group was 18.8% (121/645) versus 38.9% (239/615) in the non-handbook group. There was a statistically significant reduction of 54.0% (95% CI 49.9–57.9) in the estimated percentage error rate when the handbook was available across all scenarios 17.9% (95% CI 14.4–22.0%) versus 38.9% (95% CI 34.2–43.9%). Almost all (97%) participants said they would want to use this cognitive aid during a real medical crisis situation. Conclusion: This trial showed that by following the step-by-step, linear pathways in the handbook, clinicians more than halved their teams’ rate of error, across four simulated medical crises. The handbook improves team performance and enables healthcare teams to reduce clinical error rates and thus reduce harm for patients

The common information model for climate modelling digital repositories: The metafor project

A poster highlighting the common information model for climate modelling digital repositorie

Dictator Games: A Meta Study

Over the last 25 years, more than a hundred dictator game experiments have been published. This meta study summarizes the evidence. Exploiting the fact that most experiments had to fix parameters they did not intend to test, the meta study explores a rich set of control variables for multivariate analysis. It shows that Tobit models (assuming that dictators would even want to take money) and hurdle models (assuming that the decision to give a positive amount is separate from the choice of amount, conditional on giving) outperform mere meta-regression and OLS

Adding 6 months of androgen deprivation therapy to postoperative radiotherapy for prostate cancer: a comparison of short-course versus no androgen deprivation therapy in the RADICALS-HD randomised controlled trial

Background Previous evidence indicates that adjuvant, short-course androgen deprivation therapy (ADT) improves metastasis-free survival when given with primary radiotherapy for intermediate-risk and high-risk localised prostate cancer. However, the value of ADT with postoperative radiotherapy after radical prostatectomy is unclear. Methods RADICALS-HD was an international randomised controlled trial to test the efficacy of ADT used in combination with postoperative radiotherapy for prostate cancer. Key eligibility criteria were indication for radiotherapy after radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to radiotherapy alone (no ADT) or radiotherapy with 6 months of ADT (short-course ADT), using monthly subcutaneous gonadotropin-releasing hormone analogue injections, daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as distant metastasis arising from prostate cancer or death from any cause. Standard survival analysis methods were used, accounting for randomisation stratification factors. The trial had 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 80% to 86% (hazard ratio [HR] 0·67). Analyses followed the intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov, NCT00541047. Findings Between Nov 22, 2007, and June 29, 2015, 1480 patients (median age 66 years [IQR 61–69]) were randomly assigned to receive no ADT (n=737) or short-course ADT (n=743) in addition to postoperative radiotherapy at 121 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 9·0 years (IQR 7·1–10·1), metastasis-free survival events were reported for 268 participants (142 in the no ADT group and 126 in the short-course ADT group; HR 0·886 [95% CI 0·688–1·140], p=0·35). 10-year metastasis-free survival was 79·2% (95% CI 75·4–82·5) in the no ADT group and 80·4% (76·6–83·6) in the short-course ADT group. Toxicity of grade 3 or higher was reported for 121 (17%) of 737 participants in the no ADT group and 100 (14%) of 743 in the short-course ADT group (p=0·15), with no treatment-related deaths. Interpretation Metastatic disease is uncommon following postoperative bed radiotherapy after radical prostatectomy. Adding 6 months of ADT to this radiotherapy did not improve metastasis-free survival compared with no ADT. These findings do not support the use of short-course ADT with postoperative radiotherapy in this patient population

Duration of androgen deprivation therapy with postoperative radiotherapy for prostate cancer: a comparison of long-course versus short-course androgen deprivation therapy in the RADICALS-HD randomised trial

Background Previous evidence supports androgen deprivation therapy (ADT) with primary radiotherapy as initial treatment for intermediate-risk and high-risk localised prostate cancer. However, the use and optimal duration of ADT with postoperative radiotherapy after radical prostatectomy remains uncertain. Methods RADICALS-HD was a randomised controlled trial of ADT duration within the RADICALS protocol. Here, we report on the comparison of short-course versus long-course ADT. Key eligibility criteria were indication for radiotherapy after previous radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to add 6 months of ADT (short-course ADT) or 24 months of ADT (long-course ADT) to radiotherapy, using subcutaneous gonadotrophin-releasing hormone analogue (monthly in the short-course ADT group and 3-monthly in the long-course ADT group), daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as metastasis arising from prostate cancer or death from any cause. The comparison had more than 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 75% to 81% (hazard ratio [HR] 0·72). Standard time-to-event analyses were used. Analyses followed intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov , NCT00541047 . Findings Between Jan 30, 2008, and July 7, 2015, 1523 patients (median age 65 years, IQR 60–69) were randomly assigned to receive short-course ADT (n=761) or long-course ADT (n=762) in addition to postoperative radiotherapy at 138 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 8·9 years (7·0–10·0), 313 metastasis-free survival events were reported overall (174 in the short-course ADT group and 139 in the long-course ADT group; HR 0·773 [95% CI 0·612–0·975]; p=0·029). 10-year metastasis-free survival was 71·9% (95% CI 67·6–75·7) in the short-course ADT group and 78·1% (74·2–81·5) in the long-course ADT group. Toxicity of grade 3 or higher was reported for 105 (14%) of 753 participants in the short-course ADT group and 142 (19%) of 757 participants in the long-course ADT group (p=0·025), with no treatment-related deaths. Interpretation Compared with adding 6 months of ADT, adding 24 months of ADT improved metastasis-free survival in people receiving postoperative radiotherapy. For individuals who can accept the additional duration of adverse effects, long-course ADT should be offered with postoperative radiotherapy. Funding Cancer Research UK, UK Research and Innovation (formerly Medical Research Council), and Canadian Cancer Society

2017 Usage Report for the IPCC DDC at CEDA

<p>This report provides details of how the DDC web site, ipcc-data.org, was used in the 12 months from January 1^st 2017 to December 31^st 2017. The information presented here is generated using the Google Analytics service; providing a range of different statistics that cover both temporal and spatial trends. Only sessions which persist for longer than 10 seconds have been used in this analysis for consistency with the previous usage reports for TGICA. The Google Analytics statistics have also been filtered to remove robotic and other automated behaviour.</p

Portable Infrastructure for the Metafor Metadata System

PIMMS (Portable Infrastructure for the Metafor Metadata System) provides institutions with tools to capture information about the workflow of running simulations from the design of experiments to the implementation of experiments via simulations running models. PIMMS uses the Metafor methodology for simulation documentation which consists of a common information model (CIM), a set of controlled vocabularies (CV) and software tools. PIMMS software tools provide for the creation and consumption of CIM content via a web infrastructure and portal.PIMMS will refactor the “CMIP5 questionnaire” metadata management tool, that is collecting climate model metadata for the CMIP5 model inter-comparison project, so that it can be more easily portable into stand alone installations within the university environment and customised to address the specific requirements of individual research groups. Initial model descriptions may take time to complete but once they have been cre ated the PIMMS infrastructure can be used to document subsequent variations by describing only those elements that are changed. An established PIMMS infrastructure will fit seamlessly into the research metadata workflow and significantly reduce subsequent documentation effort. The key to the customisation of PIMMS is in the modularity of its tools and the clear separation of structure (CIM) from content (CV). The PIMMS project will extend the CMIP5 controlled vocabulary to encompass descriptions of paleoclimate models and will also demonstrate how the CIM can be used to document an Integrated Assessment Model (IAM). This proof of concept prototype will create a new controlled vocabulary in collaboration with Ermitage and use it to reconfigure PIMMS to collect metadata in a different discipline. PIMMS will further explore how the CV that is used to configure PIMMS may be of further use to our stake holders and the wider JISC community through the development of the Uni versity of Cambridge chemicaltagger tool. PIMMS will provide a local portal so that research groups can view and search their own content, as well as publish their metadata content to institutional, national and international services. In addition PIMMS will also include data node software so that data documented with PIMMS can also be published to the web, both locally, and to national and international services

Integrating PIMMS into the Simulation Workflow

The workflow of running simulations, converting from model data format to a common data format and then making model data available to the community contain many different actions. At some point along the way we expect the scientist to pause and document what they did. In an ideal world model documentation should happen early in this workflow however in practice models and simulations are very often documented only when the data is used in research publications.  The PIMMS project (Portable Infrastructure for the Metafor Metadata System) hopes to revolutionise the documentation of models and simulations by creating an infrastructure that makes model documentation easy to do very early in the workflow.  This is an interactive poster where we invite participants to indicate where the act of documenting simulations occurs in their typical workflow. And also where the act of documentation should occur in their ideal workflow. In this way the PIMMS team hope to find out those places where PIMMS would be of most benefit to the community.  An established PIMMS infrastructure should fit seamlessly into the simulation workflow and significantly reduce the effort required to fully document simulations