Issues for the sharing and re-use of scientific workflows

In this paper, we outline preliminary findings from an ongoing study we have been conducting over the past 18 months of researchers’ use of myExperiment, a Web 2.0-based repository with a focus on social networking around shared research artefacts such as workflows. We present evidence of myExperiment users’ workflow sharing and re-use practices, motivations, concerns and potential barriers. The paper concludes with. a discussion of the implications of these our findings for community formation, diffusion of innovations, emerging drivers and incentives for research practice, and IT systems design

Structuring research methods and data with the research object model:genomics workflows as a case study

Background: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e. g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. Results: We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Conclusions: Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. Availability: The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/r

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Lightning Talk:"I solemnly pledge" A Manifesto for Personal Responsibility in the Engineering of Academic Software

International audienceSoftware is fundamental to academic research work, both as part of the method and as the result of research. In June 2016 25 people gathered at Schloss Dagstuhl for a week-long Perspectives Workshop and began to develop a manifesto which places emphasis on the scholarly value of academic software and on personal responsibility. Twenty pledges cover the recognition of academic software, the academic software process and the intellectual content of academic software. This is still work in progress. Through this lightning talk, we aim to get feedback and hone these further, as well as to inspire the WSSSPE audience to think about actions they can take themselves rather than actions they want others to take. We aim to publish a more fully developed Dagstuhl Manifesto by December 2016

Four simple recommendations to encourage best practices in research software [version 1; referees: awaiting peer review]

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations. Keyword

The myGrid Project:Services, Architecture and Demonstrator

myGrid is an e-Science research project developing open source high-level middleware to support in silico experiments in biology. In silico experiments use databases and computational analysis rather than laboratory investigations to test hypothesis. This paper provides an overview of services the Grid project is developing, and the architecture in which they fit. Registries provide information about available data and computational services, while remote legacy bioinformatics applications are wrapped using a consistent distributed analysis framework Soaplab. As in conventional science, experimental method is as important as final results. myGri

Accelerating scientists’ knowledge turns

A “knowledge turn” is a cycle of a process by a professional, including the learning generated by the experience, deriving more good and leading to advance. The majority of scientific advances in the public domain result from collective efforts that depend on rapid exchange and effective reuse of results. We have powerful computational instruments, such as scientific workflows, coupled with widespread online information dissemination to accelerate knowledge cycles. However, turns between researchers continue to lag. In particular method obfuscation obstructs reproducibility. The exchange of “Re-search Objects” rather than articles proposes a technical solution; however the obstacles are mainly social ones that require the scientific community to rethink its current value systems for scholarship, data, methods and software