Posts tagged: open science

Implementing Reproducible Research: the Role of Publishers. An interview with Iain Hrynaszkiewicz, Peter Li, and Scott Edmunds


Implementing Reproducible Research, recently released by CRC Press and edited by Victoria Stodden, Friedrich Leisch, and Roger Peng, clearly describes the changes needed in science and publishing to help foster reproducible research.

With contributions from key leaders in computational science, such as Titus Brown, the book covers topics ranging from good programming practice and open source computational tools to the role of publishers in reproducible research.

Below is an interview with the authors of the chapter ‘Open Science and the Role of Publishers in Reproducible Research’, Iain Hrynaszkiewicz (Outreach Director at F1000), Peter Li (Data Organisation Manager at GigaScience) and Scott Edmunds (Executive Editor at GigaScience).


Your chapterOpen Science and the Role of Publishers in Reproducible

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BioMed Central rolls up its sleeves for citizen science

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OPAL Tree Survey staff briefing

Posted on behalf of Shreeya Nanda, Deputy Editor for Biology and Medicine, BioMed Central

At this year’s BMC Day, the once-yearly company bonding event, we got to be citizen scientists, participating in projects ranging from classifying cancer cells on a computer screen to venturing out into the unknown (not really, it was just a park in Vauxhall) to categorise trees. For some, conducting scientific research was a novel experience, for others it probably brought back memories (hopefully not painful ones) of previous lives in laboratories. But I think I can safely say that for all of us, it was an interesting and rewarding experience.

Citizen science, as the name suggests, is scientific research conducted by amateurs and non-professionals, and as a concept …

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Guest blog – Galaxy Zoo: exploring the universe from the comfort of your sofa


Last month, staff at BioMed Central took a day off from publishing science, to get involved in doing some! One of several citizen science projects engaged in was Galaxy Zoo. Grant Miller and Robert Simpson from Galaxy Zoo tell us more about the project.  

As part of his PhD in astrophysics, Kevin Schawinski was asked to look through a catalogue of almost a million galaxies to sort the spiral-shaped objects from the elliptical ones. This simple two-way split in appearances is fundamental to a galaxy’s evolution, history and astrophysical properties. It’s trivial to tell them apart but no automatic method could reliably perform the same task.

Kevin spent a week working on the problem and managed to go through 50,000 …

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Canine Genetics and Epidemiology is now accepting submissions

Jessica Keating / DPOTY 2013 / KCPL (c)

Canine Genetics and Epidemiology (CGE) is a new peer-reviewed open access journal, published by BioMed Central with the support and backing of the Kennel Club, the UK’s largest organisation dedicated to the health and welfare of dogs.

CGE is now accepting manuscript submissions via the journal’s homepage. The journal will consider genetic, genomic and epidemiological research in both domestic and wild canids, relating to breed and species diversity as well as canine evolution. It will not publish articles describing research generated through experimental procedures that inflict pain and suffering to animals.

The journal’s aim is to disseminate research not only between scientists, but also to inform veterinarians, dog breeders and owners. …

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BMC Psychology launches!


On Wednesday 27 February, the newest addition to the BMC-series portfolio was launched. This marked a significant milestone for the BMC-series family of open access journals, as it was the first truly new journal since 2008.

View the story “BMC Psychology Launches!” on Storify

Social coding and scholarly communication – open for collaboration

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Innovation in how social online tools and their features develop is frequently defined and driven by the network’s users. A collaboration between BioMed Central, some of our authors and editors, and the team behind a powerful social software development platform aims to stimulate innovation in scholarly communication.

The ‘social coding’ website, GitHub, was founded in 2008 and its primary aim is to enable users to publicly or privately share source code, and manage software development projects. But it seems that life scientists have had other ideas for quite some time.

Bioinformaticians – one of BioMed Central’s earliest and largest author groups – by definition must create and share software for life science projects. Many BioMed Central journals urge authors …

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Version control for scientific research


Guest blog post from Dr Karthik Ram (KR) and Dr C. Titus Brown (CTB) who have been working with BioMed Central on our recently announced collaboration with the social coding repository, GitHub.

We live in an increasingly collaborative era, where the Internet enables distance collaboration almost trivially – not just with e-mail and videoconferencing, but with collaborative realtime document editing and networked transmission of data and analyses. These tools allow us to collectively leverage many resources to rapidly solve problems and ultimately accelerate scientific discovery. While these tools and technologies are fundamentally changing how we collaborate on science, there is still considerable room for improvement in how we are using them.

Programmers, and especially the world of open source software …

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BioMed Central support for data publishing: enhanced handling of additional files


At BioMed Central, we encourage authors to submit additional files such as movies and datasets, and we continue to look for ways to use web technology to make these files more useful and accessible.

We have recently updated our Instructions for Authors, adding an additional file quick reference guide, which provides advice, recommendations and examples for the preparation of various types of additional file. The guide also describes what we currently do to present each type of additional file in a readily accessible way. Examples range from interactive images to enhanced 3D PDFs, chemical structures and cut-and-paste-enabled mathematical formulae. We hope the guide will encourage authors to take full advantage of the data-sharing opportunities offered by the BioMed Central …

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Exploring the Semantic Web and its relevance to clinical and life sciences


Guest blog post from the series editors of the ‘Semantic technologies in healthcare and life sciences’ thematic series, which focuses on the application of web-based technologies for knowledge representation and data integration in clinical and life sciences. 

We would like to draw your attention to a new thematic series in Journal of Biomedical Semantics. The ‘Semantic technologies in healthcare and life sciences’ series focuses on the development and application of web-based technologies for knowledge representation and data integration in clinical and life sciences, with the objective of facilitating biomedical research and healthcare practice.

This thematic series originates from research presented at two conferences; SWAT4LS (Semantic Web Application and Tools for Life Sciences) and CSHALS (Conference on Semantics …

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Studies on vaccine and drug mechanisms and effects using biomedical ontologies

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Guest blog post by Yongqun He, who is series editor for the newly launched “Vaccine and Drug Ontology in the Study of Mechanism and Effect” (VDOSME) thematic series. The VDOSME workshop provides a platform for discussing problems and solutions in the development and application of biomedical ontologies to representing and analyzing vaccines and drugs. In this blog post he explores how the cutting-edge research published in this series makes a valuable contribution to the field.

Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Although therapeutic vaccines are being invented, vaccines are classically administered to prevent the appearance of a medical problem. Chemical drugs are generally administered to treat a medical problem. Nevertheless, vaccines and …

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