Posts by Iain Hrynaszkiewicz

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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Journal of Medical Case Reports celebrates launch of Cases Database


To celebrate the launch of Cases Database, BioMed Central is offering a discounted article processing charge to Journal of Medical Case Reports authors, and expanding the scope of its Case Report of the Year Award.

Creating Cases Database, BioMed Central’s freely accessible database of peer-reviewed case reports which launched last month, was one of the original aims of Journal of Medical Case Reports. The expertise and guidance of a number of the journal’s senior editorial board members, including in particular Editor-in-Chief Prof Michael Kidd and Deputy Editor Dr Geoff Wong, have been invaluable in developing the database.

Cases Database is growing rapidly and includes several thousand more case reports than when it first launched in …

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Current Controlled Trials and DOIs – another important step towards Threaded Publications


The introduction of digital object identifiers (DOIs) to all ISRCTN records in the Current Controlled Trials database, announced today, is an essential part of achieving the aims of the Threaded Publications initiative – making the medical literature more transparent and better connected.

Prospective trial registration should be the first step in transparently disseminating all scientifically relevant information about a clinical trial. Trials can be very expensive to carry out, involve large numbers of subjects and investigators, and generate large amounts of data potentially constituting several scientific articles. The articles from the third International Stroke Trial are a case in point. But unfortunately many clinical trial-related articles are not published, leading to bias in …

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How far have we got with public disclosure of trial data?

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BioMed Central in collaboration with an Ottawa-based researcher has received the Committee on Publication Ethics (COPE) research grant for a timely project which aims to facilitate wider sharing of clinical research data.

In the last few weeks GlaxoSmithKline and Medtronic have made public commitments to share data from clinical trials they have sponsored, the BMJ have strengthened their policy on data sharing for clinical trial submissions, and Ben Goldacre‘s latest book, Bad Pharma, is causing something of a stir. These are significant and much-needed developments in transparency in clinical research.

Researchers working with human subjects are amongst the least likely to share their data, and the practicalities and legalities of sharing clinical data while …

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Encouraging data developments on the BMC series


The BMC series biology journals have joined BMC Research Notes in encouraging all authors of original research-based articles to publish supporting data permanently online and include an ‘Availability of supporting data’ section in their articles. This includes journals such as BMC Bioinformatics, BMC Systems Biology, BMC Ecology and BMC Genomics.

Different journals and publishers have different approaches to data sharing. A recent feasibility study by JISC and the Research Information Network (and other partners) has the potential to produce a comprehensive Journal Research Data Policy Bank (JoRD) cataloguing these different policies. Meanwhile, non-comprehensively, some journals such as the BMJ require a data sharing statement from all authors. Others – including all BioMed …

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Systematic Reviews joins Threaded Publications initiative


Authors of study protocols in Systematic Reviews are now entitled to a 20% discount on the article processing charge (APC) for publication of the results of the same systematic review in the journal.

Publication – and public registration in PROSPERO – of information about proposed or ongoing systematic reviews is increasingly common, and Systematic Reviews regularly publishes protocols.

To encourage authors to report the results of their research regardless of the outcome – whether positive, negative or no difference – we offer an APC discount on publication in a number of journals.

Financial incentives for transparent reporting of all components of a research project are one part of BioMed Central’s Threaded Publications initiative. See our protocol publication resources, …

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Help put the open in Open Data and Open Bibliography


Legal restrictions and uncertainties surrounding scientific data are a barrier to efficient data sharing and reuse, and ultimately the pace of research. Copyright in particular is problematic for data. It is often unclear if data are protected by copyright and the law differs greatly internationally.

To try and more universally clarify the legal status of data published in our open access journals – maximizing the potential for secondary data uses such as text mining – we have been working towards a solution: public domain dedication of data under the Creative Commons CC0 waiver.

In a detailed editorial published in BMC Research Notes we set out the case and process for evolving the copyright and licensing structure in open access …

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How do we standardize peer review of bioinformatics software?

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The 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), an international meeting positioned at the intersection of computer science and biology, took place in Long Beach last week. Bioinformaticians build software on which much of modern biological computation depends, and openness – in data, software and of course journal articles – is a refreshingly familiar concept to many scientists working in this field.

I’ve recently returned from the conference and in 2012 there were many
reasons to make the trip – not least the launch of new ‘big data’
journal GigaScience, reported elsewhere. Another reason to attend was an invitation to participate in a panel discussion at the Bioinformatics Open Source 2012
(#BOSC2012) …

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Why “We the People” should support open access


Guest blog post by Dr Bill (Craig) Hooker, Associate Editor of BMC Research Notes and open science enthusiast, and strong supporter of the access2research initiative

Sign the Petition!

I don’t suppose that readers of a BioMed Central website need a long introduction to open access, so I’ll get right to the point: there’s a “We The People” petition active until June 19th, petitioning the Obama administration to provide public access to publicly funded research:

We petition the Obama administration to:
Require free access over the Internet to scientific journal articles arising from taxpayer-funded research
We believe in the power of the Internet to foster innovation, research, and education. Requiring the published results …

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