Posts tagged: open science
Social coding and scholarly communication – open for collaboration
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 …
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 …
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 …
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 …
Studies on vaccine and drug mechanisms and effects using biomedical ontologies
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 …
The growth of open access journals – an Open Access Week twitter chat
To conclude Open Access Week 2012, BMC Medicine hosted a twitter chat with Stephen Curry, Mikael Laakso and Bo-Christer Björk to discuss the growth and future of open access publishing.
Open Access Week – highlights, and looking ahead
BMC Medicine kicked off their Open Access Week activities with the publication of a research article looking at the changing landscape of open access scientific publishing over the last decade, which, to quote Stephen Curry in his coverage of the article appearing in the Guardian, suggests that the “academic publishing game has changed irrevocably”.
To end the week the journal will be hosting a twitter chat with the article authors and Stephen Curry to discuss this growth in open access, turning our gaze to the future of open access, and the broad issues that will be relevant in next decade and beyond (Friday, 12pm UK time).
This week has seen a flurry of announcements and activity around open …
Nobel prize-winning lab releases mutant mouse data to the public domain
N-ethyl-N-nitrosourea (ENU) is a highly mutagenic chemical used in the laboratory for inducing changes in DNA and allowing study of the impact of that change. A team of researchers from the Department of Genetics at The Scripps Research Institute and Southwestern Medical Center’s Center for Genetics of Host Defense, have published a data note in BMC Research Notes, providing the data from over a decade of work to identify 185 phenotypes tracked to ENU induced mutations in 129 genes. Working on the project was Professor Bruce Beutler, winner of the Nobel Prize in Physiology or Medicine in 2011, who says of the work: “Over a period of eleven years we accumulated hundreds of mutations, induced …
No result is worthless: the value of negative results in science
Jian Tang and Renata Curty are carrying out a study which examines the academic influence of Journal of Negative Results in BioMedicine. They are doctoral students in the Information Science and Technology Program at Syracuse University, and are interested in the Open Science movement. In this guest blog post they explore the value of publishing negative results and the possible reasons behind a reticence within science to publish such data.
“Well, we failed to reject the null hypothesis for our experiments. I guess we should just put that submission idea on hold for now since we have no good results to report.” – the Professor says to his advisee in a frustrated tone while …
