It’s hard to make predictions, especially about the Future.
Yogi Berra (via Titus Brown)
What will biology look like in the year 2039? In July I attended the Bioinformatics Open Source Conference (BOSC), a friendly community of open source advocates, where I heard bioinformatician Titus Brown deliver his thoughts on this in his talk, “A History of Bioinformatics (in the Year 2039)”.
Good for my jet lag and a great start to BOSC. Talks about the future often focus on data size. Titus pointed to one such talk by Mike Schatz of Cold Spring Harbor: “The next 10 years of quantitative biology”. (Also check out the latest big data Cold Spring Harbor meeting, whose abstract deadline is August 22nd.) Sequencing …
By far one of the biggest concerns around Open Data is not whether we have the technology to enable researchers to make their data open but whether the cultural incentives are in place to make researchers freely share their data. Several publishers have recently started publishing ‘data journals’ or ‘data notes’. Is this latest publishing buzzword the answer to incentivising Open Data?
I try not to write in the first person (partly to avoid flashbacks of big red X’s from my high school essays) but this post—about something I myself have debated quite a bit—seems to demand it. As head of open data initiatives and policy here at BioMed Central, I’ve spent the last year questioning the need for ‘data notes’. …
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 chapter ‘Open Science and the Role of Publishers in Reproducible …
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 …
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 …
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. …
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
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 …
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 …
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 …