BioMed Central Blog
Biological adventures into the world of cloud computing
Cloud computing is becoming an increasingly popular phenomenon in the world of computing. Analysing data in ‘the cloud’ involves using a self-service internet infrastructure, where you pay-as-you-go and use only what you need, all managed by the third party provider, typically Amazon or Google. 
This technology has so far not been utilised for biological computing applications. The potential uses of cloud computing to analyse the mass of data pouring out of next-generation sequencing projects has, however, been a topic of hot debate in recent months amongst biologists and computational biologist alike.
In this month’s issue of Genome Biology, Ben Langmead and colleagues, from the University of Maryland and the John Hopkins Bloomberg School of Public Health, present the Crossbow algorithm for the alignment of whole-genome sequence data and the mapping of genetic variation information, such Single Nucleotide Polymorphisms (SNPs). Crossbow combines the alignment speed of the Bowtie algorithm, together with the SNP calling accuracy of the SOAPsnp algorithm, and allows them to be run on any publicly-available cloud computing cluster.
In the article presenting Crossbow Langmead and colleagues demonstrate how data from a 38-fold coverage of the human genome can be aligned, and the SNPs mapped, in less than 3 hours and for only US$ 85 using the Amazon cloud.
The authors believe this first demonstration of software for biological applications being able to utilise the technology of cloud computing will revolutionise the way we analyse our biological data.
Crossbow is open source and freely available to download here, as well as being provided online with the Genome Biology article.
Liz Gaskell, Senior Assistant Editor, Genome Biology.
Posted by Elisabeth Gaskell at 16:17 Comments (0)
Migraine—Are more effective treatments in sight?
Migraine is a
largely inherited neurological disorder leading to a combination of symptoms
including headache, visual and aural effects. As any long-time migraine
sufferer will tell you, migraine pain is debilitating, and the current
treatments are not always very effective. How well do we really understand the
mechanism of migraine, and what treatments are available? Are there better treatments coming in the
near future? How can we maximise the therapeutic effect of existing treatment?
These are just a few of the questions that Peter Goadsby and Till Springer address in their minireview “Migraine pathogenesis and state of pharmacological treatment options” in BMC Medicine this month. If you suffer from migraine, or see patients with migraine in your day to day practice, how do you feel about progress in this area?
If you’re interested in research, reviews or opinion articles covering topics of medical interest, article alerts are a great way to keep informed of developments in medical research!
Posted by Robin Cassady-Cain at 17:27 Comments (0)
Support solidifies for the U.S. Federal Research Public Access Act (FRPPA)
41 Nobel Laureates and scientists collaborated to show their support for FRPPA, by lobbying Congress thorough an open letter. The legislation seeks to enhance access to federally funded published research articles, ensuring they are made available in an online repository no later than 6 months after publication.
The bill will broaden the reach of scientific data for the benefit of researchers, companies and consumers alike. It is also hoped that the legislation will fuel innovation and entrepreneurship through increased dissemination of ideas, as well as raising the international profile of U.S. originated research.
The bill will bring the U.S. in line with many global research councils' public access policies as well as complementing the NIH public access policy. Furthermore the legislation would increase the accessibility of research for all higher education institutions regardless of size, propagating research to students who might not habitually have access.
Read the full letter to Congress here for a more detailed view.
Posted by Charlotte Webber at 15:33 Comments (0)
Open access and the developing world - read the latest
As part of Open Access Week last month, Walter H. Curioso, M.D., M.P.H, Research Professor at Universidad Peruana Cayetano Heredia, talks about his views of open access and how it can help in developing countries.
In other open access news, Denise Nicholson recently published her Tips for Developing Countries when reviewing Copyright Laws as part of the African Copyright & Access to Knowledge Project. Her recommendations include:
* ... Do not include protection for non-original databases. (It had little or no positive impact for rightsholders in the EU and created problems for users)". Original databases are protected by copyright like any original work. ...
* Promote Open Access, Open Source Software & Open Licensing (e.g. Creative Commons, etc.)
* Create and populate Open Access Institutional Repositories/Research Archives to showcase African research.
At a meeting on open access in agriculture, held at the International Centre for Crop Research for the Semi-Arid Tropics (ICRISAT), Hyderabad early September, Bruce Alberts, Editor-in-Chief or Science, called for open access to agricultural research in India to help drive development and reduce poverty. According to Alberts 'Given that agriculture is a "critical component" of India's science sector and that the country has a tremendous advantage in terms of diversity in agricultural science and practice, providing open access to agricultural research results could improve in national and state policymaking.'
In a comprehensive article recently published in the Times Higher Education Supplement, reporter Zoe Corbyn explores the pros and cons of open access, particularly in the developing world. In a blog piece entitled 'Revisiting OA', Barbara Kirsop of the Electronic Publishing Trust emphasises the need for instutional repositories in the developing world, concluding:
"Without a strong research base, the poorer countries will forever depend on donations and will be unable to contribute their essential and unique knowledge to the world's information pool."
Posted by Charlotte Webber at 14:44 Comments (0)
Journal of Hematology & Oncology and SJTREM accepted for indexing in MEDLINE
Journal of Hematology & Oncology and Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine (SJTREM) have both been recently accepted for inclusion in MEDLINE.
For Journal of Hematology & Oncology this news comes hot on the heels of the news that the journal has been accepted by Thomson Reuters and will receive its first impact factor next June. The journal was only launched in May 2008 and since published a wide range of articles and has quickly built a strong reputation in its field.
SJTREM transferred to BioMed Central in July 2008 in its 16th year of publication and is the official publication of the Scandinavian Networking Group on Trauma and Emergency Management and is also affiliated with 9 more societies involved in trauma, resuscitation, and emergency medicine in Scandinavia.
Posted by Charlotte Hubbard at 14:31 Comments (0)
All BioMed Central's journals strive to ensure the integrity of the scientific record and, as members of the Committee on Publication Ethics (COPE), have procedures in place to help prevent covert duplicate (redundant) publication. Non-transparent duplication within the citable literature is academically unethical and, even more importantly, can have severe consequences for the evidence-based assessment of medical interventions.
But growth in web technologies and increased transparency in the literature - and data - may be contributing to a shift in our perceptions of what constitutes a prior publication. Innovative online journals with virtually unlimited space provide researchers with opportunities to produce novel (original) contributions to the literature that are clearly and transparently linked to previously published articles. These include significantly extended/re-analysed reports of previously published summary findings in journals such as Trials and legitimate or incremental updates to previous studies in BMC Research Notes. Dyer et al, for example, published a clinical and cost-effectiveness analysis of two treatment options for refractory angina in Trials, where details of the randomised trial results had been previously reported.
These and other developments such as the growth of pre-print servers, availability of articles in multiple languages, mandates for sharing of scientific results, open science - often involving substantial discussion of data placed in the public domain before formal publication - and queries from the research community, have prompted BioMed Central to produce guidance for its journal editors on these issues.
'Guidance on duplicate publication for BioMed Central journal editors' can be found online and includes a quick-reference table for ease of use.
Editorial control rests with the editors of journals published by BioMed Central, and this new guidance should enable our editors to assert their judgment on a case-by-case basis, whilst also providing a useful publication ethics resource for their, and the broader scientific community's reference. It's clear there is a need for flexibility as new technologies and methods of scientific communication emerge. Therefore comments on the guidance - a 'living document' - are actively encouraged.
Posted by Iain Hrynaszkiewicz at 11:03 Comments (0)
The impact of networks on UK clinical trials
In the United Kingdom, we have an expectation of high quality, effective health services which are freely available at the point of demand in the form of the National Health Service (NHS). But have recent efforts to ensure a consistent standard of service throughout the UK had knock-on effects on the ability of clinicians to carry out essential clinical research?
Authors Ng and Weilding argue in a new commentary published in Trials that whilst managed clinical networks (MCNs) and clinical research networks (CRNs) exist to ensure both the quality and equitable distribution of health services, that in practice they actually have made the setting up and conducting of clinical trials in the UK considerably more complex.
Ng and Weilding suggest that the stringent UK Medicines for Human Use (Clinical Trials) Regulations - put in place in 2004 following the European Clinical Trials Directive - coupled with greater administrative requirements resulting from MCNs and CRNs themselves, may actually discourage clinicians from undertaking clinical studies, and could result in the failure of some trials.
Do Ng and Weilding's findings of unnecessary barriers and bureaucracy represent the best possible landscape for the testing and future approval of interventions?
Commentary
The impact of networks on clinical trials in the United Kingdom
Sze May Ng, Alan Michael Weindling
Victoria Thompson
Assistant Journal Development Editor
Posted by Iain Hrynaszkiewicz at 10:29 Comments (0)
The Coral genetic linkage map – an essential resource for Coral biology
Coral reefs are diverse marine ecosystems. Overfishing, pollution and the effects of climate change including, ocean acidification (as a result of rising carbon dioxide levels) are destroying these precious environments. Reefs are being lost at an alarming rate and understanding whether/how coral can adapt to these changes could provide clues for aiding their preservation.
In this month’s issue of Genome Biology, Mikhail Matz and colleagues from the University of Texas present a high-resolution genetic linkage map of the reef-building coral Acropora millepora, the first for any coral or any non-bilaterian animal, and the most basal metazoan genetic linkage map to date. This linkage map will enable the identification of the quantitative trait loci (QTLs) associated with adaptation-relevant physiological traits, as well as facilitating population genomics studies and coral genome assembly.
As well as facilitating future studies into coral genomics, biology and ecology, the linkage map itself reveals insights into coral biology. The consensus genetic linkage map contains more than 400 markers distributed over 14 linkage groups. Matz and colleagues also produced separate male and female linkage maps, and found that the female map was 1.3x longer than that of the male, suggesting that this coral may possess sex-specific differences in recombination. The coral map also revealed syntenic regions with other metazoan genomes, allowing the authors to build a picture of the architecture of the ancestral metazoan genome.
This new genetic linkage map provides an important resource for future studies on coral genome structure and enhances our understanding of metazoan genome evolution
You can read the article by Matz and colleagues in this month’s issue of Genome Biology.
Clare Hinkley, Senior Editor, Genome Biology
Posted by Elisabeth Gaskell at 18:01 Comments (0)
Hot on the heels of our recent announcement we have just heard that three more journals have been accepted by Thomson Reuters and are now on course to receive their first Impact Factors. The journals are:
- Biotechnology for Biofuels - Impact Factor due June 2010
- Cell Communication and Signaling - Impact Factor due June 2012
- Journal of Hematology & Oncology - Impact Factor due June 2010
Each of these journals has developed a strong reputation its field and this news is a good indicator of their success to date. We would like to congratulate the Editors-in-Chief of all of these titles.
A total of 94 BioMed Central journals are now tracked by Thomson Reuters; 59 of these currently have impact factors and another 17 are set to receive their first impact factors in June 2010. A full list of all these journals as well as further details on indexing of all BioMed Central titles is available from our website.
Posted by Charlotte Hubbard at 17:48 Comments (0)
National advocacy portals help spread the word about Open Access
The recently announced Open Access for Hong Kong portal, created by the Hong Kong Open Access Committee, is the latest in a series of such national OA advocacy portals which bring together information about the benefits of Open Access scholarly communication, focusing on the needs of academic researchers in a particular country.
These national Open Access portals now include:
- http://open-access.net (Germany)
- http://openaccess.hk (Hong Kong)
- http://openaccessjapan.com (Japan)
- http://openaccess.nl (Netherlands)
- http://openaccess.no (Norway)
- http://openaccess.se (Sweden)
Know of any more? Please let us know...
Posted by Matthew Cockerill at 19:45 Comments (0)
Announcing the launch of Allergy, Asthma & Clinical Immunology
Allergy, Asthma & Clinical
Immunology, the official journal of the Canadian Society of Allergy and
Clinical Immunology (CSACI), has now
commenced publication with BioMed Central, having transferred to our open access
publishing format with the aim of increasing the success of the
journal.Posted by Sally Robertson at 14:02 Comments (0)
Why are women predisposed to autoimmune rheumatic diseases?
In the current issue of Arthritis Research & Therapy, Jacqueline Oliver and Alan Silman explore the various factors that influence susceptibility to the major autoimmune connective tissue disorders, in search for an explanation for the high female-to-male predisposition ratio.
Autoimmune diseases of all organ sites and systems affect approximately 8% of the population, around 78% of whom are women. The majority of studies into this female predominance have focused on examining the affect of hormonal fluctuations on disease risk.
Oliver and Silman provide a detailed review of these hormonal influences, as well as genetics and gender differences in lifestyle factors, focusing on rheumatoid arthritis, systemic lupus erythematosus and scleroderma. The authors convey the complexity of autoimmune disease susceptibility and the need for further studies to disentangle the many contributing factors.
Review 
Why are women predisposed to autoimmune rheumatic diseases?
Jacqueline E Oliver, Alan J Silman
Arthritis Research & Therapy 2009, 11:252 (26 October 2009)
[Abstract] [Full text] [PDF]
The commissioned reviews published in Arthritis Research & Therapy's regular issues usually require a subscription for access, but a free 30-day trial is available. Moreover, recipients of the BioMed Central Update, in which Arthritis Research & Therapy features regularly, are provided with unique opportunities to freely access subscription review content published in BMC journals. Register for the Update here, or alternatively, recommend the journal to your librarian via the website.
Abigail Jones
Senior Assistant Editor - Arthritis Research & Therapy
Posted by Iain Hrynaszkiewicz at 12:32 Comments (0)
Automated Experimentation - a new independent, open access journal
Automated Experimentation launched today, providing a new platform for
biomedical and informatics researchers to revise, re-use
and recombine their automated experimentation processes or protocols. With
recent advances in engineering, laboratory robotics and informatics, the
automation of experiments are becoming increasingly important for expediting
large-scale research, particularly in areas such as systems biology and
translational medicine.
“Our aim is to bring together the diverse forms of automated experimentation and, by studying them in an abstract but practical way, understand how they generalise across domains”, say Editors-in-Chief, Siu-Wai Leung, Dave Robertson and Dietlind Gerloff in their launch Editorial, concluding, “In this way we hope Automated Experimentation will promote new styles of computationally inspired experimental thinking.”
Please view the journal website to read the first three articles published in Automated Experimentation. If you would like to know when new articles are published in the journal, please sign up for article alerts
Posted by Anne Braae at 12:21 Comments (0)
Speedy diagnosis for mitochondrial disorders
A team led by Sihoun Hahn and Jay Shendure from Seattle Children’s Research Institute and the University of Washington present a molecular diagnostic tool for mitochondrial disease in their article titled “Next generation sequence analysis for mitochondrial disorders”, recently published in Genome Medicine. This is the 100th article published in Genome Medicine, BioMed Central’s premier medical journal, since its launch in January 2009.
Next-generation sequencing technologies herald an era when personal genome information may be used to guide medical decisions. While complete genome sequences are not yet cost-effective for routine clinical use, methods which target specific genomic regions have already become practical for disease diagnosis.
The method described by Hahn and colleagues uses array-based technology and genetic sequencing to screen patients’ DNA for variations in 362 genes which have been associated with mitochondrial disease or mitochondrial function. Thanks to its lower cost and faster turnaround, this approach could replace the protracted tests currently needed to determine some rare mitochondrial mutations and it may also lead to discovery of new mutations and genes which affect mitochondrial function.
Genome Medicine publishes high-quality genomic and post-genomic research that significantly advances our understanding and management of human health and disease. Thanks to the active involvement of exceptional section editors and editorial board members, Genome Medicine has published a wide range of research articles, reviews, meeting reports and commentaries in the past ten months, and we look forward to continued growth and involvement with the research community.
Read the article by Hahn and colleagues, register for article updates and submit your next outstanding research manuscript to Genome Medicine. For quick feedback on the suitability of your manuscript, we welcome presubmission enquiries.
Rebecca Furlong
Assistant Editor, Genome Medicine
Posted by Rebecca Furlong at 10:49 Comments (0)
Arthritis Research & Therapy's 10th anniversary issue published in full
This month Arthritis Research & Therapy (AR&T) published the final installment of its 10th anniversary issue, 'The Scientific Basis of Rheumatology: A Decade of Progress' - a comprehensive, up-to-date and freely available rheumatology reference work spanning more than 400 pages.
This special, four-part collection of 38 review articles - commissioned to celebrate AR&T's 10 years of publication and published over the past 12 months - has been written by an internationally recognised group of experts with the aim of providing clinicians and researchers with a detailed overview of the current status of basic, translational and clinical research in rheumatology. The articles outline the biologic processes underlying rheumatic diseases and analyse the most significant developments in specific rheumatic diseases from the past decade.
View the full table of contents on the journal website.
“The past 10 years have seen an explosion of new information in rheumatology research” said AR&T Editors-in-Chief, Peter E Lipsky and Ravinder N. Maini. “This collection produced for AR&T’s 10th anniversary will help readers around the world understand the nature of the new developments that not only should stimulate additional interdisciplinary research on unsolved problems but also foster the timely application of this new knowledge into better patient care.”
All articles in this collection have been freely available immediately on publication without a subscription, along with all editorials, letters and research articles published in the AR&T. Reviews
in the regular journal issues published more than 6 months previously
are also available to non-subscribers. A free 30-day online trial
subscription is available via the website.
Posted by Iain Hrynaszkiewicz at 11:58 Comments (0)