Posts by Gabriella Anderson

Crowdsourcing the Corpasome

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The post-genomic era has seen an upsurge in direct-to-consumer testing services.  Members of the public are now able to access their genetic information without involving a healthcare professional. There are advantages to this approach to genetic testing: it allows people to gain an insight into diseases they may be predisposed to develop and play a more proactive role in their healthcare. Despite this progress in personal genomics, most people choose to keep their genetic data private, and a consequence of this is that very little personal genomics data is made available in the public domain.

Dr Manuel Corpas, a Bioinformatician and author for Source Code for Biology and Medicine, has taken steps to …

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Call for papers for a special GCC2013 Galaxy series

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Guest blog post by Scott Edmunds, Executive Editor for GigaScience, a BioMed Central journal which is collaborating with the 2013 Galaxy Community Conference (GCC2013) to publish a special thematic series on studies utilizing large-scale datasets and workflows. GigaScience is a journal which is co-published in collaboration between BioMed Central and BGI Shenzhen, and publishes ‘big-data’ studies from the entire spectrum of life and biomedical sciences.

The 2013 Galaxy Community Conference (GCC2013) and GigaScience are announcing a call for papers for a special thematic focused series on studies utilizing large-scale datasets and workflows. Galaxy is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. GigaScience, with …

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EvoBIO 2013: Seeking creative solutions to complex biological problems

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Guest blog post by William S. Bush, co-organiser of EvoBIO 2013, which is the leading European event on bio-inspired and evolutionary computation. This year EvoBIO will be held on 3rd – 5th April in Vienna, Austria. It is also collaborating with BioMed Central’s BioData Mining journal to offer free publication to the winner of this year’s best paper award.

For over 15 years, members of the computer science, machine learning, and data mining communities have gathered in a beautiful European location each spring to share ideas about biologically-inspired computation.  Stemming from the work of Holland who pioneered the field of genetic algorithms, the evolutionary optimization work of Rechenberg and Schwefel, and the evolutionary programming technique …

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

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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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Confronting the scale and complexity of big data: a new thematic series

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Guest blog post by Prof Jason Moore, co-Editor-in-Chief of BioData Mining, a journal which publishes research on data mining applied to high-dimensional biological and biomedical data. Jason is Professor of Genetics at Dartmouth College and Director of the Institute for Quantitative Biomedical Sciences; his research focuses on understanding how DNA sequence variations increase or decrease susceptibility to common diseases.

A rapid increase in the amount of data produced by the life sciences, has led to a new era of ‘big data’. Much work has been completed in recent years to address issues such as the storage and curation of large amounts of data, and progress has been made with encouraging researchers to deposit …

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No result is worthless: the value of negative results in science

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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 …

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Why publish your negative results?

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During an interview with Journal of Negative Results in BioMedicine (JNRBM), Dr Haiko Sprott (below) provides some interesting and thought-provoking views on why the publication of negative results is valuable to the scientific community. Dr Sprott is Head of the Pain Clinic Basel, Switzerland, and carries out research into chronic pain, pain genes and multimodal pain therapy. He is also an Editorial Board member for JNRBM.

Why is the publication of negative results so important?

In general, the researcher is following a hypothesis which he or she suspects has a probability of occurring. Based on my own experience, in some cases this is not necessarily what will happen at the end of the study, and this …

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Deep space, data analysis and dealing with uncertainty

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In July Source Code for Biology and Medicine, a forward-looking bioinformatics journal with an emphasis on the practical utilization of source code within biomedicine, attended the Ninth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) in Houston, Texas. This meeting took place at the Methodist Hospital Research Institute (TMHRI), which is one of the many hospitals in the renowned Texas Medical Center.

Texas Medical Center is internationally recognized for such prestigious institutions as Baylor College of Medicine, the University of Texas MD Anderson Cancer Center and the Methodist Hospital System. These institutions provide some of the world’s most advanced treatment available and also carry out ground-breaking research. The conference covered …

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The Crowdfunding Genome Project: a personal genomics community with open source values

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Guest blog post by Manuel Corpas, author for Source Code for Biology and Medicine, strong supporter of the open source movement and originator of the Crowdfunding Genome Project

 

Source Code for Biology and Medicine constitutes an ideal platform for dissemination of code developed for the biomedical fields. One particular field in which the development of source code is particularly critical at the moment is personal genomics. We live in a moment in which the accessibility of Direct-to-consumer (DTC) genetic testing services is not being matched by our ability to interpret results. Sequencing technologies have advanced so much that it has become almost trivial to sequence a personal genome. What is not trivial though is its interpretation, and …

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