Welcome to Source Code for Biology and Medicine

This editorial introduces Source Code for Biology and Medicine, a new journal for publication of programming source code used in biology and medicine. Source Code for Biology and Medicine is an open access independent journal published by BioMed Central. We describe the journal aims, scope, benefits of open access, article processing charges, competing interests, content and article format, peer review policy and publication, and introduce the Editorial Board

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

Ontology-based specific and exhaustive user profiles for constraint information fusion for multi-agents

Intelligent agents are an advanced technology utilized in Web Intelligence. When searching information from a distributed Web environment, information is retrieved by multi-agents on the client site and fused on the broker site. The current information fusion techniques rely on cooperation of agents to provide statistics. Such techniques are computationally expensive and unrealistic in the real world. In this paper, we introduce a model that uses a world ontology constructed from the Dewey Decimal Classification to acquire user profiles. By search using specific and exhaustive user profiles, information fusion techniques no longer rely on the statistics provided by agents. The model has been successfully evaluated using the large INEX data set simulating the distributed Web environment

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

The Cure: Making a game of gene selection for breast cancer survival prediction

Motivation: Molecular signatures for predicting breast cancer prognosis could greatly improve care through personalization of treatment. Computational analyses of genome-wide expression datasets have identified such signatures, but these signatures leave much to be desired in terms of accuracy, reproducibility and biological interpretability. Methods that take advantage of structured prior knowledge (e.g. protein interaction networks) show promise in helping to define better signatures but most knowledge remains unstructured. Crowdsourcing via scientific discovery games is an emerging methodology that has the potential to tap into human intelligence at scales and in modes previously unheard of. Here, we developed and evaluated a game called The Cure on the task of gene selection for breast cancer survival prediction. Our central hypothesis was that knowledge linking expression patterns of specific genes to breast cancer outcomes could be captured from game players. We envisioned capturing knowledge both from the players prior experience and from their ability to interpret text related to candidate genes presented to them in the context of the game. Results: Between its launch in Sept. 2012 and Sept. 2013, The Cure attracted more than 1,000 registered players who collectively played nearly 10,000 games. Gene sets assembled through aggregation of the collected data clearly demonstrated the accumulation of relevant expert knowledge. In terms of predictive accuracy, these gene sets provided comparable performance to gene sets generated using other methods including those used in commercial tests. The Cure is available at http://genegames.org/cure

The use of Human Subjects in Biomedical Research: A Problematic Scientific Past Shapes Present Ethical Challenges

The ethics of human experimentation is a relatively new phenomenon in medicine. The Nuremberg Code and the Helsinki Declaration focused on informed consent in human experimentation. More recently, ethicists have begun to emphasize that, beyond the need for consent, the \"content\" of the experiment also needs to be ethical. The method and process of the experiment must be humanizing and affirming of the subject as moral agent. The religious perspective has provided a comprehensive moral foundation, demanding respect for the subjects\' moral agency and their right to he treated as equally worthy members of the human community, thus ensuring the integrity of the subject as person