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

Identification of blood biomarkers for use in point of care diagnosis tool for Alzheimer's disease.

Early diagnosis of Alzheimer's Disease (AD) is widely regarded as necessary to allow treatment to be started before irreversible damage to the brain occur and for patients to benefit from new therapies as they become available. Low-cost point-of-care (PoC) diagnostic tools that can be used to routinely diagnose AD in its early stage would facilitate this, but such tools require reliable and accurate biomarkers. However, traditional biomarkers for AD use invasive cerebrospinal fluid (CSF) analysis and/or expensive neuroimaging techniques together with neuropsychological assessments. Blood-based PoC diagnostics tools may provide a more cost and time efficient way to assess AD to complement CSF and neuroimaging techniques. However, evidence to date suggests that only a panel of biomarkers would provide the diagnostic accuracy needed in clinical practice and that the number of biomarkers in such panels can be large. In addition, the biomarkers in a panel vary from study to study. These issues make it difficult to realise a PoC device for diagnosis of AD. An objective of this paper is to find an optimum number of blood biomarkers (in terms of number of biomarkers and sensitivity/specificity) that can be used in a handheld PoC device for AD diagnosis. We used the Alzheimer's disease Neuroimaging Initiative (ADNI) database to identify a small number of blood biomarkers for AD. We identified a 6-biomarker panel (which includes A1Micro, A2Macro, AAT, ApoE, complement C3 and PPP), which when used with age as covariate, was able to discriminate between AD patients and normal subjects with a sensitivity of 85.4% and specificity of 78.6%

Early Detection of Alzheimer\u27s Disease with Blood Plasma Proteins Using Support Vector Machines

\ua9 2013 IEEE. The successful development of amyloid-based biomarkers and tests for Alzheimer\u27s disease (AD) represents an important milestone in AD diagnosis. However, two major limitations remain. Amyloid-based diagnostic biomarkers and tests provide limited information about the disease process and they are unable to identify individuals with the disease before significant amyloid-beta accumulation in the brain develops. The objective in this study is to develop a method to identify potential blood-based non-amyloid biomarkers for early AD detection. The use of blood is attractive because it is accessible and relatively inexpensive. Our method is mainly based on machine learning (ML) techniques (support vector machines in particular) because of their ability to create multivariable models by learning patterns from complex data. Using novel feature selection and evaluation modalities, we identified 5 novel panels of non-amyloid proteins with the potential to serve as biomarkers of early AD. In particular, we found that the combination of A2M, ApoE, BNP, Eot3, RAGE and SGOT may be a key biomarker profile of early disease. Disease detection models based on the identified panels achieved sensitivity (SN) > 80%, specificity (SP) > 70%, and area under receiver operating curve (AUC) of at least 0.80 at prodromal stage (with higher performance at later stages) of the disease. Existing ML models performed poorly in comparison at this stage of the disease, suggesting that the underlying protein panels may not be suitable for early disease detection. Our results demonstrate the feasibility of early detection of AD using non-amyloid based biomarkers

Quiet in class: classification, noise and the dendritic cell algorithm

Theoretical analyses of the Dendritic Cell Algorithm (DCA) have yielded several criticisms about its underlying structure and operation. As a result, several alterations and fixes have been suggested in the literature to correct for these findings. A contribution of this work is to investigate the effects of replacing the classification stage of the DCA (which is known to be flawed) with a traditional machine learning technique. This work goes on to question the merits of those unique properties of the DCA that are yet to be thoroughly analysed. If none of these properties can be found to have a benefit over traditional approaches, then “fixing” the DCA is arguably less efficient than simply creating a new algorithm. This work examines the dynamic filtering property of the DCA and questions the utility of this unique feature for the anomaly detection problem. It is found that this feature, while advantageous for noisy, time-ordered classification, is not as useful as a traditional static filter for processing a synthetic dataset. It is concluded that there are still unique features of the DCA left to investigate. Areas that may be of benefit to the Artificial Immune Systems community are suggested

Bayesian inference on compact binary inspiral gravitational radiation signals in interferometric data

Presented is a description of a Markov chain Monte Carlo (MCMC) parameter estimation routine for use with interferometric gravitational radiational data in searches for binary neutron star inspiral signals. Five parameters associated with the inspiral can be estimated, and summary statistics are produced. Advanced MCMC methods were implemented, including importance resampling and prior distributions based on detection probability, in order to increase the efficiency of the code. An example is presented from an application using realistic, albeit fictitious, data.Comment: submitted to Classical and Quantum Gravity. 14 pages, 5 figure