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Source Code for Biology and Medicine

Toshiki Takeuchi, Atsuo Yamada, Takashi Aoki, Kunihiro Nishimura
BACKGROUND: Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast...
2016: Source Code for Biology and Medicine
Lindsay V Clark, Erik J Sacks
BACKGROUND: In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine...
2016: Source Code for Biology and Medicine
Brigitte Glanzmann, Hendri Herbst, Craig J Kinnear, Marlo Möller, Junaid Gamieldien, Soraya Bardien
BACKGROUND: Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them...
2016: Source Code for Biology and Medicine
John M Macdonald, Paul C Boutros
BACKGROUND: To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results. RESULTS: Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution...
2016: Source Code for Biology and Medicine
Caleb F Davis, Deborah I Ritter, David A Wheeler, Hongmei Wang, Yan Ding, Shannon P Dugan, Matthew N Bainbridge, Donna M Muzny, Pulivarthi H Rao, Tsz-Kwong Man, Sharon E Plon, Richard A Gibbs, Ching C Lau
BACKGROUND: Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich source of information in which to detect breakpoints of structural variations at base-pair resolution. However, accurate prediction of SVs remains challenging, and existing informatics tools predict rearrangements with significant rates of false positives or negatives. RESULTS: To address this challenge, we developed 'Structural Variation detection by STAck and Tail' (SV-STAT) which implements a novel scoring metric...
2016: Source Code for Biology and Medicine
Ana Gabriella de Oliveira Sardinha, Ceres Nunes de Resende Oyama, Armando de Mendonça Maroja, Ivan F Costa
BACKGROUND: The aim of this paper is to provide a general discussion, algorithm, and actual working programs of the deformation method for fast simulation of biological tissue formed by fibers and fluid. In order to demonstrate the benefit of the clinical applications software, we successfully used our computational program to deform a 3D breast image acquired from patients, using a 3D scanner, in a real hospital environment. RESULTS: The method implements a quasi-static solution for elastic global deformations of objects...
2016: Source Code for Biology and Medicine
Deena M A Gendoo, Benjamin Haibe-Kains
BACKGROUND: Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had resulted in improvement of human subtype classification methods, and the parallel development of MB mouse models towards identification of subtype-specific disease origins and signaling pathways. Despite these advances, MB classification schemes remained inadequate for personalized prediction of MB subtypes for individual patient samples and across model systems...
2016: Source Code for Biology and Medicine
Fuquan Zhang
BACKGROUND: Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. However, resources to visualize the genomic map of candidate SNPs in a programming manner are limited. We have previously created an R package, mapsnp v0.1, to plot the genomic map for a panel of SNPs within a genomic region of interest. It failed to work under the latest version of Gviz package. RESULTS: We updated the mapsnp package to keep up with the latest package environment and improved its functionality by adding more parameters to fine tune plotting outputs...
2016: Source Code for Biology and Medicine
Samson S Kiware, Tanya L Russell, Zacharia J Mtema, Alpha D Malishee, Prosper Chaki, Dickson Lwetoijera, Javan Chanda, Dingani Chinula, Silas Majambere, John E Gimnig, Thomas A Smith, Gerry F Killeen
BACKGROUND: Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often in resource-limited tropical settings lacking specialized software or informatics support. RESULTS: Data from the majority of mosquito studies conformed to a generic schema, with data collection forms recording the experimental design, sorting of collections, details of sample pooling or subdivision, and additional observations...
2016: Source Code for Biology and Medicine
Refat Sharmin, Abul B M M K Islam
BACKGROUND: MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the degree of conserved antigenic sites among them. It is of importance to elucidate the shared antigenic-sites and extent of conservation between them to understand the evolutionary dynamics of MERS-CoV. RESULTS: Multiple sequence alignment of the spike (S), membrane (M), enveloped (E) and nucleocapsid (N) proteins was employed to identify the sequence conservation among MERS and Bat (HKU4, HKU5) coronaviruses...
2016: Source Code for Biology and Medicine
Vasanth R Singan, Jeremy C Simpson
BACKGROUND: Quantitative co-localization studies strengthen the analysis of fluorescence microscopy-based assays and are essential for illustrating and understanding many cellular processes and interactions. In our earlier study, we presented a rank-based intensity weighting scheme for the quantification of co-localization between structures in fluorescence microscopy images. This method, which uses a combined pixel co-occurrence and intensity correlation approach, is superior to conventional algorithms and provides a more accurate quantification of co-localization...
2016: Source Code for Biology and Medicine
Jitsuki Sawamura, Shigeru Morishita, Jun Ishigooka
BACKGROUND: We previously presented a group theoretical model that describes psychiatric patient states or clinical data in a graded vector-like format based on modulo groups. Meanwhile, the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5, the current version), is frequently used for diagnosis in daily psychiatric treatments and biological research. The diagnostic criteria of DSM-5 contain simple binominal items relating to the presence or absence of specific symptoms...
2016: Source Code for Biology and Medicine
Elliot J Yates, Louise C Dixon
BACKGROUND: Optimal ranking of literature importance is vital in overcoming article overload. Existing ranking methods are typically based on raw citation counts, giving a sum of 'inbound' links with no consideration of citation importance. PageRank, an algorithm originally developed for ranking webpages at the search engine, Google, could potentially be adapted to bibliometrics to quantify the relative importance weightings of a citation network. This article seeks to validate such an approach on the freely available, PubMed Central open access subset (PMC-OAS) of biomedical literature...
2015: Source Code for Biology and Medicine
Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski, Adam Godzik
BACKGROUND: One of the recent challenges of computational biology is development of new algorithms, tools and software to facilitate predictive modeling of big data generated by high-throughput technologies in biomedical research. RESULTS: To meet these demands we developed PROPER - a package for visual evaluation of ranking classifiers for biological big data mining studies in the MATLAB environment. CONCLUSION: PROPER is an efficient tool for optimization and comparison of ranking classifiers, providing over 20 different two- and three-dimensional performance curves...
2015: Source Code for Biology and Medicine
Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A Swertz
BACKGROUND: Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols...
2015: Source Code for Biology and Medicine
Madison Flannery, David M Budden, Alexandre Mendes
BACKGROUND: With the continued exponential growth in data volume, large-scale data mining and machine learning experiments have become a necessity for many researchers without programming or statistics backgrounds. WEKA (Waikato Environment for Knowledge Analysis) is a gold standard framework that facilitates and simplifies this task by allowing specification of algorithms, hyper-parameters and test strategies from a streamlined Experimenter GUI. Despite its popularity, the WEKA Experimenter exhibits several limitations that we address in our new FlexDM software...
2015: Source Code for Biology and Medicine
Alice Mantoan, Claudio Pizzolato, Massimo Sartori, Zimi Sawacha, Claudio Cobelli, Monica Reggiani
BACKGROUND: Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust tools for the pre-processing of experimental movement data for their use in neuromusculoskeletal modeling software. RESULTS: This paper presents MOtoNMS (matlab MOtion data elaboration TOolbox for NeuroMusculoSkeletal applications), a toolbox freely available to the community, that aims to fill this lack...
2015: Source Code for Biology and Medicine
Maciej Fronczuk, Adrian E Raftery, Ka Yee Yeung
BACKGROUND: Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implementations are programming libraries that require users to write code, which limits their accessibility. RESULTS: We have developed a tool called CyNetworkBMA for inferring gene networks from expression data that integrates with Cytoscape. Our application offers a graphical user interface for networkBMA, an efficient implementation of Bayesian Model Averaging methods for network construction...
2015: Source Code for Biology and Medicine
Connor H Fortin, Katharina V Schulze, Gregory A Babbitt
BACKGROUND: It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity...
2015: Source Code for Biology and Medicine
Carol L Ecale Zhou
BACKGROUND: In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. RESULTS: This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA)...
2015: Source Code for Biology and Medicine
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