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Source Code for Biology and Medicine

Kridsadakorn Chaichoompu, Fentaw Abegaz, Sissades Tongsima, Philip James Shaw, Anavaj Sakuntabhai, Luísa Pereira, Kristel Van Steen
Background: Resolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target. Results: This work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure...
2019: Source Code for Biology and Medicine
Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino, Dario Greco
Background: Application of microarrays in omics technologies enables quantification of many biomolecules simultaneously. It is widely applied to observe the positive or negative effect on biomolecule activity in perturbed versus the steady state by quantitative comparison. Community resources, such as Bioconductor and CRAN, host tools based on R language that have become standard for high-throughput analytics. However, application of these tools is technically challenging for generic users and require specific computational skills...
2019: Source Code for Biology and Medicine
Daniel A Machlab, Gabriel Velez, Alexander G Bassuk, Vinit B Mahajan
Background: In proteomics studies, liquid chromatography tandem mass spectrometry data (LC-MS/MS) is quantified by spectral counts or by some measure of ion abundance. Downstream comparative analysis of protein content (e.g. Venn diagrams and network analysis) typically does not include this quantitative data and critical information is often lost. To avoid loss of spectral count data in comparative proteomic analyses, it is critical to implement a tool that can rapidly retrieve this information...
2018: Source Code for Biology and Medicine
Christina Nieuwoudt, Samantha J Jones, Angela Brooks-Wilson, Jinko Graham
Background: Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, rare variants from next-generation sequencing data. Results: We present the R package SimRVPedigree, which allows researchers to simulate pedigrees ascertained on the basis of multiple, affected relatives. By incorporating the ascertainment process in the simulation, SimRVPedigree allows researchers to better understand the within-family patterns of relationship amongst affected individuals and ages of disease onset...
2018: Source Code for Biology and Medicine
Tong Liu, Zheng Wang
Background: The segment overlap score (SOV) has been used to evaluate the predicted protein secondary structures, a sequence composed of helix (H), strand (E), and coil (C), by comparing it with the native or reference secondary structures, another sequence of H, E, and C. SOV's advantage is that it can consider the size of continuous overlapping segments and assign extra allowance to longer continuous overlapping segments instead of only judging from the percentage of overlapping individual positions as Q3 score does...
2018: Source Code for Biology and Medicine
Jiho Kim, Yury Tsoy, Jan Persson, Regis Grailhe
Background: Despite the broad use of FRET techniques, available methods for analyzing protein-protein interaction are subject to high labor and lack of systematic analysis. We propose an open source software allowing the quantitative analysis of fluorescence lifetime imaging (FLIM) while integrating the steady-state fluorescence intensity information for protein-protein interaction studies. Findings: Our developed open source software is dedicated to fluorescence lifetime imaging microscopy (FLIM) data obtained from Becker & Hickl SPC-830...
2017: Source Code for Biology and Medicine
Brian D Bennett, Pierre R Bushel
BACKGROUND: Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times there are hundreds of statistically significant GO terms per gene set. Comparing enriched categories between a large number of analyses and identifying the term within the GO hierarchy with the most connections is challenging. Furthermore, ascertaining biological themes representative of the samples can be highly subjective from the interpretation of the enriched categories...
2017: Source Code for Biology and Medicine
Jörn Bethune, Lars Kraemer, Ingo Thomsen, Andreas Keller, David Ellinghaus, Andre Franke
BACKGROUND: In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities...
2017: Source Code for Biology and Medicine
Jana Lasser, Eleni Katifori
BACKGROUND: The analysis of complex networks both in general and in particular as pertaining to real biological systems has been the focus of intense scientific attention in the past and present. In this paper we introduce two tools that provide fast and efficient means for the processing and quantification of biological networks like Drosophila tracheoles or leaf venation patterns: the Network Extraction Tool (NET) to extract data and the Graph-edit-GUI (GeGUI) to visualize and modify networks...
2017: Source Code for Biology and Medicine
Maria Rubega, Claudia Cecchetto, Stefano Vassanelli, Giovanni Sparacino
BACKGROUND: Local field potentials (LFPs) evoked by sensory stimulation are particularly useful in electrophysiological research. For instance, spike timing and current transmembrane current flow estimated from LFPs recorded in the barrel cortex in rats and mice are exploited to investigate how the brain represents sensory stimuli. Recent improvements in microelectrodes technology enable neuroscientists to acquire a great amount of LFPs during the same experimental session, calling for algorithms for their quantitative automatic analysis...
2017: Source Code for Biology and Medicine
Yan Li, Jorge Andrade
BACKGROUND: A growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is however still challenging, as it requires sufficient computer programing and command-line knowledge. Furthermore, researchers often need to evaluate and visualize interactively the effect of using differential statistical and error models, assess the impact of selecting different parameters and cutoffs, and finally explore the overlapping consensus of cross-validated results obtained with different methods...
2017: Source Code for Biology and Medicine
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C Boutros
[This corrects the article DOI: 10.1186/s13029-016-0059-5.].
2017: Source Code for Biology and Medicine
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C Boutros
BACKGROUND: Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annotation, merging multiple experiments together and subsequently quantifying and visualizing the overlap. The most widely-used tools for these tasks work at the command-line (e.g. BEDTools) and the small number of available R packages are either slow or have distinct semantics and features from command-line interfaces...
2016: Source Code for Biology and Medicine
Markus Riester, Angad P Singh, A Rose Brannon, Kun Yu, Catarina D Campbell, Derek Y Chiang, Michael P Morrissey
BACKGROUND: Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known somatic alterations in cancer genes and often only sequence tumors. Therefore, an algorithm that reliably classifies variants would be helpful for retrospective exploratory analyses. Contamination of tumor samples with normal cells results in differences in expected allelic fractions of germline and somatic variants, which can be exploited to accurately infer genotypes after adjusting for local copy number...
2016: 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
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