166 results match your criteria Source Code for Biology and Medicine [Journal]


ProSave: an application for restoring quantitative data to manipulated subsets of protein lists.

Source Code Biol Med 2018 12;13. Epub 2018 Nov 12.

1Omics Laboratory, Stanford University, Palo Alto, CA USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-018-0070-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233572PMC
November 2018
5 Reads

Simulating pedigrees ascertained for multiple disease-affected relatives.

Source Code Biol Med 2018 15;13. Epub 2018 Oct 15.

1Department of Statistics and Actuarial Science, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, Canada.

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. Read More

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https://scfbm.biomedcentral.com/articles/10.1186/s13029-018-
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http://dx.doi.org/10.1186/s13029-018-0069-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6190569PMC
October 2018
4 Reads

SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity.

Authors:
Tong Liu Zheng Wang

Source Code Biol Med 2018 20;13. Epub 2018 Apr 20.

Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL 33124 USA.

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. However, we have found a drawback from its previous definition, that is, it cannot ensure increasing allowance assignment when more residues in a segment are further predicted accurately. Read More

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http://dx.doi.org/10.1186/s13029-018-0068-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909207PMC

FLIM-FRET analyzer: open source software for automation of lifetime-based FRET analysis.

Source Code Biol Med 2017 3;12. Epub 2017 Nov 3.

Technology Development Platform, Institut Pasteur Korea, 463-400, 16, Daewangpangyo-ro 712 beon-gi,l Bundang-gu, Seongnam-si, Gyeonggi-do Republic of Korea.

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. Read More

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http://dx.doi.org/10.1186/s13029-017-0067-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670528PMC
November 2017
1 Read

goSTAG: gene ontology subtrees to tag and annotate genes within a set.

Source Code Biol Med 2017 13;12. Epub 2017 Apr 13.

Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, 27709 NC USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-017-0066-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390446PMC
April 2017
2 Reads

LitDB - Keeping Track of Research Papers From Your Institute Made Simple.

Source Code Biol Med 2017 21;12. Epub 2017 Mar 21.

Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.

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. Read More

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http://dx.doi.org/10.1186/s13029-017-0065-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5361695PMC
March 2017
9 Reads

NET: a new framework for the vectorization and examination of network data.

Source Code Biol Med 2017 8;12. Epub 2017 Feb 8.

Department of Physics & Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, 19104-6396 PA USA.

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 tracheoles or leaf venation patterns: the Network Extraction Tool () to extract data and the Graph-edit-GUI () to visualize and modify networks.

Results: NET is especially designed for high-throughput semi-automated analysis of biological datasets containing digital images of networks. Read More

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http://dx.doi.org/10.1186/s13029-017-0064-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299731PMC
February 2017
3 Reads

Algorithm and software to automatically identify latency and amplitude features of local field potentials recorded in electrophysiological investigation.

Source Code Biol Med 2017 7;12. Epub 2017 Feb 7.

Department of Information Engineering, University of Padova, Padova, 35131 Italy.

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. Read More

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http://dx.doi.org/10.1186/s13029-017-0062-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297145PMC
February 2017
7 Reads

DEApp: an interactive web interface for differential expression analysis of next generation sequence data.

Source Code Biol Med 2017 3;12. Epub 2017 Feb 3.

Center for Research Informatics, University of Chicago, Knapp Center for Biomedical Discovery, 900 East 57th St., Chicago, 60637 USA.

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. Read More

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http://scfbm.biomedcentral.com/articles/10.1186/s13029-017-0
Publisher Site
http://dx.doi.org/10.1186/s13029-017-0063-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291987PMC
February 2017
4 Reads

Erratum to: A bedr way of genomic interval processing.

Source Code Biol Med 2017 9;12. Epub 2017 Jan 9.

Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.

[This corrects the article DOI: 10.1186/s13029-016-0059-5.]. Read More

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http://dx.doi.org/10.1186/s13029-016-0061-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223540PMC
January 2017
4 Reads

A bedr way of genomic interval processing.

Source Code Biol Med 2016 15;11:14. Epub 2016 Dec 15.

Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0059-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5157088PMC
December 2016
9 Reads

PureCN: copy number calling and SNV classification using targeted short read sequencing.

Source Code Biol Med 2016 15;11:13. Epub 2016 Dec 15.

Novartis Institutes for BioMedical Research, Cambridge, MA USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0060-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5157099PMC
December 2016
16 Reads

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

Source Code Biol Med 2016 17;11:12. Epub 2016 Aug 17.

Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0058-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987990PMC
August 2016
12 Reads

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data.

Source Code Biol Med 2016 11;11:11. Epub 2016 Jul 11.

Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802 USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0057-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940913PMC
July 2016
9 Reads

A new tool for prioritization of sequence variants from whole exome sequencing data.

Source Code Biol Med 2016 1;11:10. Epub 2016 Jul 1.

Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

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.

Results: We designed a novel method for the filtration of WES data called TAPER™ (Tool for Automated selection and Prioritization for Efficient Retrieval of sequence variants). Read More

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http://dx.doi.org/10.1186/s13029-016-0056-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929716PMC
July 2016
13 Reads

Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.

Source Code Biol Med 2016 24;11. Epub 2016 Jun 24.

Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Suite 510, MaRS Centre, 661 University Ave, Toronto, Ontario Canada.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0055-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919834PMC
June 2016
5 Reads

SV-STAT accurately detects structural variation via alignment to reference-based assemblies.

Source Code Biol Med 2016 18;11. Epub 2016 Jun 18.

Structural and Computational Biology and Molecular Biophysics (SCBMB) Program, Baylor College of Medicine, Houston, TX 77030 USA ; Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030 USA ; W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX 77005 USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0051-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913042PMC
June 2016
17 Reads

Implementation and clinical application of a deformation method for fast simulation of biological tissue formed by fibers and fluid.

Source Code Biol Med 2016 15;11. Epub 2016 Apr 15.

Faculdade UnB Planaltina, University of Brasilia, 70919-970 Brasilia, DF Brazil.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0054-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832498PMC
April 2016
3 Reads

MM2S: personalized diagnosis of medulloblastoma patients and model systems.

Source Code Biol Med 2016 11;11. Epub 2016 Apr 11.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Ontario Canada ; Department of Computer Science, University of Toronto, Toronto, Ontario Canada.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0053-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827218PMC
April 2016
7 Reads

A flexible tool to plot a genomic map for single nucleotide polymorphisms.

Authors:
Fuquan Zhang

Source Code Biol Med 2016 2;11. Epub 2016 Apr 2.

Wuxi Mental Health Center, Nanjing Medical University, 156 Qianrong Road, Wuxi, Jiangsu Province 214151 China.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0052-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818925PMC
April 2016
5 Reads

A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes.

Source Code Biol Med 2016 28;11. Epub 2016 Mar 28.

Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania ; Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK.

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. Generically applicable forms with standardized attribute definitions enabled rigorous, consistent data and sample management with generic software and minimal expertise. Read More

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http://dx.doi.org/10.1186/s13029-016-0050-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809029PMC
March 2016
12 Reads

Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis.

Source Code Biol Med 2016 9;11. Epub 2016 Mar 9.

Department of Genetic Engineering and Biotechnology, University of Dhaka, Science Complex Building, Dhaka, 1000 Bangladesh.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0049-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784407PMC
March 2016
5 Reads

Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images.

Source Code Biol Med 2016 16;11. Epub 2016 Feb 16.

School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin 4, Ireland.

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. Read More

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http://dx.doi.org/10.1186/s13029-016-0048-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754806PMC
February 2016
8 Reads

Symmetrical treatment of "Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition", for major depressive disorders.

Source Code Biol Med 2016 19;11. Epub 2016 Jan 19.

Department of Psychiatry, Tokyo Women's Medical University, Tokyo, Japan.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0041-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717580PMC
January 2016
1 Read

PageRank as a method to rank biomedical literature by importance.

Source Code Biol Med 2015 9;10:16. Epub 2015 Dec 9.

College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0046-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674919PMC
December 2015
9 Reads

PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB.

Source Code Biol Med 2015 3;10:15. Epub 2015 Dec 3.

Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92307 USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0047-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668683PMC
December 2015
4 Reads

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

Source Code Biol Med 2015 19;10:14. Epub 2015 Nov 19.

University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Postbus 30 001, Groningen, 9700 RB The Netherlands.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0042-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652372PMC
November 2015
6 Reads

FlexDM: Simple, parallel and fault-tolerant data mining using WEKA.

Source Code Biol Med 2015 17;10:13. Epub 2015 Nov 17.

School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, 2308 NSW Australia.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0045-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647584PMC
November 2015
3 Reads

MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation.

Source Code Biol Med 2015 16;10:12. Epub 2015 Nov 16.

Department of Management and Engineering, University of Padova, Stradella San Nicola, 3, Vicenza, 36100 Italy.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0044-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647340PMC
November 2015
8 Reads

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks.

Source Code Biol Med 2015 11;10:11. Epub 2015 Nov 11.

Institute of Technology, University of Washington, Tacoma, 98402 WA USA.

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. Read More

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http://dx.doi.org/10.1186/s13029-015-0043-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642660PMC
November 2015
10 Reads

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

Source Code Biol Med 2015 25;10:10. Epub 2015 Sep 25.

Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623 USA.

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). Read More

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http://dx.doi.org/10.1186/s13029-015-0040-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583169PMC
September 2015
6 Reads

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

Source Code Biol Med 2015 5;10. Epub 2015 Aug 5.

Computational Biology Group, Global Security Computing Applications Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 USA.

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). Read More

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http://dx.doi.org/10.1186/s13029-015-0039-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526201PMC
August 2015
2 Reads

Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment.

Source Code Biol Med 2015 22;10. Epub 2015 May 22.

Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh.

Background: Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Read More

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http://dx.doi.org/10.1186/s13029-015-0037-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472393PMC
June 2015
29 Reads
1 Citation

Membrainy: a 'smart', unified membrane analysis tool.

Source Code Biol Med 2015 7;10. Epub 2015 Mar 7.

Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, UK.

Background: The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These interactions often result in changes to the properties of the lipids which can modify the behaviour of the membrane. Membrainy is a unified membrane analysis tool that contains a broad spectrum of analytical techniques to enable: measurement of acyl chain order parameters; presentation of 2D surface and thickness maps; determination of lateral and axial headgroup orientations; measurement of bilayer and leaflet thickness; analysis of the annular shell surrounding membrane-embedded objects; quantification of gel percentage; time evolution of the transmembrane voltage; area per lipid calculations; and quantification of lipid mixing/demixing entropy. Read More

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http://dx.doi.org/10.1186/s13029-015-0033-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460882PMC
June 2015
49 Reads

PrimerView: high-throughput primer design and visualization.

Source Code Biol Med 2015 4;10. Epub 2015 Jun 4.

Department of Biological Sciences, The George Washington University, Science & Engineering Hall 5685, 800 22nd St N.W., Washington, DC 20052 USA ; Institute for Neuroscience, The George Washington University, 636 Ross Hall, 2300 I St. N.W., Washington, DC 20052 USA.

Background: High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer walking experiments. Batch primer design is also required in validation experiments from RNA-seq transcriptome sequencing projects, as well as in generating probes for microarray experiments. The growing popularity of next generation sequencing and microarray technology has created a greater need for more primer design tools to validate large numbers of candidate genes and markers. Read More

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http://dx.doi.org/10.1186/s13029-015-0038-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456780PMC
June 2015
1 Read

popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator.

Source Code Biol Med 2015 11;10. Epub 2015 Apr 11.

Departments of Biology and Biomedical Informatics, Stanford University, Stanford, CA 94305 USA ; Departments of Biomedical Informatics, Stanford University, Stanford, CA 94305 USA.

Background: Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). Read More

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http://dx.doi.org/10.1186/s13029-015-0036-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399400PMC
April 2015
2 Reads

Wormpath: searching for molecular interaction networks in Caenorhabditis elegans.

Source Code Biol Med 2015 2;10. Epub 2015 Apr 2.

CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany ; Systems Biology of Aging Cologne (SyBACol), University of Cologne, Cologne, Germany ; Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.

Background: High-throughput transcriptional profiling using Next-Generation Sequencing (RNA-Seq) or microarray technology have become standard tools in molecular biology. Successful investigations of gene regulatory mechanisms from these data typically employ mathematical models of biological networks.

Results: We have developed Wormpath, a software for molecular network discovery which operates on the genetic and physical interaction data of the Wormbase, a comprehensive resource of molecular data on Caenorhabditis elegans. Read More

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http://dx.doi.org/10.1186/s13029-015-0034-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392734PMC
April 2015
4 Reads

MagiCMicroRna: a web implementation of AgiMicroRna using shiny.

Source Code Biol Med 2015 26;10. Epub 2015 Mar 26.

Department of Toxicogenomics, P.O. Box 616, 6200 MD Maastricht, The Netherlands.

Background: MicroRNA expression can be quantified using sequencing techniques or commercial microRNA-expression arrays. Recently, the AgiMicroRna R-package was published that enabled systematic preprocessing and statistical analysis for Agilent microRNA arrays. Here we describe MagiCMicroRna, which is a user-friendly web interface for this package, together with a new filtering approach. Read More

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http://dx.doi.org/10.1186/s13029-015-0035-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383057PMC
April 2015
7 Reads

LocusTrack: Integrated visualization of GWAS results and genomic annotation.

Source Code Biol Med 2015 3;10. Epub 2015 Feb 3.

Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia.

Background: Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci.

Results: We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservation, chromatin state, and other genomic and regulatory elements. Read More

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http://dx.doi.org/10.1186/s13029-015-0032-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351846PMC
March 2015
3 Reads

Mega2: validated data-reformatting for linkage and association analyses.

Source Code Biol Med 2014 5;9(1):26. Epub 2014 Dec 5.

Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261 USA ; Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261 USA.

Background: In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of these analysis programs use differing input formats. Writing scripts to facilitate this can be tedious, time-consuming, and error-prone. Read More

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http://dx.doi.org/10.1186/s13029-014-0026-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269913PMC
February 2015
3 Reads

AdmixKJump: identifying population structure in recently diverged groups.

Source Code Biol Med 2015 3;10(1). Epub 2015 Feb 3.

Institute for Genome Sciences, Program in Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, 801 W Baltimore St, Baltimore, 21201 MD USA.

Motivation: Correctly modeling population structure is important for understanding recent evolution and for association studies in humans. While pre-existing knowledge of population history can be used to specify expected levels of subdivision, objective metrics to detect population structure are important and may even be preferable for identifying groups in some situations. One such metric for genomic scale data is implemented in the cross-validation procedure of the program ADMIXTURE, but it has not been evaluated on recently diverged and potentially cryptic levels of population structure. Read More

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http://dx.doi.org/10.1186/s13029-014-0031-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325960PMC
February 2015
1 Read

Using the value of Lin's concordance correlation coefficient as a criterion for efficient estimation of areas of leaves of eelgrass from noisy digital images.

Source Code Biol Med 2014 20;9(1):29. Epub 2014 Dec 20.

Instituto Tecnológico de Tijuana, Tijuana, Baja California México.

Background: Eelgrass is a cosmopolitan seagrass species that provides important ecological services in coastal and near-shore environments. Despite its relevance, loss of eelgrass habitats is noted worldwide. Restoration by replanting plays an important role, and accurate measurements of the standing crop and productivity of transplants are important for evaluating restoration of the ecological functions of natural populations. Read More

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http://dx.doi.org/10.1186/s13029-014-0029-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302588PMC
February 2015
3 Reads

Robust dose-response curve estimation applied to high content screening data analysis.

Source Code Biol Med 2014 10;9(1):27. Epub 2014 Dec 10.

Videometer A/S, Horsholm, Denmark.

Background And Method: Successfully automated sigmoidal curve fitting is highly challenging when applied to large data sets. In this paper, we describe a robust algorithm for fitting sigmoid dose-response curves by estimating four parameters (floor, window, shift, and slope), together with the detection of outliers. We propose two improvements over current methods for curve fitting. Read More

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http://dx.doi.org/10.1186/s13029-014-0027-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279979PMC
January 2015
30 Reads

Erratum: BatTool: an R package with GUI for assessing the effect of white-nose syndrome and other take events on Myotis spp. of bats.

Source Code Biol Med 2014 20;9(1):122. Epub 2014 Dec 20.

Division of Endangered Species, U.S. Fish and Wildlife Service, 555 Lester Avenue, 54650 Onalaksa, WI USA.

[This corrects the article DOI: 10.1186/1751-0473-9-9.]. Read More

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http://dx.doi.org/10.1186/s13029-014-0028-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289230PMC
March 2015
3 Reads

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

Source Code Biol Med 2014 5;9(1):25. Epub 2014 Dec 5.

Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.

Background: Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centres, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. Read More

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http://dx.doi.org/10.1186/s13029-014-0025-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288629PMC
January 2015
4 Reads

HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline.

Source Code Biol Med 2014 24;9(1):30. Epub 2014 Dec 24.

Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136 FL USA.

Background: The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expression levels, such as those measured with RNAseq and microarray experiments, to provide qualitative large-scale views of the transcriptonomic landscape. Creating high-quality heatmaps is a computationally intensive task, often requiring considerable programming experience, particularly for customizing features to a specific dataset at hand. Read More

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http://dx.doi.org/10.1186/s13029-014-0030-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279803PMC
December 2014
31 Reads

Methylation plotter: a web tool for dynamic visualization of DNA methylation data.

Source Code Biol Med 2014 7;9:11. Epub 2014 Jun 7.

Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Ctra. de Can Ruti, camí de les escoles, s/n, 08916 Badalona, Spain ; Health Research Institute Germans Trias i Pujol (IGTP), Ctra. de Can Ruti, camí de les escoles, s/n, 08916 Badalona, Spain.

Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Read More

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http://dx.doi.org/10.1186/1751-0473-9-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066318PMC
September 2014
13 Reads

EC2KEGG: a command line tool for comparison of metabolic pathways.

Authors:
Aleksey Porollo

Source Code Biol Med 2014 2;9:19. Epub 2014 Sep 2.

Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.

Background: Next-generation sequencing and metagenome projects yield a large number of new genomes that need further annotations, such as identification of enzymes and metabolic pathways, or analysis of metabolic strategies of newly sequenced species in comparison to known organisms. While methods for enzyme identification are available, development of the command line tools for high-throughput comparative analysis and visualization of identified enzymes is lagging.

Methods: A set of perl scripts has been developed to perform automated data retrieval from the KEGG database using its new REST program application interface. Read More

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http://scfbm.biomedcentral.com/articles/10.1186/1751-0473-9-
Publisher Site
http://dx.doi.org/10.1186/1751-0473-9-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157228PMC
September 2014
4 Reads

VIRAPOPS2 supports the influenza virus reassortments.

Source Code Biol Med 2014 17;9:18. Epub 2014 Aug 17.

Univ Paris Diderot, Sorbonne Paris Cité, F-75013 Paris, France ; CNRS, UMR7592, Institut Jacques Monod, F-75013 Paris, France ; Atelier de Bio Informatique, F-75005 Paris, France.

Background: For over 400 years, due to the reassortment of their segmented genomes, influenza viruses evolve extremely quickly and cause devastating epidemics. This reassortment arises because two flu viruses can infect the same cell and therefore the new virions' genomes will be composed of segment reassortments of the two parental strains. A treatment developed against parents could then be ineffective if the virions' genomes are different enough from their parent's genomes. Read More

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http://scfbm.biomedcentral.com/articles/10.1186/1751-0473-9-
Publisher Site
http://dx.doi.org/10.1186/1751-0473-9-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144320PMC
September 2014
10 Reads

Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains.

Source Code Biol Med 2014 10;9:16. Epub 2014 Jul 10.

Centre for High-Throughput Biology, University of British Colombia, Vancouver, BC V6T 1Z4, Canada ; Department of Biochemistry & Molecular Biology, University of British Colombia, Vancouver, BC V6T 2A1, Canada.

Background: A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties of very diverse polymers. To date, determining these properties is the privilege of a limited circle of biophysicists and engineers with appropriate technical skills.

Findings: Easyworm is a user-friendly software suite coded in MATLAB that simplifies the image analysis of individual polymeric chains and the extraction of the mechanical properties of these chains. Read More

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http://dx.doi.org/10.1186/1751-0473-9-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4106204PMC
August 2014
7 Reads