Articles

BioFlow: a web based workflow management software for design and execution of genomics pipelines

Bioinformatics data analysis is usually done sequentially by chaining together multiple tools. These are created by writing scripts and tracking the inputs and outputs of all stages. Writing such scripts requi...

Authors: Harold Garner and Ashwin Puthige

EC2KEGG: a command line tool for comparison of metabolic pathways

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 strategi...

Authors: Aleksey Porollo

VIRAPOPS2 supports the influenza virus reassortments

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 t...

Authors: Michel Petitjean and Anne Vanet

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

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 o...

Authors: Guillaume Lamour, Julius B Kirkegaard, Hongbin Li, Tuomas PJ Knowles and Jörg Gsponer

A dedicated database system for handling multi-level data in systems biology

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic...

Authors: Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew and Jens Nielsen

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

The NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual sear...

Authors: Daniel J Park, Tú Nguyen-Dumont, Sori Kang, Karin Verspoor and Bernard J Pope

biobambam: tools for read pair collation based algorithms on BAM files

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of ...

Authors: German Tischler and Steven Leonard

Second generation registry framework

Information management systems are essential to capture data be it for public health and human disease, sustainable agriculture, or plant and animal biosecurity. In public health, the term patient registry is ...

Authors: Matthew I Bellgard, Lee Render, Maciej Radochonski and Adam Hunter

Modular and configurable optimal sequence alignment software: Cola

The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignm...

Authors: Neda Zamani, Görel Sundström, Marc P Höppner and Manfred G Grabherr

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

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 methylatio...

Authors: Izaskun Mallona, Anna Díez-Villanueva and Miguel A Peinado

H3Africa: a tipping point for a revolution in bioinformatics, genomics and health research in Africa

A multi-million dollar research initiative involving the National Institutes of Health (NIH), Wellcome Trust and African scientists has been launched. The initiative, referred to as H3Africa, is an acronym tha...

Authors: Moses P Adoga, Segun A Fatumo and Simon M Agwale

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

Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind ...

Authors: Richard A Erickson, Wayne E Thogmartin and Jennifer A Szymanski

Software for pre-processing Illumina next-generation sequencing short read sequences

When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specif...

Authors: Chuming Chen, Sari S Khaleel, Hongzhan Huang and Cathy H Wu

BLASTPLOT: a PERL module to plot next generation sequencing NCBI-BLAST results

The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based B...

Authors: Jesus Enrique Herrera-Galeano, Kenneth G Frey, Regina Z Cer, Alfred J Mateczun, Kimberly A Bishop-Lilly and Vishwesh P Mokashi

Identifying large sets of unrelated individuals and unrelated markers

Genetic Analyses in large sample populations are important for a better understanding of the variation between populations, for designing conservation programs, for detecting rare mutations which may be risk f...

Authors: Kuruvilla Joseph Abraham and Clara Diaz

PFClust: an optimised implementation of a parameter-free clustering algorithm

A well-known problem in cluster analysis is finding an optimal number of clusters reflecting the inherent structure of the data. PFClust is a partitioning-based clustering algorithm capable, unlike many widely...

Authors: Khadija Musayeva, Tristan Henderson, John BO Mitchell and Lazaros Mavridis

Erratum to: Dispelling myths about rare disease registry system development

Authors: Matthew Bellgard, Christophe Beroud, Kay Parkinson, Tess Harris, Segolene Ayme, Gareth Baynam, Tarun Weeramanthri, Hugh Dawkins and Adam Hunter

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end...

Authors: Bernard J Pope, Tú Nguyen-Dumont, Fleur Hammet and Daniel J Park

TrigNER: automatically optimized biomedical event trigger recognition on scientific documents

Cellular events play a central role in the understanding of biological processes and functions, providing insight on both physiological and pathogenesis mechanisms. Automatic extraction of mentions of such eve...

Authors: David Campos, Quoc-Chinh Bui, Sérgio Matos and José Luís Oliveira

MOSAL: software tools for multiobjective sequence alignment

Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of the...

Authors: Luís Paquete, Pedro Matias, Maryam Abbasi and Miguel Pinheiro

Combining de novo and reference-guided assembly with scaffold_builder

Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes i...

Authors: Genivaldo GZ Silva, Bas E Dutilh, T David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A Dinsdale and Robert A Edwards

[COMMODE] a large-scale database of molecular descriptors using compounds from PubChem

Molecular descriptors have been extensively used in the field of structure-oriented drug design and structural chemistry. They have been applied in QSPR and QSAR models to predict ADME-Tox properties, which sp...

Authors: Andreas Dander, Laurin AJ Mueller, Ralf Gallasch, Stephan Pabinger, Frank Emmert-Streib, Armin Graber and Matthias Dehmer

Dispelling myths about rare disease registry system development

Rare disease registries (RDRs) are an essential tool to improve knowledge and monitor interventions for rare diseases. If designed appropriately, patient and disease related information captured within them ca...

Authors: Matthew Bellgard, Christophe Beroud, Kay Parkinson, Tess Harris, Segolene Ayme, Gareth Baynam, Tarun Weeramanthri, Hugh Dawkins and Adam Hunter

MIA - A free and open source software for gray scale medical image analysis

Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisitio...

Authors: Gert Wollny, Peter Kellman, María-Jesus Ledesma-Carbayo, Matthew M Skinner, Jean-Jaques Hublin and Thomas Hierl

Superplot3d: an open source GUI tool for 3d trajectory visualisation and elementary processing

When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to ra...

Authors: Luke J Whitehorn, Frances M Hawkes and Ian AN Dublon

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments

Protein-protein interaction (PPI) plays a core role in cellular functions. Massively parallel supercomputing systems have been actively developed over the past few years, which enable large-scale biological pr...

Authors: Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida and Yutaka Akiyama

GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses

The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoper...

Authors: Hidetoshi Itaya, Kazuki Oshita, Kazuharu Arakawa and Masaru Tomita

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, ...

Authors: Erlend Hodneland, Tanja Kögel, Dominik Michael Frei, Hans-Hermann Gerdes and Arvid Lundervold

Implementing a new EPR lineshape parameter for organic radicals in carbonaceous matter

Electron Paramagnetic Resonance (EPR) is a non-destructive, non-invasive technique useful for the characterization of organic moieties in primitive carbonaceous matter related to the origin of life. The classi...

Authors: Mathilde Bourbin, Yann Le Du, Laurent Binet and Didier Gourier

GenePattern flow cytometry suite

Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have i...

Authors: Josef Spidlen, Aaron Barsky, Karin Breuer, Peter Carr, Marc-Danie Nazaire, Barbara Allen Hill, Yu Qian, Ted Liefeld, Michael Reich, Jill P Mesirov, Peter Wilkinson, Richard H Scheuermann, Rafick-Pierre Sekaly and Ryan R Brinkman

Crowdsourcing the Corpasome

The suffix -ome conveys “comprehensiveness” in some way. The idea of the Corpasome started half-jokingly, acknowledging the efforts to sequence five members of my family. After the unexpected response from man...

Authors: Manuel Corpas

EEGgui: a program used to detect electroencephalogram anomalies after traumatic brain injury

Identifying and quantifying pathological changes in brain electrical activity is important for investigations of brain injury and neurological disease. An example is the development of epilepsy, a secondary co...

Authors: Justin Sick, Eric Bray, Amade Bregy, W Dalton Dietrich, Helen M Bramlett and Thomas Sick

BioPatRec: A modular research platform for the control of artificial limbs based on pattern recognition algorithms

Processing and pattern recognition of myoelectric signals have been at the core of prosthetic control research in the last decade. Although most studies agree on reporting the accuracy of predicting predefined...

Authors: Max Ortiz-Catalan, Rickard Brånemark and Bo Håkansson

The non-negative matrix factorization toolbox for biological data mining

Non-negative matrix factorization (NMF) has been introduced as an important method for mining biological data. Though there currently exists packages implemented in R and other programming languages, they eith...

Authors: Yifeng Li and Alioune Ngom

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes

The annotation of surface exposed bacterial membrane proteins is an important step in interpretation and validation of proteomic experiments. In particular, proteins detected by cell surface protease shaving e...

Authors: Andrew J Perry and Bosco K Ho

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or ...

Authors: Mehdi Pirooznia, Fayaz Seifuddin, Fernando S Goes, Jeffrey T Leek and Peter P Zandi

Git can facilitate greater reproducibility and increased transparency in science

Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but al...

Authors: Karthik Ram

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics

The whole-genome sequences of many non-model organisms have recently been determined. Using these genome sequences, next-generation sequencing based experiments such as RNA-seq and ChIP-seq have been performed...

Authors: Akiko Izawa and Jun Sese

CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals

In population association studies, standard methods of statistical inference assume that study subjects are independent samples. In genetic association studies, it is therefore of interest to diagnose undocume...

Authors: Annick Nembot-Simo, Jinko Graham and Brad McNeney

BlaSTorage: a fast package to parse, manage and store BLAST results

Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all infor...

Authors: Massimiliano Orsini and Simone Carcangiu

FCC – An automated rule-based processing tool for life science data

Data processing in the bioinformatics field often involves the handling of diverse software programs in one workflow. The field is lacking a set of standards for file formats so that files have to be processed...

Authors: Simon Barkow-Oesterreicher, Can Türker and Christian Panse

Knowledge Driven Variable Selection (KDVS) – a new approach to enrichment analysis of gene signatures obtained from high–throughput data

High–throughput (HT) technologies provide huge amount of gene expression data that can be used to identify biomarkers useful in the clinical practice. The most frequently used approaches first select a set of ...

Authors: Grzegorz Zycinski, Annalisa Barla, Margherita Squillario, Tiziana Sanavia, Barbara Di Camillo and Alessandro Verri

MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data

MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing and represent critical regulators of cell and tissue differentiation. Microarray expression profiling of miRNAs is ...

Authors: Guy N Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia Webb, Robert M Greene and M Michele Pisano

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads

MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies...

Authors: Alexander V Tyakht, Anna S Popenko, Maxim S Belenikin, Ilya A Altukhov, Alexander V Pavlenko, Elena S Kostryukova, Oksana V Selezneva, Andrei K Larin, Irina Y Karpova and Dmitry G Alexeev

RMol: a toolset for transforming SD/Molfile structure information into R objects

The graph-theoretical analysis of molecular networks has a long tradition in chemoinformatics. As demonstrated frequently, a well designed format to encode chemical structures and structure-related information...

Authors: Martin Grabner, Kurt Varmuza and Matthias Dehmer

A CellML simulation compiler and code generator using ODE solving schemes

Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully si...

Authors: Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda and Akira Amano

PathNet: a tool for pathway analysis using topological information

Identification of canonical pathways through enrichment of differentially expressed genes in a given pathway is a widely used method for interpreting gene lists generated from high-throughput experimental stud...

Authors: Bhaskar Dutta, Anders Wallqvist and Jaques Reifman

CADLIVE optimizer: web-based parameter estimation for dynamic models

Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complex...

Authors: Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi and Hiroyuki Kurata

JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility

Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, ...

Authors: Daniel Jaschob and Michael Riffle

How Not to Be a Bioinformatician

Although published material exists about the skills required for a successful bioinformatics career, strangely enough no work to date has addressed the matter of how to excel at not being a bioinformatician. A se...

Authors: Manuel Corpas, Segun Fatumo and Reinhard Schneider