Tools and techniques for computational reproducibility

A Quick Introduction to Version Control with Git and GitHub

(2016) John D. Blischak et al.   PLoS Computational Biology

Rebooting review

(2015)   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

The fickle P value generates irreproducible results

(2015) Lewis G Halsey et al.   NATURE METHODS

The probability of improvement in Fisher’s geometric model: A probabilistic approach

(2015) Yoav Ram et al.   THEORETICAL POPULATION BIOLOGY

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

(2015) Andreas Bremges et al.   GigaScience

Bioboxes: standardised containers for interchangeable bioinformatics software

(2015) Peter Belmann et al.   GigaScience

Virtual Reference Environments: a simple way to make research reproducible

(2014) Daniel G. Hurley et al.   BRIEFINGS IN BIOINFORMATICS

Interactive notebooks: Sharing the code

(2014) Helen Shen   NATURE

Code share

(2014)   NATURE

Policy: NIH plans to enhance reproducibility

(2014) Francis S. Collins et al.   NATURE

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss

(2014) Andrew M Gross et al.   NATURE GENETICS

Software with impact

(2014)   NATURE METHODS

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

A Field Guide to Genomics Research

(2014) Andrea H. Bild et al.   PLOS BIOLOGY

Best Practices for Scientific Computing

(2014) Greg Wilson et al.   PLOS BIOLOGY

A data repository and analysis framework for spontaneous neural activity recordings in developing retina

(2014) Stephen John Eglen et al.   GigaScience

Bacterial communities on classroom surfaces vary with human contact

(2014) James F Meadow et al.   Microbiome

All hail reproducibility in microbiome research

(2014) Jacques Ravel et al.   Microbiome

OpenStructure: an integrated software framework for computational structural biology

(2013) M. Biasini et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

If a job is worth doing, it is worth doing twice

(2013) Jonathan F. Russell   NATURE

Announcement: Reducing our irreproducibility

(2013)   NATURE

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

(2013) Victoria Stodden et al.   PLoS One

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

(2013) Daniel Garijo et al.   PLoS One

Revised standards for statistical evidence

(2013) V. E. Johnson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

(2013) Erhan Bilal et al.   PLoS Computational Biology

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Creating reusable tools from scripts: the Galaxy Tool Factory

(2012) R. Lazarus et al.   BIOINFORMATICS

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

(2012) Konstantinos Krampis et al.   BMC BIOINFORMATICS

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection

(2012) J. A. Neuman et al.   BRIEFINGS IN BIOINFORMATICS

Abstract 3966: GenomeSpace: An environment for frictionless bioinformatics

(2012) Michael Reich et al.   CANCER RESEARCH

Virtual Appliances, Cloud Computing, and Reproducible Research

(2012) Bill Howe   COMPUTING IN SCIENCE & ENGINEERING

Reproducible research for scientific computing: Tools and strategies for changing the culture

(2012) Randall J. LeVeque et al.   COMPUTING IN SCIENCE & ENGINEERING

Error prone

(2012)   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

(2012) Ed H. B. M. Gronenschild et al.   PLoS One

Shining Light into Black Boxes

(2012) A. Morin et al.   SCIENCE

Computing for the Large Hadron Collider

(2011) Ian Bird   Annual Review of Nuclear and Particle Science

Case studies in reproducibility

(2011) T. Hothorn et al.   BRIEFINGS IN BIOINFORMATICS

Harnessing cloud computing with Galaxy Cloud

(2011) Enis Afgan et al.   NATURE BIOTECHNOLOGY

Reproducible Research in Computational Science

(2011) R. D. Peng   SCIENCE

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

(2010) Keith A. Baggerly et al.   Annals of Applied Statistics

An invitation to reproducible computational research

(2010) D. L. Donoho   BIOSTATISTICS

In silico research in the era of cloud computing

(2010) Joel T Dudley et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Prepublication data sharing

(2009)   NATURE

Post-publication sharing of data and tools

(2009) Paul N. Schofield et al.   NATURE

Repeatability of published microarray gene expression analyses

(2009) John P A Ioannidis et al.   NATURE GENETICS