(Q29002201)

21 June 2017

2 references

8 April 2021

Tools and techniques for computational reproducibility (English)

1 reference

21 June 2017

0 references

computational biology

1 reference

PubMed

Computational reproducibility

8 April 2021

1 reference

Stephen R Piccolo

1

1 reference

21 June 2017

Michael B Frampton

series ordinal

2

1 reference

21 June 2017

language of work or name

English

0 references

publication date

11 July 2016

2 references

21 June 2017

8 April 2021

2 references

21 June 2017

8 April 2021

5

1 reference

21 June 2017

30

1 reference

21 June 2017

1

1 reference

Creative Commons Attribution 4.0 International

21 June 2017

1 reference

describes a project that uses

8 April 2021

copyright status

copyrighted

0 references

Jupyter notebook file

1 reference

https://scigraph.springernature.com/pub.10.1186/s13742-016-0135-4

exact match

0 references

cites work

A Quick Introduction to Version Control with Git and GitHub

1 reference

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Bioboxes: standardised containers for interchangeable bioinformatics software

22 March 2017

1 reference

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Orchestrating high-throughput genomic analysis with Bioconductor

22 March 2017

1 reference

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Interactive notebooks: Sharing the code

22 March 2017

1 reference

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Software Carpentry: lessons learned

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Best practices for scientific computing

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

A field guide to genomics research

22 March 2017

1 reference

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Ten simple rules for reproducible computational research

22 March 2017

1 reference

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

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

22 March 2017

1 reference

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NIH Image to ImageJ: 25 years of image analysis

22 March 2017

1 reference

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

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Reproducible Research in Computational Science

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

In silico research in the era of cloud computing

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

An invitation to reproducible computational research

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Post-publication sharing of data and tools

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Prepublication data sharing

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Repeatability of published microarray gene expression analyses

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Sharing Detailed Research Data Is Associated with Increased Citation Rate

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Galaxy: a platform for interactive large-scale genome analysis

22 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Policy: NIH plans to enhance reproducibility

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

The fickle P value generates irreproducible results

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Virtual Reference Environments: a simple way to make research reproducible.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Dynamics and associations of microbial community types across the human body

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

All hail reproducibility in microbiome research

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Bacterial communities on classroom surfaces vary with human contact

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Quantifying reproducibility in computational biology: the case of the tuberculosis drugome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Revised standards for statistical evidence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Visibility of retractions: a cross-sectional one-year study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Improving breast cancer survival analysis through competition-based multidimensional modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

OpenStructure: an integrated software framework for computational structural biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Creating reusable tools from scripts: the Galaxy Tool Factory

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Snakemake--a scalable bioinformatics workflow engine

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Bpipe: a tool for running and managing bioinformatics pipelines

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Research priorities. Shining light into black boxes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Harnessing cloud computing with Galaxy Cloud

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

COMPUTING: Screen Savers of the World Unite!

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

Quantification of modelling uncertainties in a large ensemble of climate change simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4940747

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Design and Analysis of Computer Experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Electronic documents give reproducible research a new meaning

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Case studies in reproducibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

IPython: A System for Interactive Scientific Computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

The probability of improvement in Fisher's geometric model: a probabilistic approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Examining the Challenges of Scientific Workflows

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

What Every Computer Scientist Should Know About Floating-Point Arithmetic

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Bias as a threat to the validity of cancer molecular-marker research

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

The LONI Pipeline Processing Environment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Kepler: an extensible system for design and execution of scientific workflows

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

Announcement: Reducing our irreproducibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13742-016-0135-4

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/27401684

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

https://pubmed.ncbi.nlm.nih.gov/27401684

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13742-016-0135-4

1 reference

Dimensions Publication ID

21 June 2017

1053407686

0 references

Fatcat ID

release_37345ilcb5cebo7o5selinor5m

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/37345ilcb5cebo7o5selinor5m

mapped directly with Wikidata item

24 November 2022

based on heuristic

OpenCitations bibliographic resource ID

133395

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference