Experiences with workflows for automating data-intensive bioinformatics (Q30987801)

11 August 2017

Experiences with workflows for automating data-intensive bioinformatics (English)

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11 August 2017

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PubMed publication ID

28 June 2017

2

Erik Bongcam-Rudloff

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Ognyan Kulev

Ognyan Kulev

12

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Paweł P Łabaj

Paweł P Łabaj

13

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Dimitar Vassilev

Dimitar Vassilev

18

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Lukas Forer

Lukas Forer

4

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Luca Pireddu

Luca Pireddu

15

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Samuel Lampa

Samuel Lampa

14

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author name string

Guillermo Carrasco Hernández

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11 August 2017

Mario Giovacchini

5

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11 August 2017

Roman Valls Guimera

6

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11 August 2017

Aleksi Kallio

7

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11 August 2017

Eija Korpelainen

8

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11 August 2017

Maciej M Kańduła

9

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11 August 2017

Milko Krachunov

10

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11 August 2017

David P Kreil

11

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11 August 2017

Sebastian Schönherr

16

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11 August 2017

Alexey Siretskiy

17

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11 August 2017

19 August 2015

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11 August 2017

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11 August 2017

10

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11 August 2017

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A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

HTSeq--a Python framework to work with high-throughput sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Detecting and correcting systematic variation in large-scale RNA sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Genetic variants regulating immune cell levels in health and disease.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

The Cancer Genome Atlas Pan-Cancer analysis project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Biology: The big challenges of big data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Snakemake--a scalable bioinformatics workflow engine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Bpipe: a tool for running and managing bioinformatics pipelines

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Chipster: user-friendly analysis software for microarray and other high-throughput data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

SEAL: a distributed short read mapping and duplicate removal tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Conveyor: a workflow engine for bioinformatic analyses.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Galaxy CloudMan: delivering cloud compute clusters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Ruffus: a lightweight Python library for computational pipelines

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

BioXSD: the common data-exchange format for everyday bioinformatics web services

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Cloud computing and the DNA data race

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

The case for cloud computing in genome informatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Hybridization thermodynamics of NimbleGen microarrays.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Galaxy: a web-based genome analysis tool for experimentalists

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Model-based probe set optimization for high-performance microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

XML schemas for common bioinformatic data types and their application in workflow systems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Galaxy: a platform for interactive large-scale genome analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Taverna: a tool for the composition and enactment of bioinformatics workflows

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539931

Make — a program for maintaining computer programs

21 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

Molecular Modelling of G Protein-Coupled Receptors Through the Web.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

Design and implementation of GXP make — A workflow system based on make

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

Delivering bioinformatics MapReduce applications in the cloud

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

Computational science: ...Error

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13062-015-0071-8

10.1186/S13062-015-0071-8

21 January 2018

Identifiers

DOI

1 reference

Dimensions Publication ID

11 August 2017

0 references

1 reference

11 August 2017

PubMed publication ID

26282399

1 reference