Evidence map›Paper›PMID 26605000›Full record

ArticleProcedia computer science

Using Kepler for Tool Integration in Microarray Analysis Workflows.

Zhuohui Gan, Jennifer C Stowe, Ilkay Altintas, Andrew D McCulloch, Alexander C Zambon

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Procedia computer science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Zhuohui GanDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
Jennifer C StoweDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
Ilkay AltintasSan Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
Andrew D McCullochDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
Alexander C ZambonDepartments of Pharmacology, University of California, San Diego, La Jolla, CA, USA.

Funding

San Diego Clinical and Translational Research InstituteUL1TR000100 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S · 2012 to 2015
$19.7M
iDASH: Integrating Data for Analysis, Anonymization, and SharingU54HL108460 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI OHNO-MACHADO, LUCILA · 2010 to 2015
$19.1M
National Biomedical Computation Resource - Competitive Revision SupplementP41GM103426 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AMARO, ROMMIE E · 2012 to 2019
$14.0M
Systems Biology CoreP01HL098053 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HADDAD, GABRIEL G · 2010 to 2014
$10.2M
Multi-scale Systems Model of Murine Heart FailureR01HL105242 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BERS, DONALD M, MCCULLOCH, ANDREW D. · 2012 to 2016
$3.5M
NCATS NIH HHS UL1 TR000100NHLBI NIH HHS P01 HL098053NHLBI NIH HHS R01 HL105242NHLBI NIH HHS U54 HL108460NIGMS NIH HHS P41 GM103426
6 · The paper itself

Abstract

Increasing numbers of genomic technologies are leading to massive amounts of genomic data, all of which requires complex analysis. More and more bioinformatics analysis tools are being developed by scientist to simplify these analyses. However, different pipelines have been developed using different software environments. This makes integrations of these diverse bioinformatics tools difficult. Kepler provides an open source environment to integrate these disparate packages. Using Kepler, we integrated several external tools including Bioconductor packages, AltAnalyze, a python-based open source tool, and R-based comparison tool to build an automated workflow to meta-analyze both online and local microarray data. The automated workflow connects the integrated tools seamlessly, delivers data flow between the tools smoothly, and hence improves efficiency and accuracy of complex data analyses. Our workflow exemplifies the usage of Kepler as a scientific workflow platform for bioinformatics pipelines.

Indexed as

AltAnalyzeIntegrationKeplerMicroarrayWorkflow

Identifiers

PMID26605000
PMCPMC4655117

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.