Long-Term Reduction of T-Cell Intracellular Antigens Reveals a Transcriptome Associated with Extracellular Matrix and Cell Adhesion Components

Nunez, M.; Sánchez-Jiménez, Carmen; Alcalde, José; Izquierdo, José M.

doi:10.1371/journal.pone.0113141

Cited by 3 publications

(2 citation statements)

References 51 publications

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“…The reported experiment with this dataset measured gene expression in normal HeLa cells and HeLa cells with TIA1 and TIAR knocked down 15 . We ran the same source code using the same dataset altering only the version of the BrainArray Custom CDF library (versions 18, 19 and 20).…”

Section: Resultsmentioning

confidence: 99%

Reproducibility of computational workflows is automated using continuous analysis

2017

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Replication, validation and extension of experiments are crucial for scientific progress. Computational experiments are inherently scriptable and should be easy to reproduce. However, it remains difficult and time consuming to reproduce computational results because analyses are designed and run in a specific computing environment, which may be difficult or impossible to match from written instructions. We report a workflow named continuous analysis that can build reproducibility into computational analyses. Continuous analysis combines Docker, a container technology akin to virtual machines, with continuous integration, a software development technique, to automatically re-run a computational analysis whenever updates or improvements are made to source code or data. This allows results to be accurately reproduced without needing to contact the study authors. Continuous analysis allows reviewers, editors or readers to verify reproducibility without manually downloading and re-running any code and can provide an audit trail for analyses of data that cannot be shared.

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Section: Resultsmentioning

confidence: 99%

Reproducibility of computational workflows is automated using continuous analysis

2017

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“…To evaluate the impact of differing CDF versions, we downloaded a recently published public gene expression dataset (GEO Series Ascension number GSE47664). This experiment examined differential expression between normal HeLa cells and HeLa cells with TIA1 and TIAR knocked down 42 . We performed a parallel analysis using each of the three versions that we found installed on machines that we could access (18, 19, and 20).…”

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confidence: 99%

Reproducible Computational Workflows with Continuous Analysis

Beaulieu‐Jones

Greene

2016

Preprint

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Reproducing experiments is vital to science. Being able to replicate, validate and extend previous work also speeds new research projects. Reproducing computational biology experiments, which are scripted, should be straightforward. But reproducing such work remains challenging and time consuming. In the ideal world we would be able to quickly and easily rewind to the precise computing environment where results were generated. We would then be able to reproduce the original analysis or perform new analyses. We introduce a process termed “continuous analysis” which provides inherent reproducibility to computational research at a minimal cost to the researcher. Continuous analysis combines Docker, a container service similar to virtual machines, with continuous integration, a popular software development technique, to automatically re-run computational analysis whenever relevant changes are made to the source code. This allows results to be reproduced quickly, accurately and without needing to contact the original authors. Continuous analysis also provides an audit trail for analyses that use data with sharing restrictions. This allows reviewers, editors, and readers to verify reproducibility without manually downloading and rerunning any code. Example configurations are available at our online repository (https://github.com/greenelab/continuous_analysis).

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Proteomic profile changes associated with diminished expression of T-cell intracellular antigens reveal a hormesis response

Alcalde

Izquierdo

2018

Biochemical and Biophysical Research Communications

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Long-Term Reduction of T-Cell Intracellular Antigens Reveals a Transcriptome Associated with Extracellular Matrix and Cell Adhesion Components

Cited by 3 publications

References 51 publications

Reproducibility of computational workflows is automated using continuous analysis

Reproducibility of computational workflows is automated using continuous analysis

Reproducible Computational Workflows with Continuous Analysis

Proteomic profile changes associated with diminished expression of T-cell intracellular antigens reveal a hormesis response

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