SoS notebook: An interactive multi-language data analysis environment

Bo Peng; Gao Wang; Jun Ma; Man Chong Leong; Chris Wakefield; James Melott; Yulun Chiu; Di Du; John N. Weinstein

doi:10.1093/bioinformatics/bty405

SoS notebook: An interactive multi-language data analysis environment

Bo Peng, Gao Wang, Jun Ma, Man Chong Leong, Chris Wakefield, James Melott, Yulun Chiu, Di Du, John N. Weinstein

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

Motivation: Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking. Results: We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.

Original language	English (US)
Pages (from-to)	3768-3770
Number of pages	3
Journal	Bioinformatics
Volume	34
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/bty405
State	Published - Nov 1 2018

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

MD Anderson CCSG core facilities

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10.1093/bioinformatics/bty405

Cite this

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title = "SoS notebook: An interactive multi-language data analysis environment",

abstract = "Motivation: Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking. Results: We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.",

author = "Bo Peng and Gao Wang and Jun Ma and Leong, {Man Chong} and Chris Wakefield and James Melott and Yulun Chiu and Di Du and Weinstein, {John N.}",

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T2 - An interactive multi-language data analysis environment

AU - Peng, Bo

AU - Wang, Gao

AU - Ma, Jun

AU - Leong, Man Chong

AU - Wakefield, Chris

AU - Melott, James

AU - Chiu, Yulun

AU - Du, Di

AU - Weinstein, John N.

PY - 2018/11/1

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N2 - Motivation: Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking. Results: We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.

AB - Motivation: Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking. Results: We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.

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SoS notebook: An interactive multi-language data analysis environment

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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