Automated composition of scientific workflows in mass spectrometry-based proteomics

Anna Lena Lamprecht; Magnus Palmblad; Jon Ison; Veit Schwammle

doi:10.1109/eScience.2018.00098

Automated composition of scientific workflows in mass spectrometry-based proteomics

Anna Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwammle

IT Service

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Abstract

Numerous software utilities operating on mass spectrometry (MS) data are described in the literature that provide specific operations as building blocks for the assembly of purposespecific workflows. Working out which tools and combinations are applicable or optimal is often hard: insufficient annotation of tool functions and interfaces impedes finding viable tool combinations, and potentially compatible tools may not, in practice, operate together. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.

Original language	English
Title of host publication	Proceedings of 14th International Conference on eScience
Publisher	IEEE
Publication date	24 Dec 2018
Pages	360-361
Article number	8588717
ISBN (Electronic)	9781538691564
DOIs	https://doi.org/10.1109/eScience.2018.00098
Publication status	Published - 24 Dec 2018
Event	14th IEEE International Conference on eScience, e-Science 2018 - Amsterdam, Netherlands Duration: 29 Oct 2018 → 1 Nov 2018 https://www.escience2018.com/

Conference

Conference	14th IEEE International Conference on eScience, e-Science 2018
Country/Territory	Netherlands
City	Amsterdam
Period	29/10/2018 → 01/11/2018
Internet address	https://www.escience2018.com/

Keywords

Automated workflow composition
Bio.tools
ELIXIR
Mass spectrometry
Proteomics
Scientific workflows
Semantic domain modeling
Workflow management systems

Access to Document

10.1109/eScience.2018.00098

OpenUrl availability

Full text

Cite this

@inproceedings{a90fb5bb390e488d97875e105533c420,

title = "Automated composition of scientific workflows in mass spectrometry-based proteomics",

abstract = "Numerous software utilities operating on mass spectrometry (MS) data are described in the literature that provide specific operations as building blocks for the assembly of purposespecific workflows. Working out which tools and combinations are applicable or optimal is often hard: insufficient annotation of tool functions and interfaces impedes finding viable tool combinations, and potentially compatible tools may not, in practice, operate together. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.",

keywords = "Automated workflow composition, Bio.tools, ELIXIR, Mass spectrometry, Proteomics, Scientific workflows, Semantic domain modeling, Workflow management systems",

author = "Lamprecht, {Anna Lena} and Magnus Palmblad and Jon Ison and Veit Schwammle",

year = "2018",

month = dec,

day = "24",

doi = "10.1109/eScience.2018.00098",

language = "English",

pages = "360--361",

booktitle = "Proceedings of 14th International Conference on eScience",

publisher = "IEEE",

address = "United States",

note = "14th IEEE International Conference on eScience, e-Science 2018, eScience 2018 ; Conference date: 29-10-2018 Through 01-11-2018",

url = "https://www.escience2018.com/",

}

Lamprecht, AL, Palmblad, M, Ison, J & Schwammle, V 2018, Automated composition of scientific workflows in mass spectrometry-based proteomics. in Proceedings of 14th International Conference on eScience., 8588717, IEEE, pp. 360-361, 14th IEEE International Conference on eScience, e-Science 2018, Amsterdam, Netherlands, 29/10/2018. https://doi.org/10.1109/eScience.2018.00098

TY - GEN

T1 - Automated composition of scientific workflows in mass spectrometry-based proteomics

AU - Lamprecht, Anna Lena

AU - Palmblad, Magnus

AU - Ison, Jon

AU - Schwammle, Veit

PY - 2018/12/24

Y1 - 2018/12/24

N2 - Numerous software utilities operating on mass spectrometry (MS) data are described in the literature that provide specific operations as building blocks for the assembly of purposespecific workflows. Working out which tools and combinations are applicable or optimal is often hard: insufficient annotation of tool functions and interfaces impedes finding viable tool combinations, and potentially compatible tools may not, in practice, operate together. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.

AB - Numerous software utilities operating on mass spectrometry (MS) data are described in the literature that provide specific operations as building blocks for the assembly of purposespecific workflows. Working out which tools and combinations are applicable or optimal is often hard: insufficient annotation of tool functions and interfaces impedes finding viable tool combinations, and potentially compatible tools may not, in practice, operate together. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.

KW - Automated workflow composition

KW - Bio.tools

KW - ELIXIR

KW - Mass spectrometry

KW - Proteomics

KW - Scientific workflows

KW - Semantic domain modeling

KW - Workflow management systems

U2 - 10.1109/eScience.2018.00098

DO - 10.1109/eScience.2018.00098

M3 - Article in proceedings

AN - SCOPUS:85061388801

SP - 360

EP - 361

BT - Proceedings of 14th International Conference on eScience

PB - IEEE

T2 - 14th IEEE International Conference on eScience, e-Science 2018

Y2 - 29 October 2018 through 1 November 2018

ER -

Automated composition of scientific workflows in mass spectrometry-based proteomics

Abstract

Conference

Keywords

Access to Document

OpenUrl availability

Fingerprint

Cite this