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myExperiment specifications


Unique identifier OMICS_18311
Name myExperiment
Restrictions to use None
Community driven Yes
Data access Browse, Application programming interface
User data submission Allowed
Maintained Yes



  • person_outline Peter Li
  • person_outline myExperiment team

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Publications for myExperiment

myExperiment citations


Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

J Cheminform
PMCID: 5736515
PMID: 29260340
DOI: 10.1186/s13321-017-0252-9

[…] results presented in this paper have been produced making use of the open source workflow RetroPath2.0. RetroPath2.0 and the associated data are provided as Additional file and can be downloaded at The only differences between the various usages we have made of the RetroPath2.0 are within (1) the set of reaction rules and (2) the way molecules are selected at each iteration dur […]


Spatiotemporal analysis of tropical disease research combining Europe PMC and affiliation mapping web services

PMCID: 5658975
PMID: 29093641
DOI: 10.1186/s41182-017-0073-6

[…] c.) and publication type (full text, open access, reviews, books, and documents). A Taverna [] workflow profilePublications_over_time integrating this service is shown in Fig.  and also shared on the myExperiment [] website ( This workflow takes as input one or more Europe PMC search queries. From each of these, the Build_Queries_1900_2016 component gen […]


Integration of EGA secure data access into Galaxy

PMCID: 5302147
PMID: 28232859
DOI: 10.5256/f1000research.11010.r19733

[…] up to the final results. As a result, we have: shared molecular data via EGA;created new Galaxy tools;shared the workflow, including all parameters, via a URL for Galaxy (as a shared history) and via myExperiment ;shared the interpreted data as a Galaxy history;shared a manual as a Galaxy page on how to set up such an experiment. shared molecular data via EGA;created new Galaxy tools;shared the wo […]


From linked open data to molecular interaction: studying selectivity trends for ligands of the human serotonin and dopamine transporter† †The authors declare no competing interests. ‡ ‡Electronic supplementary information (ESI) available. See DOI: 10.1039/c6md00207b Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

PMCID: 5100691
PMID: 27891211
DOI: 10.1039/c6md00207b

[…] . All further data filtering, preprocessing, and analyses were done in a single KNIME (version 2.11) workflow, which is fully flexible to be adopted to other protein targets and openly available from myExperiment ( workflows consist of the following steps: […]


Scientific workflows for bibliometrics

PMCID: 4833826
PMID: 27122644
DOI: 10.1007/s11192-016-1885-6

[…] eliminate manual steps in analysis pipelines and provide reusability and repeatability of bibliometrics analyses. All workflows for bibliometrics and scientometrics presented here can be found in the myExperiment group for Bibliometrics and Scientometrics ( […]


Scientific workflow optimization for improved peptide and protein identification

BMC Bioinformatics
PMCID: 4558836
PMID: 26335531
DOI: 10.1186/s12859-015-0714-x
call_split See protocol

[…] not only parameters but also algorithms, we included a retention time prediction in the workflow. The workflow in Fig. , shown in grey was used for the optimization. It can be accessed at In addition to peptide-spectrum matching, we may choose to incorporate additional information about the peptides in the identification or removal of false positiv […]


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myExperiment institution(s)
School of Computer Science, The University of Manchester, Manchester UK; School of Electronics and Computer Science, University of Southampton, Southampton UK; BioSemantics group, Human Genetics Department, Leiden University Medical Centre, Leiden, Netherlands; Adaptive Information Disclosure group, Informatics Institute, University of Amsterdam, Amsterdam, Netherlands
myExperiment funding source(s)
Supported by three European Commission 7th Framework Programme (FP7) projects: BioVeL (Grant 283359), SCAPE (Grant 270137), and the Wf4Ever Project (Grant 270192) as well as the e-Research South and myGrid EPSRC Platform grants and previously by JISC and the Microsoft Technical Computing Initiative.

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