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Protocols specifications


Unique identifier OMICS_30565
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes


  • person_outline Jon Ison

Additional information

Publication for citations


mORCA: ubiquitous access to life science web services

BMC Genomics
PMCID: 5771032
PMID: 29338691
DOI: 10.1186/s12864-018-4439-x

[…] arily active BIBM research field, there is continuous growth in the already high number of available software as novel tools, demands, and data types emerge (e.g. over 2000 services are registered in [], which is the most recent attempt to create a BIBM catalogue). This considerable amount of resources motivates the creation of an intelligent software organisation to make easier the inte […]


Using to generate and annotate workbench tool descriptions

PMCID: 5747335
PMID: 29333231
DOI: 10.5256/f1000research.14069.r28566

[…] The ToolDog utility allows a developer to generate new tool descriptions for tools which are compatible with the code analysis module, and reuse the metadata provided by to enrich existing tool descriptions. There are some limitations to this approach: 1. The “plugin” libraries used for code analysis are specific to the programming languages, libraries or fr […]


An architecture for genomics analysis in a clinical setting using Galaxy and Docker

PMCID: 5691353
PMID: 29048555
DOI: 10.1093/gigascience/gix099

[…] M uses a PostgresSQL database to store the user operations. Asynchronous Tasks jobs are performed with Celery and Redis [, ].ReGaTE [] aims at automating the publication of Galaxy tools in the ELIXIR bio-tools registry by generating EDAM ontologies annotations []. The EDAM ontology goal is to describe and characterize bioinformatics operations such as data types and format. We choose to Dockerize […]


Mitochondria and lipid raft located FOF1 ATP synthase as major therapeutic targets in the antileishmanial and anticancer activities of ether lipid edelfosine

PLoS Negl Trop Dis
PMCID: 5568728
PMID: 28829771
DOI: 10.1371/journal.pntd.0005805

[…] tion, and centroid algorithm for monoisotopic peak assignment. In all cases, resolution was higher than 9000. The generated peaks were submitted to Mascot Server (version 2.2, February 2007) [] using Bio Tools 3.1 (Bruker Daltonics) software, and searched against Uniprot database for human sequences and NCBI database for Leishmania sequences. Search parameters were set as follow: searches were res […]


BioCIDER: a Contextualisation InDEx for biological Resources discovery

PMCID: 5870719
PMID: 28407033
DOI: 10.1093/bioinformatics/btx213

[…] for biological Resource discovery. BioCIDER automatically collects information (metadata and source description) from a variety of centralized registries, including the GOBLET training portal (), the service registry (Ison et al., 2015), the iAnn collaborative event dissemination portal () and TeSS, the ELIXIR training portal (; others (e.g.; ) […]


ReGaTE: Registration of Galaxy Tools in Elixir

PMCID: 5530318
PMID: 28402416
DOI: 10.1093/gigascience/gix022

[…] nputs and outputs are available.The mapping from a Galaxy tool definition file (detailed documentation of this format is available at to a file is handled by the ReGaTE code, taking advantage of the important number of common properties between such workbench wrappers and registry entries []. A few properties are not natively a […]


Looking to check out a full list of citations? institution(s)
Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark; Centre d’Informatique pour la Biologie, C3BI, Institut Pasteur, France; [etc.] funding source(s)
Supported by the European Union Seventh Framework Programme within Research Infrastructures of the FP7 Capacities Specific Programme [284209], the European Commission within the Research Infrastructures programme of Horizon 2020 [676559], the Danish Infrastructure Roadmap grant to the Danish ELIXIR Node and the National Human Genome Research Institute (NHGRI) [grant 5U41HG002273-14]. reviews

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