Search results for "openms"

Search filter terms
Filter by category
Filter by type
Filter by tag
Filter by user
Filter by licence
Filter by group
Results per page:
Sort by:
Showing 5 results. Use the filters on the left and the search box below to refine the results.

Workflow HLA ligandomics workflow using OpenMS and ... (2)

Thumb
HLA ligandomics workflow combining native KNIME, OpenMS, and ImmunoNodes nodes. The workflow extracts MS data from PRIDE and performs mass spectra identification with X!Tandem, annotates the results with details of the given target/decoy database, calculates false discovery rates and filters for 5% FDR using OpenMS’ nodes. The identified peptides are annotated with their respective binding affinity predicted by NetMHC using the EpitopePrediction node. Finally, simple summary statistics ...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: User Mathias Walzer

Uploader

Workflow RetroPath2.0-Mods-metabolomics (1)

Thumb
Set of workflows for the "Metabolome completion and metabolomics" use case:1) Produces a list of molecules using a user defined set of rules (RetroPath2.0 workflow).2) Takes as input the products generated by RetroPath2.0 and prepare the files to be read by OpenMS nodes.3) The last workflow finally searches for each produced compound the corresponding peak in some MS spectra.See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflo...

Created: 2017-06-30 | Last updated: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

Creator

Pack Pack #4 - Metabolome completion and metabolomics


Created: 2017-06-30 16:36:44 | Last updated: 2017-06-30 18:04:28

This pack provides part of the supporting material for M. Koch et. al., Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 2017.The pack contains (i) the RetroPath2.0-Mods-metabolomics workflow as well as (ii) all the associated data for the metabolome completion use case (see the main text for details, section 2.4 Metabolome completion and metabolomics).

2 items in this pack

Comments: 0 | Viewed: 3 times | Downloaded: 0 times

Tags:

Member

User Thomas Duigou

Joined: Wednesday 07 June 2017 11:36:28 (UTC)

No description

Last active:Monday 03 July 2017 08:33:36 (UTC)

Email (public):thomas.duigou [at] inra.fr

Field/Industry:Biotechnology | Occupation/Role(s):Research engineer

Uploader

Workflow Scan range splitting for untargeted metabo... (1)

Thumb
This workflow analyzes untargeted HPLC-Orbitrap measurements split into separate or alternating scan ranges. The input nodes expect OpenMS consensusXML files that were exported using TextExporter. The workflow then combines the separate scan ranges, filters them utilizing blank and QC measurements, and performs a statistical analysis.Requirements:- KNIME Interactive R Statistics Integration

Created: 2016-01-14 | Last updated: 2016-01-14

Credits: User Marc Rurik

Results per page:
Sort by: