microbiomedata/metams issues and pull requests

#62 - 61 update gc ms workflow figure

Pull Request - State: open - Opened by kaijli 2 months ago - 1 comment

#61 - Update GC-MS workflow figure

Issue - State: open - Opened by kaijli 2 months ago

#60 - Add CI/CD to test wdl validity

Issue - State: closed - Opened by kheal 6 months ago - 1 comment

#59 - Upgrade wdl to version 1.0

Issue - State: closed - Opened by kheal 6 months ago - 1 comment

#58 - Add DatabaseInterface module and classes for pulling and organizing spectra from MetabRef

Issue - State: closed - Opened by kheal 8 months ago - 1 comment

#57 - Load Configuration and Calibration objects for berkeley-schema implementation

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#56 - Generate updated metadata and upload

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#55 - Modify metadata generation scripts for GC-MS Metabolomics workflow to berkeley-schema-fy24

Issue - State: closed - Opened by kheal 9 months ago - 2 comments

#54 - Merge lcms_dev into main branch of CoreMS

Issue - State: closed - Opened by kheal 9 months ago

#53 - Re-render documentation on lcms_dev branch on CoreMS

Issue - State: closed - Opened by kheal 9 months ago

#52 - Format lcms_dev branch according to PEP8 guidelines

Issue - State: closed - Opened by kheal 9 months ago

#51 - Add lipidomics-specific exporter to lcms_dev on CoreMS

Issue - State: closed - Opened by kheal 9 months ago

#50 - Remove `to_json` method from `LCMSParameters` in `encapsulation/factory/parameters` module to `encapsulation/output/parameter_to_json` and adjust usage throughout.

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#49 - Remove api token path parameter and usage from LCMSBase object

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#48 - Modify peak picking parameters to call by relative abundance (not absolute value)

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#47 - Add functionality for parameter import/export using a tmol file

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#47 - Add functionality for parameter import/export using a tmol file

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#46 - Add private attributes and associated properties to LCMSMassFeatures class to lcms_dev on CoreMS

Issue - State: closed - Opened by kheal 9 months ago - 3 comments

#45 - Harmonize GC and LC spectral library creation and interfacing with MetabRef

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#44 - Apply properties to ChromaPeak attributes

Issue - State: closed - Opened by kheal 9 months ago - 1 comment

#43 - Develop MetabRef-specific database interface

Issue - State: closed - Opened by smcolby 10 months ago

#42 - Develop database interface base class for flexible database linking

Issue - State: closed - Opened by smcolby 10 months ago

#41 - Add lipid workflow as a test to corems

Issue - State: closed - Opened by kheal 10 months ago

#40 - Add LCMS hdf5 import and export to lcms_dev on CoreMS

Issue - State: closed - Opened by kheal 10 months ago

#39 - Add LCMS spectra searching to lcms_dev on CoreMS

Issue - State: closed - Opened by kheal 10 months ago

#38 - Add LCMS peak picking functionality to lcms_dev on CoreMS

Issue - State: closed - Opened by kheal 10 months ago

#37 - Add LCMSMassFeature Class to chroma_peak/factory to lcms_dev on CoreMS

Issue - State: closed - Opened by kheal 10 months ago - 1 comment

#36 - Update GC-MS workflow

Issue - State: open - Opened by smcolby 10 months ago

#35 - Modify GC-MS workflow to use internal standard FAMEs

Issue - State: closed - Opened by smcolby 10 months ago

#34 - Verify RT/RI calculations and test GC-MS workflow implementation to connect with Fiehn lab database

Issue - State: closed - Opened by smcolby 10 months ago - 1 comment

#33 - Modify GC-MS workflow to source MetabRef database

Issue - State: closed - Opened by smcolby 10 months ago

#32 - Add lipidomics workflow to MetaMS (cli, wdl)

Issue - State: open - Opened by kheal 10 months ago - 1 comment

#31 - Document lipidomics workflow

Issue - State: open - Opened by kheal 10 months ago

#30 - Benchmark lipidomics workflow and parameter optimization based on data in NMDC portal

Issue - State: open - Opened by kheal 10 months ago

#29 - Design and enable metadata generation for lipidomics workflow

Issue - State: closed - Opened by kheal 10 months ago - 6 comments
Labels: berkeley-rollout-post-mvp-eligible

#28 - META ISSUE: Create lipidomics workflow

Issue - State: closed - Opened by kheal 10 months ago

#27 - META ISSUE: Add modules and functions to CoreMS needed for lipidomics workflow

Issue - State: closed - Opened by kheal 10 months ago - 1 comment

#26 - Create in silico lipid database and load into MetabRef

Issue - State: closed - Opened by kheal 10 months ago

#24 - LC-MS metabolomics WDL development and Github deployment

Issue - State: open - Opened by ssarrafan over 2 years ago - 11 comments
Labels: SMALL, backlog

#23 - LC-MS metabolomics CLI development

Issue - State: open - Opened by ssarrafan over 2 years ago - 12 comments
Labels: MEDIUM, backlog

#22 - Check & confirm missing components once template and example are complete (@yuricorilo ) (September)

Issue - State: closed - Opened by ssarrafan over 2 years ago

#21 - Generate metadata template (September)

Issue - State: closed - Opened by ssarrafan over 2 years ago

#20 - Identify metadata components captured by DMS that are required when data is received from other institutions

Issue - State: open - Opened by ssarrafan over 2 years ago - 1 comment

#19 - MetaB-GCMS: Identify metadata components that need captured at PNNL (what isn't captured by DMS)

Issue - State: closed - Opened by ssarrafan over 2 years ago - 1 comment

#18 - Collect metadata prep, QC, and Blanks / what is used at PNNL

Issue - State: open - Opened by ssarrafan over 2 years ago - 1 comment
Labels: backlog

#17 - Check & confirm missing components once template and example are complete (@yuricorilo ) (December)

Issue - State: closed - Opened by ssarrafan over 2 years ago

#15 - Identify metadata components captured by DMS that are required when data is received from other institutions

Issue - State: open - Opened by ssarrafan over 2 years ago

#14 - Identify metadata components that need captured at PNNL (what isn't captured by DMS) (November)

Issue - State: closed - Opened by ssarrafan over 2 years ago

#13 - Collect metadata for how QC and Blanks are prepped / what is used at PNNL (October)

Issue - State: open - Opened by ssarrafan over 2 years ago

#12 - LC-MS workflow for metabolomics data dependent analysis

Issue - State: closed - Opened by ssarrafan over 3 years ago - 14 comments

#11 - Preparation Metadata: Sample Prep/Extraction

Issue - State: closed - Opened by mslarae13 over 3 years ago - 1 comment
Labels: LARGE

#8 - Preparation Metadata: Metabolomics

Issue - State: closed - Opened by mslarae13 over 3 years ago - 8 comments
Labels: X LARGE, backlog

#7 - Issue with running MetaMS and minwidl

Issue - State: closed - Opened by Michal-Babins over 3 years ago - 4 comments
Labels: X LARGE, workflows

#6 - Metabolomics pipeline prototype

Issue - State: closed - Opened by ssarrafan over 3 years ago
Labels: X LARGE, workflows

#5 - Metabolomics workflow distribution outside PNNL

Issue - State: closed - Opened by ssarrafan almost 4 years ago - 1 comment
Labels: workflows

#4 - identify additional metadata / configuration data needed for metabolomics including the use of blanks

Issue - State: closed - Opened by dehays almost 4 years ago - 8 comments
Labels: X LARGE

#3 - Workflows - Test large data sets for workflows (metaMS)

Issue - State: closed - Opened by ssarrafan almost 4 years ago

#2 - Workflows - Test small data sets for workflows (metaMS)

Issue - State: closed - Opened by ssarrafan almost 4 years ago - 1 comment

#1 - documentation

Issue - State: closed - Opened by hubin-keio over 4 years ago

GitHub / microbiomedata/metams issues and pull requests