diff --git a/docs/index.rst b/docs/index.rst index 2aff296..94e2941 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,33 +1,23 @@ +:github_url: https://github.com/microbiomedata/metaMS/blob/master/docs/index.rst + +.. + Note: The above `github_url` field is used to force the target of the "Edit on GitHub" link + to be the specified URL. That makes it so the link will work, regardless of the Sphinx + site the file is incorporated into. You can learn more about the `github_url` field at: + https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-github_url + Metabolomics Workflow ============================== -Summary +.. image:: metams_workflow2024.svg + +Workflow Overview ------- The gas chromatography-mass spectrometry (GC-MS) based metabolomics workflow (metaMS) has been developed by leveraging PNNL's CoreMS software framework. The current software design allows for the orchestration of the metabolite characterization pipeline, i.e., signal noise reduction, m/z based Chromatogram Peak Deconvolution, abundance threshold calculation, peak picking, spectral similarity calculation and molecular search, similarity score calculation, and confidence filtering, all in a single step. - -Workflow Diagram ------------------- - -.. image:: metamsworkflow.png - - -Workflow Dependencies ---------------------- - -Third party software -~~~~~~~~~~~~~~~~~~~~ - -- CoreMS (2-clause BSD) -- Click (BSD 3-Clause "New" or "Revised" License) - -Database -~~~~~~~~~~~~~~~~ -- PNNL Metabolomics GC-MS Spectral Database - Workflow Availability --------------------- @@ -43,18 +33,47 @@ https://pypi.org/project/metaMS/ The databases are available by request. Please contact NMDC (support@microbiomedata.org) for access. -Test datasets -------------- -https://github.com/microbiomedata/metaMS/blob/master/data/GCMS_FAMES_01_GCMS-01_20191023.cdf +Requirements for Execution +-------------------------- +- Docker Container Runtime + + or +- Python Environment >= 3.10 +- Python Dependencies are listed on requirements.txt Execution Details ---------------------- +~~~~~~~~~~~~~~~~ Please refer to: https://github.com/microbiomedata/metaMS#metams-installation +Hardware Requirements +-------------------------- +- To run this application, you need a processor with at least 2.0 GHz speed, 8GB of RAM, 10GB of free hard disk space + + +Workflow Dependencies +--------------------- + +Software +~~~~~~~~~~~~~~~~~~~~ + +- CoreMS (2-clause BSD) +- Click (BSD 3-Clause "New" or "Revised" License) + +Database +~~~~~~~~~~~~~~~~ +- PNNL Internal Metabolomics GC-MS Spectral Database, version 20191015 +- Test database provided at db/EMSL_lowres_gcms_test_database.sqlite +- Database will be provided via an API in FY25 + +Test datasets +------------- +https://github.com/microbiomedata/metaMS/tree/master/data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf + + Inputs ~~~~~~~~ @@ -76,15 +95,6 @@ Outputs - Workflow Metadata: - JSON -Requirements for Execution --------------------------- - -- Docker Container Runtime - - or -- Python Environment >= 3.6 -- Python Dependencies are listed on requirements.txt - Version History --------------- @@ -94,4 +104,4 @@ Version History Point of contact ---------------- -Package maintainer: Yuri E. Corilo +Package maintainer: Yuri E. Corilo \ No newline at end of file diff --git a/docs/metams_workflow2024.png b/docs/metams_workflow2024.png new file mode 100644 index 0000000..72dd335 Binary files /dev/null and b/docs/metams_workflow2024.png differ diff --git a/docs/metams_workflow2024.svg b/docs/metams_workflow2024.svg new file mode 100644 index 0000000..725b1aa --- /dev/null +++ b/docs/metams_workflow2024.svg @@ -0,0 +1,286 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CoreMS + SimilarityScoreControl + Reference Database + GC-MS Control + Raw GC-MS + IdentifiedMetabolites + MetabolitesData Table + + \ No newline at end of file