data provenance metadata files

JSON version

kinome/meta.json:

{
    "init": {
        "datestamp": ,
        "init_path": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit":
    }
}

kinome/targets/meta.json:

{
    "init": {
    } ,
    "gather_targets: {
        "datestamp": ,
        "method": TargetExplorerDB ,
        "ntargets": ,
        "gather_from_target_explorer": {
            "uniprot_query_string": ,
            "uniprot_domain_regex": ,
            "species_selector": 9606,
            "database_path":
        } ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit":
    }
}

kinome/templates/meta.json:

{
    "init": {
    } ,
    "gather_templates: {
        "datestamp": ,
        "method": UniProt ,
        "ntemplates": ,
        "gather_from_uniprot": {
            "uniprot_query_string": ,
            "uniprot_domain_regex": ,
        } ,
        "structure_paths": [
            "..." ,
            "..."
        ] ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit":
    }
}

kinome/models/[target_name]/meta.json:

{
    "init": {
    } ,
    "gather_targets": {
    } ,
    "gather_templates": {
    } ,
    "build_models": {
        "target_id": ,
        "datestamp": ,
        "nsuccesful_models": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "modeller_version": ,
        "biopython_version":
    } ,
    "sort_by_sequence_identity": {
        "target_id": ,
        "datestamp": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "biopython_version":
    } ,
    "cluster_models": {
        "target_id": ,
        "datestamp": ,
        "nunique_models": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "biopython_version": ,
        "mdtraj_version":
    } ,
    "refine_implicit_md": {
        "target_id": ,
        "datestamp": ,
        "nsuccessful_refinements": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "biopython_version": ,
        "openmm_version":
        "openmm_commit":
    } ,
    "solvate_models": {
        "target_id": ,
        "datestamp": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "biopython_version": ,
        "openmm_version":
        "openmm_commit":
    } ,
    "determine_nwaters": {
        "target_id": ,
        "datestamp": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "biopython_version":
    } ,
    "refine_explicit_md": {
        "target_id": ,
        "datestamp": ,
        "nsuccessful_refinements": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "biopython_version": ,
        "openmm_version":
        "openmm_commit":
    }
}

kinome/packaged-models/fah-project/[target_name]/meta.xml:

{
    "init": {
    } ,
    "gather_targets": {
    } ,
    "gather_templates": {
    } ,
    "build_models": {
    } ,
    "sort_by_sequence_identity": {
    } ,
    "cluster_models": {
    } ,
    "refine_implicit_md": {
    } ,
    "solvate_models": {
    } ,
    "refine_explicit_md": {
    } ,
    "package_for_fah": {
        "datestamp": ,
        "python_version": ,
        "python_full_version": ,
        "msmseeder_version": ,
        "msmseeder_commit": ,
        "openmm_version":
        "openmm_commit":
    }
}

XML version

kinome/meta.xml:

<init datestamp= init_path=>
  <python version=2.7.8>
    <full_version>
      2.7.8 |Anaconda 1.9.2 (x86_64)| (default, Jul  2 2014, 15:36:00)
      [GCC 4.2.1 (Apple Inc. build 5577)]
  <msmseeder version= commit=>

kinome/targets/meta.xml:

<init datestamp=>
  <python version=>
  <msmseeder version= commit=>
<gather_targets datestamp= method=TargetExplorerDB ntargets=>
  <gather_from_target_explorer>
    <uniprot_query_string>
      domain:"Protein kinase" and species:"Human"
    <uniprot_domain_regex>
      ...
    <database_path>
      /cbio/jclab/home/parton/dev/TargetExplorerDB/database/database.xml
  <python version=>
  <msmseeder version= commit=>

kinome/templates/meta.xml:

<init datestamp=>
  <python version=>
  <msmseeder version= commit=>
<gather_templates datestamp= method=UniProt ntemplates=>
  <gather_from_uniprot>
    <uniprot_query_string>
      domain:"Protein kinase"
    <uniprot_domain_regex>
      ...
  <structure_paths>
    <path>
      ...
  <python version=>
  <msmseeder version= commit=>

kinome/models/[target_name]/meta.xml:

<init datestamp=>
  <python version=>
  <msmseeder version= commit=>
<gather_targets datestamp= method=TargetExplorerDB ntargets=>
  <gather_from_target_explorer>
    <uniprot_query_string>
      domain:"Protein kinase" and species:"Human"
    <uniprot_domain_regex>
      ...
    <database_path>
<gather_templates datestamp= method=UniProt ntemplates=>
  <gather_from_uniprot>
    <uniprot_query_string>
      domain:"Protein kinase"
    <uniprot_domain_regex>
      ...
  <structure_paths>
    <path>
      ...
  <python version=>
  <msmseeder version= commit=>
<build_models datestamp= nsuccessful_models=>
  <python version=>
  <msmseeder version= commit=>
  <modeller version=>
  <biopython version=>
<sort_by_sequence_identity datestamp=>
  <python version=>
  <msmseeder version= commit=>
  <biopython version=>
<cluster_models datestamp=>
  <python version=>
  <msmseeder version= commit=>
  <biopython version=>
  <mdtraj version=>
<refine_implicit_md datestamp= nsuccessful_refinements=>
  <python version=>
  <msmseeder version= commit=>
  <openmm version= commit=>
  <biopython version=>
<solvate_models datestamp=>
  <python version=>
  <msmseeder version= commit=>
  <openmm version= commit=>
  <biopython version=>
<determine_nwaters datestamp=>
  <python version=>
  <msmseeder version= commit=>
  <biopython version=>
<refine_explicit_md datestamp= nsuccessful_refinements>
  <python version=>
  <msmseeder version= commit=>
  <openmm version= commit=>
  <biopython version=>

kinome/packaged-models/fah-project/[target_name]/meta.xml:

[all of models/[target_name]/meta.xml]
<package_for_fah datestamp=>
  <python version=>
  <msmseeder version= commit=>
  <openmm version= commit=>
  <biopython version=>