Enhanced, improved and novel NMDC workflows to advance microbiome science
Similar to the entire field of genomics, all NMDC workflows (Appendix 15) are subject to an iterative
improvement process. To stay relevant to the scientific community, the NMDC must be able to keep up
with advancements in bioinformatics. Major leaps in bioinformatic algorithms occasionally force a
wholesale re-evaluation of previously processed data. The ongoing expansion of taxonomic and functional
knowledge can also result in older analyses needing to be refreshed. When a new component of the
workflow is updated (an algorithm/tool or a queried database), the NMDC works with the upstream
workflow developers (e.g., JGI, EMSL, and LANL) to determine next steps. This could include deciding
whether there is a need for the NDMC workflow to adopt the latest version and if so, whether application
of the updated workflow on previously processed data is necessary and whether an update to the
workflow output data schema is necessary (see Governance, Milestone 0.4). We anticipate several
enhancements and improvements to existing workflows, as well as new workflows, to be developed and
integrated as standardized NMDC workflows (Milestone 2.12 - 2.21), and will be integrated within NMDC
EDGE (NMDC EDGE, Milestone 5.4) with updated documentation and training materials (NMDC EDGE,
Milestone 5.5).
ssarrafan
commented
9 months ago
Enhanced, improved and novel NMDC workflows to advance microbiome science Similar to the entire field of genomics, all NMDC workflows (Appendix 15) are subject to an iterative improvement process. To stay relevant to the scientific community, the NMDC must be able to keep up with advancements in bioinformatics. Major leaps in bioinformatic algorithms occasionally force a wholesale re-evaluation of previously processed data. The ongoing expansion of taxonomic and functional knowledge can also result in older analyses needing to be refreshed. When a new component of the workflow is updated (an algorithm/tool or a queried database), the NMDC works with the upstream workflow developers (e.g., JGI, EMSL, and LANL) to determine next steps. This could include deciding whether there is a need for the NDMC workflow to adopt the latest version and if so, whether application of the updated workflow on previously processed data is necessary and whether an update to the workflow output data schema is necessary (see Governance, Milestone 0.4). We anticipate several enhancements and improvements to existing workflows, as well as new workflows, to be developed and integrated as standardized NMDC workflows (Milestone 2.12 - 2.21), and will be integrated within NMDC EDGE (NMDC EDGE, Milestone 5.4) with updated documentation and training materials (NMDC EDGE, Milestone 5.5).
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