Micro.biotech #752
Micro.biotech #752
Conversation
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| #### Considerations | ||
| ### Description | ||
| Approriate and detailed description of the systethic parts design is critical for reproducibility. It is important to consider how to record metadata at each point in the design process in a standard way, so that it can be clear to others and reproducible. |
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Small typos in this sentence. Change to:
Appropriate and detailed description of the synthetic parts design is critical for reproducibility.
| * The database collection from the [International Nucleotide Sequence Database Collaboration](http://www.insdc.org/) provides an umbrella for gathering and sharing a variety of sequence data from different sequence databases internationally. | ||
| * Other databases such as [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) and the [DNA Data Bank of Japan (DDBJ)](https://www.ddbj.nig.ac.jp/index-e.html) also cater for sequence information. | ||
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| ### Genetic parts, device and systems | ||
| ## Design: Syntethic parts - Existing data, metadata collection and publication |
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Typo, change to:
Design: Synthetic parts - Existing data, metadata collection and publication
| * Enzymes can be assigned EC numbers, according to the guidance from the [International Union of Biochemistry and Molecular Biology (IUBMB)](https://www.qmul.ac.uk/sbcs/iubmb/), to indicate their function and an entry made in the [BRaunschweig ENzyme DAtabase](https://www.brenda-enzymes.org/) (BRENDA). | ||
| * More generally, the [IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN)](https://www.qmul.ac.uk/sbcs/iupac/jcbn/) encourages the communication of biochemical information using generally understood terminology. | ||
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| ### Model based designs | ||
| #### (Meta)Data publication | ||
| * SBOL. |
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Should remove this bullet point as SBOL is best described as a data standard or ontology which was described above
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| ### Solutions | ||
| * Various DNA synthesis companies build DNA from a computer specification of the sequence and also a variety of experimental approaches for assembling DNA molecules. This information can be shared as free text attached to a design in SBOL format and uploaded to a repository that supports SBOL2 format and above such as SynBioHub. | ||
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| #### Documentation | ||
| * To the authors’ knowledge, there are no proposed standards that exist that are able to capture this diverse set of data. Currently, from a pragmatic point of view, the best a data manager can do is to make sure data is captured in some form from the lab scientist and grouped together with as much metadata as possible.The metadata standards for a build exercise are still to be defined and so at the discretion of the data manager. |
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Missing a space between sentences.
Change to:
To the authors’ knowledge, there are no proposed standards that exist that are able to capture this diverse set of data. Currently, from a pragmatic point of view, the best a data manager can do is to make sure data is captured in some form from the lab scientist and grouped together with as much metadata as possible. The metadata standards for a build exercise are still to be defined and so at the discretion of the data manager.
| #### Test | ||
| The test stage of a biotechnological study is the most variable in terms of the types of data produced. This stage is mostly about: | ||
| * [testing](https://floradanna.github.io/rdm-toolkit/microbial_biotechnology.html#test-outcome-tests---metadata-standards-and-metadata-publication) the outcome or output variables and analyse the modified organism. | ||
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Add additional bullet point:
• Characterising the synthetic parts using experimental data
| The learning stage consists in interpreting the obtained results, share the acquired knowledge and reuse it in combination with other existing data to improve the creation of the modified organism. | ||
| * Publish and share data and results. | ||
| * Reuse existing data and combine it with new data. | ||
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Add additional bullet point:
• Feed data back into model(s) to inform the next iteration
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| ### Description: | ||
| ### Description | ||
| The build stage in the microbial biotechnology and/or synthetic biology life cycle involves the application of any number of a range of experimental techniques and, since these techniques are so varied, the domain is therefore very difficult to standardise in terms of the data and metadata to be shared. |
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There is repeated information here from the overall introduction. This is fine if it is intentional as it reminds the reader of the build stage.
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I think it is intentional indeed.
Implementing davidcmarkham review.
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@davidcmarkham I think I implemented all the changes you suggested. Please, double check. If you approve the PR, I will merge. Thank you very much for your corrections and contribution! |
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Yes, I think that's everything. Happy to merge the changes. Thanks! |
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