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lims-guide-data-prep-tutorial [2023/04/10 18:32] – csdunhamlims-guide-data-prep-tutorial [2024/03/04 22:39] (current) – csdunham
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-==== Step-by-step tutorial: generating metadata and submitting to LIMS ==== +===== Tutorial: LIMS Data Upload ===== 
-Each data item submitted to the LIMS requires a metadata file.  The LIMS system provides tools to generate these metadata files.  If you are generating metadata for less than three (< 3) samples, it's recommended that you use the metadata form, as this will be the fastest method to produce your metadata files.  If you are generating metadata for more than three (> 3) samples, it's recommended that you use the metadata batch processor to generate your metadata files.  This tutorial provides step-by-step instructions for both methods. +This is going to be revised...
----- +
-==== Metadata Form (< 3 samples) ==== +
-  - Go to the [[https://bpm-lims.cnsi.ucsb.edu/metadata/ | LIMS metadata form]]. +
-  - Enter information to the required fields (those with a blue asterisk) +
-    - **Required fields summary**: +
-      - //__LIMS Account__//: The LIMS account is your account name: you can see this at the top right corner of the page. If you enter a non-existent account name, the system will tell you the account is invalid when you submit the form. +
-      - //__Experimental ID__//: The experimental ID is the serial number analog for your sample. If you previously characterized your sample in the LIMS and are now submitting additional characterization information (e.g. you previously submitted an NMR spectrum and now you're submitting a mass spectrum), you **must** use the same experimental ID.  If this is a new sample, then click the "Generate ID" button to generate a new unique identifier. +
-      - //__Component__//: The simplest kind of molecule/chemical species as understood by the LIMS. Specify your component by common name or PubChem CID number (the latter is preferred!) and mark its component class: monomer, solvent, catalyst, or additional reagent (i.e. other). +
-      - //__Experiment, Synthesis Dates__//: The date the experiment (characterization) was performed and the date the sample was synthesized.  Recommendation: use the calendar tool over manual entry. +
-      - //__Exp. Synopsis__//: A brief synopsis, or summary, of what's going on in this experiment.  Recommendation: include a truncated version of your methods and instrument parameters here. +
-      - //__Synthesis Platform__//: Indicate where/how the sample was synthesized. +
-      - //__Instrument__//: Indicate the instrument from which the data you are submitting was acquired. +
-      - //__Data File(s)__//: Indicate which instrument data files are included as part of this metadata submission. +
-      - //__Data Category__//: Indicate the manner in which the data should be interpreted (i.e., is this a spectrum, or a chromatogram, or a mean squared displacement measurement?). Data categories are used to distinguish between different data representations that might be available from a singular raw data source file. +
-      - //__Data Integrity__//: Indicate whether the identity or identities of the component(s)/polymer(s)/composite is confirmed.  In other words: have you confirmed that your sample is as you've described above?  If so, mark it as verified.  If not, mark it as unverified. +
-      - //__Data Availability__//: Indicate whether the data is accessible to all qualified BioPACIFIC MIP users or whether it should be restricted. __For the LIMS beta phase, all data should be marked as available to all users__. +
-    - **Conditional fields summary**: +
-      - //__Polymer__//: If your sample is a polymer (i.e. an assembly of multiple components), then you will provide the common name or abbreviation (or, if available, PubChem CID number) in this field.  You must also provide information concerning the following: +
-        - Polymer components +
-        - Component ratios +
-        - Chemical formula +
-        - Molecular weight +
-        - Polymerization mechanism(s) employed to construct the polymer +
-  - After completing all of the required fields for your sample, click "Generate Metadata File". +
- +
----- +
-==== Metadata Batch (> 3 samples) ==== +
-  - Go to the [[https://bpm-lims.cnsi.ucsb.edu/metadata/batch/ | LIMS metadata batch processor]]. +
-  - +
lims-guide-data-prep-tutorial.1681151568.txt.gz · Last modified: 2023/04/10 18:32 by csdunham