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--- eln-guide-basic-page-annotations [2026/01/27 17:22] – csdunham
+++ eln-guide-basic-page-annotations [2026/01/27 17:49] (current) – csdunham
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 ==== Chemspeed Annotations ====
-The Chemspeed annotation module is designed to facilitate and streamline experimental access to the Chemspeed instrument. The module provides a mechanism for designating a Chemspeed experiment, with parameters including temperature and atmospheric conditions alongside the employed polymerization scheme. Once the Chemspeed experiment is registered, you can add chemicals to the stock solutions table and assign volumes for each reaction in each reaction container. (Figures 6, 7, 8, to be added shortly).
+The Chemspeed annotation module is designed to facilitate and streamline experimental access to the Chemspeed instrument. The module provides a mechanism for designating a Chemspeed experiment (Fig 6), with parameters including temperature and atmospheric conditions alongside the employed polymerization scheme. Once the Chemspeed experiment is registered, you can add chemicals (Figs 7, 8, 9) to the stock solutions table and assign volumes for each reaction in each reaction vessel (Fig 10). You may then download stock reagent files for the Chemspeed instrument by clicking the Download Text File button. Note: double-check the file for accuracy and make sure you save your table before doing so to prevent data loss, as there is no auto-save functionality for these tables.
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+{{:chemspeed_exp_reg_2026.png?400|}}
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+//Fig 6. Chemspeed experiment registration. Allows you to name and provide input parameters for your Chemspeed experiment, including: polymerization mechanism, temperature, time, and atmosphere.//
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+{{:chemspeed_stock_search_2026.png?700|}}
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+//Fig 7. Chemspeed add/search for stock chemicals. This feature allows you to search for chemicals in the BioPACIFIC MIP LIMS based on common name, chemical formula, or SMILES string. Additionally, this search is expanded beyond the LIMS to return results from the public chemical database found at PubChem.//
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+{{:chemspeed_stock_search_add_new_2026.png?200|}}
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+//Fig 8. Chemspeed add chemical to LIMS. You may add chemicals directly to the LIMS by clicking the Add New Chemical button, which will result in the window shown here. You must upload a representative structure image file and input some basic parameters. Upon save, the chemical is registered in the LIMS and added to the Stocks table.//
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+{{:chemspeed_stock_search_add_pubchem_2026.png?200|}}
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+//Fig 9. Chemspeed add chemical from PubChem. Allows you to add the chemical returned from PubChem to the LIMS database in addition to your stocks table. A few values are requested which cannot be retrieved from PubChem, including density. Successful addition adds the chosen chemical to the LIMS database for future reference.//
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+{{:chemspeed_stocks_table_2026.png?700|}}
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+//Fig 10. Chemspeed stocks table. Displays all chemicals added to the stocks table with a thumbnail image of their structure. Each row of the stocks table represents a reaction in a reaction vessel. Volumes are then added and must follow any limitations imposed by the instrument. Consult with your project scientist for more details about volume limitations for viscous and non-viscous materials.//
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 ==== Symphony Annotations ====
-The Symphony module is designed to greatly simplify the provision of Symphony data files to your ELN page(s). Data from the Symphony X Peptide Synthesizer is automatically transmitted to the BioPACIFIC MIP LIMS, where it is then parsed and registered into the database and made available to the ELN through simple search and point-and-click addition of your Symphony methods files (Fig 9). Each attached Symphony methods collection is displayed as an information card (Fig 10). Clicking on the individual files associated with the method (e.g., an amino acid file or program file) displays a table with all of the values belonging to the original file (Fig 11).
+The Symphony module is designed to greatly simplify the provision of Symphony data files to your ELN page(s). Data from the Symphony X Peptide Synthesizer is automatically transmitted to the BioPACIFIC MIP LIMS, where it is then parsed and registered into the database and made available to the ELN through simple search and point-and-click addition of your Symphony methods files (Fig 11). Each attached Symphony methods collection is displayed as an information card (Fig 12). Clicking on the individual files associated with the method (e.g., an amino acid file or program file) displays a table with all of the values belonging to the original file (Fig 13).
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 {{:symphony_annotation_module_2026.png?700|}}
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-//Fig 9. Symphony module. Displays the search results of querying the system for Symphony methods files. These methods can be linked to your ELN page simply by clicking the button.//
+//Fig 11. Symphony module. Displays the search results of querying the system for Symphony methods files. These methods can be linked to your ELN page simply by clicking the button.//
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 {{:symphony_attached_annotations_2026.png?700|}}
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-//Fig 10. Symphony module file cards. Displays the attached/linked Symphony methods files.//
+//Fig 12. Symphony module file cards. Displays the attached/linked Symphony methods files.//
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 {{:symphony_attached_file_contents_2026.png?700|}}
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-//Fig 11. Symphony module file card file view. Displays the parsed methods file/file dependent's information in tabular format.//
+//Fig 13. Symphony module file card file view. Displays the parsed methods file/file dependent's information in tabular format.//
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