Differences

This shows you the differences between two versions of the page.

--- eln-guide-basic-page-annotations [2026/01/27 17:49] – csdunham
+++ eln-guide-basic-page-annotations [2026/08/14 22:15] (current) – csdunham
@@ Line 3: / Line 3: @@
 \\
 \\
-{{::annotations_expanded.png?700|}}
+{{:annotations_expanded2.png?700|}}
 \\
-//Fig 1. Page annotation menu. From left to right: Chemistry, Biology, Well Plates, ChemSpeed, and Symphony X/Peptide Synthesizers.//
+//Fig 1. Page annotation menu. From left to right: Chemical synthesis, Biological information, Well plates, Chemspeed annotation tools, Symphony X Peptide Synthesizer, small angle X-ray scattering (SAXS), chemical Structure Editor, Flow Chemistry, and Tecan SPARK (BNL).//
 \\
 \\
-==== Chemistry Annotations ====
+==== Chemical Synthesis ====
 Basic information about the chemical reagents used and products produced in an experiment are recorded in the Chemical Annotation module (Fig 2). This information is used to populate Chemical data entries in the LIMS database and provides a simple, historical account of the reagent quantities and product yields in the synthesis.
 \\
@@ Line 26: / Line 26: @@
 \\
 \\
-==== Well Plate Annotations ====
+==== Well Plates ====
 Well plate annotations (Fig 4) in the ELN come in two different forms: **[[eln-guide-basic-chemical-formulation-plate-annotations|chemical]]** and **[[eln-guide-basic-biological-plate-annotations|biological]]**. Depending on the plate choice you specify, you will walk through a process for capturing formulation information (chemical) or well-by-well culture information (biological). Once saved, the plate is given a unique ID and a QR code, and is made available in a visual display with your other well plates. Plates can then be edited or removed from your ELN page.
 \\
@@ Line 43: / Line 43: @@
 \\
 \\
-==== Chemspeed Annotations ====
+==== Chemspeed ====
 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.
 \\
@@ Line 72: / Line 72: @@
 \\
 \\
-==== Symphony Annotations ====
+==== Symphony ====
 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).
 \\
@@ Line 90: / Line 90: @@
 //Fig 13. Symphony module file card file view. Displays the parsed methods file/file dependent's information in tabular format.//
 \\
+\\
+==== SAXS ====
+This module provides a mechanism to link and view data from the small angle X-ray scattering (SAXS) instrument at BioPACIFIC MIP. It works similarly to the Symphony, in that there's a retrieval/data search window (Fig 14) from which you may link data files to your ELN page.
+\\
+\\
+{{:saxs_anno.png?700|}}
+\\
+//Fig 14. SAXS retrieval/data search window. This functions identically to the Symphony workflow, but displays different information, such as a (post-processed) image thumbnail preview.//
+\\
+\\
+Upon linking, you can then further preview your SAXS data by browsing the various SAXS data cards (Fig 15). These cards provide an expanded thumbnail image of the scattering pattern (which is a post-processed image) and a plot trace of I vs q from the raw text files. You may download the original *.tiff image and *.txt files by clicking their respective links.
+\\
+\\
+{{:saxs_anno2.png?700|}}
+\\
+//Fig 15. Display of attached (linked) SAXS file cards. These cards provide a larger version of the search thumbnail image preview and also give you an interactive plot by which to perform a cursory examination of the raw data (I vs q, with error bars).//
+\\
+==== Structures ====
+The Structures annotation module of the ELN provides users with a chemical structure editor (Fig 16) that has many of the functionalities found in ChemDraw, including the ability to load/read ChemDraw files. The editor leverages the open-source chemical structure tool known as [[https://github.com/epam/ketcher|Ketcher]]. Users can generate both chemical and biological structures (e.g. proteins, genes, nucleotide sequences, etc) in this editor via the Molecules and Macromolecules editor modes, respectively.
+\\
+\\
+{{:strucs_anno.png?700|}}
+\\
+//Fig 16. Structure annotation module. Users can generate, save, export, and load molecule and macromolecule structures.//
+\\
+\\
+Structures can be stored in the ELN page and/or exported out as image files (or other formats, where permitted). Saved structures appear as cards, which can be loaded back into the editor. The structures themselves are stored as JSON objects, making them useful candidates for feeding into AI/ML models!
+==== Flow ====
+This section will be written at a later date.
+==== Tecan SPARK (BNL) ====
+The Tecan SPARK is a UV-Vis spectrophotometer designed to analyze well plates. It is housed in the Biological Nanostructures Laboratory in CNSI at UCSB. This module, as shown in Fig 17, serves to link BioPACIFIC MIP-related data from the Tecan SPARK to their corresponding ELN pages. It functions similarly to the other retrieval-and-link modules (Symphony, SAXS), but offers little in the way of additional features at this time.
+\\
+\\
+{{:spark_anno.png?700|}}
+\\
+//Fig 17. Tecan SPARK ELN annotation module. This module allows users to link their Tecan SPARK data from the BNL to their ELN pages.//
 \\