NSF BioPACIFIC MIP Wiki

A National User Facility Dedicated to Biomaterials

User Tools

Site Tools

Trace:
eln-guide-basic-page-annotations

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
eln-guide-basic-page-annotations [2026/08/14 21:31] – csdunhameln-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).//
 \\ \\
 \\ \\
Line 98: Line 98:
 \\ \\
 //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.// //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. 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.
Line 107: Line 108:
 \\ \\
 ==== Structures ==== ==== Structures ====
-In draft+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 ==== ==== Flow ====
Line 113: Line 122:
  
 ==== Tecan SPARK (BNL) ==== ==== Tecan SPARK (BNL) ====
-In draft+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.// 
 +\\
eln-guide-basic-page-annotations.1786743090.txt.gz · Last modified: by csdunham