NSF BioPACIFIC MIP Wiki

Page Annotations are a unique feature of the ELN (Fig 1). These annotations come in the form of various modules, located at the top of any given ELN page, that collect information about different processes. This information helps to annotate the page about details such as: chemical reagent and product information for a synthesis; biological protocols used in a synthetic biology experiment; descriptions for the contents of well plates; and so on. This information remains linked to the ELN page, is stored in the LIMS for programmatic access, and is shared via page snapshots.


Fig 1. Page annotation menu. From left to right: Chemistry, Biology, Well Plates, ChemSpeed, and Symphony X/Peptide Synthesizers.

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.


Fig 2. Reagent and product tables in the ELN's Chemical Annotation module. Rows can be added/removed as needed by the user inputting values to the table.

Biological page annotations (Fig 3) are meant to capture the wealth of information available in conducting synthetic biology experiments. In this annotation tool, users can add, view, and edit information regarding organisms, nucleotides, plasmids, and protocols utilized in their synthetic biology experiments.


Fig 3. Biological annotation panel. These annotations capture information about organisms, nucleotides, plasmids, and various protocols applicable to synthetic biology experiments.

Well plate annotations (Fig 4) in the ELN come in two different forms: chemical and 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.


Fig 4. Plate annotation panel. Users first specify a plate type (chemistry or biology) and then follow the prompts. Biological plates have another layer of detail, allowing well-by-well annotation and file uploads. Once a well plate is created, it shows in the list with other plates, along with their QR codes.

Note for Microrheology and Optics11 Indenter Users: If you are using either of these instruments, or another instrument with a program that asks for your well plate serial number before going forward, please note that you can find that number above the QR code of your well plate, as shown in Fig 5.


Fig 5. Individual well plate. The blue circle indicates the universal unique identifier (UUID) used to represent the serial number of the plate. This is the number embedded in the QR code, and is the number expected by access-granting scripts that ask for the well plate serial number.

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 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).


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 10. Symphony module file cards. Displays the attached/linked Symphony methods files.


Fig 11. Symphony module file card file view. Displays the parsed methods file/file dependent's information in tabular format.