11.06 How would I use LabArchives as a chemist?

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Chemists may add calculations, observations, safety information, photos, chemical reactions, citations, and even equipment maintenance information to LabArchives. The Lab notebook should contain enough information that a colleague can read the information and replicate the experiment without speaking to you.  

Many Chemists that use LabArchives will develop standardized templates that are used frequently. These templates can be a page with a variety of rich text entries, headings, attachments, or other files that can be copied frequently. A well-thought-out template can ensure that a page of the notebook contains all necessary information, makes it easier to review a colleague’s work, and it makes your lab or group more efficient. You may organize these templates in a designated “templates” folder so your team will use the copying tools to use the template. To learn more about copying a page, click here. 

It is recommended to set up naming conventions or policies with your team to improve data retrieval and makes it easier to review a colleague’s notebook. If everyone uses a consistent naming or numbering convention, it will be easier to find the data in the future. As an example, you may use a list of standard abbreviations like IR, NMR, or a term or phrase that may be confusing to an external viewer. You can document these terms in a data dictionary or in your data management plan. In the same way, it is important to name experiments or files in a consistent way. As an example, “2019/11/21 JD aspirin synthesis 001” can indicate that the file, page or experiment was completed by Jane Doe on November 21, 2019, the data covers synthesis and it is the first experiment. 

A single chemical experiment or page in LabArchives may contain the following:

  1. Chemical Name and Experiment Number
  2. Purpose of the Experiment 
  3. Chemical Structures or Reactions 
    1. LabArchives Chemical Sketcher Widget
    2. Drawing Chemical Structures in external Applications
    3. Hand-Drawn Chemical Sketches
  4. Lists of Reagents and products:  manufacturer, lot number, purity, and more 
  5. Calculations, Formulas and Data tables 
    1. Calculations as Rich Text Entries
    2. Calculations as Office Documents
    3. Calculations as Widgets
  6. Procedure, Notes, Observations 
  7. Photos and videos of the experiment or equipment 
  8. Results including Data Analysis, chromatography, or Spectral Analysis 
  9. Lists of Equipment or software used: settings, model, manufacturer, and calibration information 
  10. Safety information and Waste disposal forms 

1. Chemical Name and Experiment Numbering 

In LabArchives, all recognized text can be indexed in the LabArchives search tool. This makes it easy to find a specific file, entry, or page in your notebook. You can also search by chemical structure. To learn about search in LabArchives Click Here and to learn more about chemical structure searching, click here.

Chemicals can be described in many ways, including the common name, systematic name, chemical formula, IUPAC name, and more. In some cases, this can make it difficult to find the correct information. As an example, if you list “Aspirin” as a reagent for a certain experiment, searching for “acetylsalicylic acid” may not return this reagent. 

2. Purpose of the Experiment

Your Lab notebook should have a short description of the work that is completed. This can be as simple as a couple of sentences at the top of the page or it can be a more complex overview of the project that is completed. 

  • In the example below, the page is named with the researcher’s initials, an experiment number, and the compound that will be synthesized. The researcher also added several names for the compound as a rich text entry.  

 

3. Drawing Chemical Structures and Reactions 

A. LabArchives Chemical Sketcher Widget 

On the list of widgets, you can select the “Chemical Sketcher.” This is a simple and easy way to draw a chemical structure, reaction, or scheme. You can also import a mol file. To learn more about the Chemical Structure widget, click here.

 

B. Draw Chemical Structures or reactions in external programs and upload the structure files to LabArchives 

Many researchers have a dedicated chemical structure drawing tool like ChemDraw. These applications have several export tools to download the structureThe export formats may be .mol, .sdf, .cdx, or you can also export the structure as a common image format. You can upload the exported chemical structure or reaction to LabArchives as an attachment. It is important to include things like a file name, file description, or tags to improve search results. To learn more about attachments, click here. 

If the file is a supported file type, you may see a thumbnail of the structure or be able to search your lab notebook for this structure. To learn more about chemical structure searching click here.

Some files will show a generic file icon like the one below.  

 

C. Upload photos of hand-drawn chemical sketches 

Some researchers prefer to quickly draw a chemical structure by hand and take a photo or scan of the drawing. To improve search results. be sure to include a description, tag, or file name. 

 

3. Calculations and data tables 

A. Calculations as Rich Text Entries

Some researchers will set up standard tables or rich text entries for calculations or measured values. Rich text entries are also a great place to include information about the formulas that are used. To learn more about rich text entries, click here.

b. Add Calculations or data tables to an Office Document in LabArchives 

You can edit Office documents in LabArchives using Microsoft Office Online. This can be a convenient way to perform calculations and it makes it easy to export the information. You can setup a standard Word, Excel, or PowerPoint document that has the necessary fields and calculations. When someone needs to use the document, they can upload the file to a page or copy the template. To learn more about working with Office Documents, Click Here.

C. Show calculations or data tables in a widget 

You can also develop custom widgets to display an HTML form that you design. This widget can have simple calculations for things like a stoichiometry table. To learn more about designing your own widgets, Click Here. 

 

6. Procedures, Notes, and Observations 

Your lab notebook can contain notes, observations, procedures, and other information about the experiment. Typically, text is added to LabArchives using a combination of rich text entries and headings. In the example below, the researchers follow a standardized procedure, however they are expected to insert comments, notes or observations within the rich text entry.  

 

7. Photos and Videos 

Photos and videos can be incredibly useful to reproduce results in the future. They are a great way to document visual clues like a chemical changing color or the amount of gas or bubbles produced from an experiment. You can upload photos of results from NMR or IR analysis. As an example, take a photo of the equipment or glassware that was used or record videos to train other colleagues on a specific process or protocol.

   

8. Results: Data Analysis, Chromatagrophy, or Spectral Analysis 

You can upload attachments of any file type to LabArchives. For chemists, it can be convenient to store the data analysis or raw files that are generated from equipment. You can upload these files as an attachment to LabArchives so that everything is stored in the same place. To learn more about attachments click here and to learn more about using LabArchives for code, click here.

If the files are large, you may prefer to store them outside of LabArchives and provide a link or reference to the data. To learn more about linking to files click here.

9. Lists of Equipment used: settings, model, manufacturer, and calibration information 

If you need specific equipment or hardware to perform an experiment, it’s important to document this information in your lab notebook.  If the equipment has been cleaned, calibrated, or repaired, this can impact the final results. You can log these activities in a formal equipment maintenance log or calendar shared with your team. If you recognize a pattern of unusual results, a maintenance log makes it easy to identify faulty parts or calibration issues.  

If you work with a lot of glassware, it can be useful to take photos of your setup and include descriptions to help you reproduce the same experiment in the future. 

10. Safety and health information and Waste disposal forms 

There are many important documents (COSHH Forms, SDS Sheets, calibration reports, or EPA Forms) that must be maintained by a lab. Many labs will store these forms in LabArchives because it is easy to share the information with everyone in your team and you can access the data quickly. You can also add links to these forms if they are stored in another location. To learn more about links, click here.