C370 | Lab Notebooks

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<h1 style = "text-align: left;">
  Chem 370 | Instrumental Analysis
</h1>
<h1 style = "text-align: left; font-weight: bold;">
  Keeping a Lab Notebook for Reproducible Research
</h1>

**Dr. Al Fischer**   |  Western Carolina University

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<img src="https://media.nature.com/lw800/magazine-assets/d41586-021-02211-4/d41586-021-02211-4_19567708.png
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> If a spreadsheet alters the gene names, those genes are lost when the data are imported into gene-network-analysis software, and this can distort results. The program “will tell you you've lost a bunch of your genes”, she says, but won’t indicate which ones. And when dealing with data sets that contain 20,000 genes, manually comparing lists to identify which genes have been lost is an onerous task, Purdie adds.

.image-credit[[Nature](https://www.nature.com/articles/d41586-021-02211-4)]

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> One solution is to avoid using spreadsheets, he suggests. Although some — such as the open-source programs LibreOffice and Gnumeric — don’t have the problem, spreadsheets are hard to audit. “If there’s a problem, it’s not readily apparent where the problem happened,” because there’s no record of what steps the software took, he says.
>
>  Some computational biologists use scripted computer languages, such as Python and R. These don’t autocorrect gene symbols, says Ziemann, and researchers can trace the source of errors.

.image-credit[[Nature](https://www.nature.com/articles/d41586-021-02211-4)]

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# lab notebooks | **guidelines**

- Create one notebook per lab/instrument.

- You should continue to add to each notebook throughout the semester as needed.

- See [my lab notebook guidelines](https://chem370.github.io/course-information/lab-notebooks/) for specific requirements and examples.

- Templates are available on the course website and may be loaded directly into Julia via the links provided.

- Follow the *specific* instructions in each template for the assessment.

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# lab notebooks | **organizing files**

- Organize your labs!
- Use the following directory structure to organize your labs:

```
    > lab-notebooks/[labN_lab-name]
        |------> /labN_lab-name.jl (this is your lab notebook file)
        |------> /datafile.csv (this is your data file - there may be several)
```
          
<img src="/assets/images/lab-0/notebooks-files.png">

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# lab notebooks | **instrument tables**

Every lab notebook should contain an [instrument table](https://chem370.github.io/course-information/lab-notebooks/#creating-instrument-tables).

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# lab notebooks | **grading**

Lab notebooks are graded for thoroughness and overall quality according to the [rubrics](https://chem370.github.io/course-information/lab-notebooks/#notebook-rubric) at the end of each lab.

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# lab notebooks | **grading**

Lab notebooks are graded for **accuracy**.  Your calculations are independently verified using your specific data.

This may be done by your instructor or in real-time during your data analysis.

*You must turn in your data and answer* ***exactly*** *as specified!*

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# lab notebooks | **reproducible research**

Youtube playlist about reproducible research:

https://youtube.com/playlist?list=PLDWboTZnRm5sF3hkjESXw1EpeI5Q4gbSC