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Updating intro blurb
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wood-chris authored Jan 10, 2023
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Expand Up @@ -126,35 +126,25 @@ Documents Library Music Public
## Nelle's Pipeline: A Typical Problem
Nelle Nemo, a marine biologist,
has just returned from a six-month survey of the
[North Pacific Gyre](http://en.wikipedia.org/wiki/North_Pacific_Gyre),
where she has been sampling gelatinous marine life in the
[Great Pacific Garbage Patch](http://en.wikipedia.org/wiki/Great_Pacific_Garbage_Patch).
She has 1520 samples that she's run through an assay machine to measure the relative abundance
of 300 proteins.
She needs to run these 1520 files through an imaginary program called `goostats.sh` she inherited.
On top of this huge task, she has to write up results by the end of the month so her paper
can appear in a special issue of *Aquatic Goo Letters*.
The bad news is that if she has to run `goostats.sh` by hand using a GUI,
she'll have to select and open a file 1520 times.
If `goostats.sh` takes 30 seconds to run each file, the whole process will take more than 12 hours
of Nelle's attention.
With the shell, Nelle can instead assign her computer this mundane task while she focuses
her attention on writing her paper.
The next few lessons will explore the ways Nelle can achieve this.
Phillipa Frogg, an ecologist, wants to use the [Living Planet Index dataset](https://www.livingplanetindex.org/)
to help her with her research. However, she is unable to use the raw data directly; instead, she has to
edit the data so it's in a suitable format for her to make best use of. Although she could do this by hand in
a text editor, this would be laborious, time-consuming, and error-prone. With the shell, Phillipa can instead assign her computer this mundane task while she focuses
her attention on writing her latest paper.
The next few lessons will explore the ways Phillipa can achieve this.
More specifically,
they explain how she can use a command shell to run the `goostats.sh` program,
using loops to automate the repetitive steps of entering file names,
they explain how she can use a command shell to run shell programs,
and use loops to automate the repetitive steps of entering file names,
so that her computer can work while she writes her paper.
As a bonus,
once she has put a processing pipeline together,
she will be able to use it again whenever she collects more data.
In order to achieve her task, Nelle needs to know how to:
In order to achieve her task, Phillipa needs to know how to:
- navigate to a file/directory
- create a file/directory
- check the length of a file
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