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docs: tweak manuscript
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kalekundert committed Nov 25, 2020
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19 changes: 3 additions & 16 deletions docs/manuscript/bmc_article.tex
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\begin{abstract}

\parttitle{Background}
Microplates are ubiquitous in biological research because they make it easy to
collect data for hundreds of different conditions in a single experiment.
Despite this, there is no standard method to annotate the wealth of data
contained in each plate.
Microplates are ubiquitous in biological research because they make it easy to collect data for hundreds of different conditions in a single experiment. Despite this, there is no standard method to annotate the wealth of data contained in each plate.

\parttitle{Results}
We introduce a new file format, called wellmap, for describing the layout of
wells on microplates. The format is text-based and emphasizes being easy to
read, write, and share. It is capable of describing any layout for any
experiment. It is also accompanied by a tool for generating clear
visualizations of layout files, and a simple API for parsing layout files in
analysis scripts written in python or R.
We introduce a new file format, called wellmap, for describing the layout of wells on microplates. The format is text-based and emphasizes being easy to read, write, and share. It is capable of describing any layout for any experiment. It is also accompanied by a tool for generating clear visualizations of layout files, and a simple API for parsing layout files in analysis scripts written in python or R.

\parttitle{Conclusions}
We have used wellmap in our own research to annotate data from a
wide variety of experiments, including qPCR and flow cytometry. Given
the large number of experiments that make use of microplates, it is
our hope that other researchers will find this file format as useful
as we have. For complete instructions on how to install and use wellmap,
visit: \url{https://wellmap.rtfd.io}
We have used wellmap in our own research to annotate data from a wide variety of experiments, including qPCR and flow cytometry. Given the large number of experiments that make use of microplates, it is our hope that other researchers will find this file format as useful as we have. For complete instructions on how to install and use wellmap, visit: \url{https://wellmap.rtfd.io}

\end{abstract}

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5 changes: 2 additions & 3 deletions docs/manuscript/cover_letter.lyx
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Expand Up @@ -133,9 +133,8 @@ Wellmap: A file format for 96-well plates
In this manuscript, I introduce a clear and succinct text file format for
describing the layout of wells on microplates.
Compared to other methods of annotating these experiments, the wellmap
file format has several advantages: it's easy to read, easy to write, easy
to share, easy to check for mistakes, and easy to incorporate into analysis
scripts.
file format is easier to read, easier to write, easier to share, easier
to check for mistakes, and easier to incorporate into analysis scripts.
Considering both these advantages and the widespread use of microplates
in modern biology, I believe that this software will be of broad interest
to the readers of this journal.
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