buf 1.0.0

For easily making chemical buffers and solutions

Welcome to buf!

Buf is a command line based toolkit for making chemical buffers/solutions. Tired of calculating how much of each chemical you need to add when making solutions? Buf can help. Specifically, buf:

1. Allows you to develop a chemical library, saving the molar masses of frequently used chemicals.
2. Allows you to use those chemicals to define recipes for your buffers/solutions, in which you specify the concentration of each ingredient required to make the buffer.
3. Will ‘make’ those recipes for you, calculating how much of each ingredient you require to produce the volume of solution you specify.

For more information, visit buf’s homepage.

Installation

To install the buf toolkit, simply use pip install buf.

Getting Started

To introduce you to buf, let’s imagine that we want to make a solution containing 50mM NaCl, is 10% glycerol by volume, and contains a constant 5g of KCl, regardless of the volume of our solution. We want to make 5L of this solution.

Developing Our Chemical Library

In our recipe, we specify the concentration of NaCl with molarity. Before buf can calculate the mass of NaCl we will need to add to our buffer when we make it, we must first tell buf the molar mass of NaCl (58.44 g/mol) by adding the chemical to our library. This can be done with buf chemical -a 58.44 NaCl. We don’t need to tell buf about the molar masses of glycerol or KCl, since the amounts of those chemicals we will add to our buffer aren’t dependent on their molar masses.

Defining Our Recipe

Now that our chemical library has been defined, it is time to do the same with our recipe library. Here we will tell buf what we want to make. We define our recipe by giving it a name and listing its contents, using buf recipe -a best_recipe 50mM NaCl 10% glycerol 5g KCl. Now buf knows the ingredients of our solution; it’s finally time to make it!

Making Our Solution

To calculate how much of each chemical we’ll need for our 5L solution, all we need to use is buf make 5L best_recipe. Buf will use our stored chemical and recipe libraries to calculate the required amounts of each ingredient, and display the results.

Learning More

This tutorial only provides a brief overview of buf; for more details about the toolkit’s usage and functionality, see buf help. For specific information about a subcommand, see buf help <subcommand_name>. Alternatively, visit buf’s online documentation on Read the Docs here. You can also access the toolkit’s GitHub repository. Happy buffer making!

Version History

• 1.0.0: Creation of documentation on Read the Docs! Repository commented and published on GitHub.
• 1.0.0a11: Fixing README format.
• 1.0.0a10: Deleting old buf/library directory (since library files are now stored outside the package), updating README to describe new changes.
• 1.0.0a9: Chemical/recipe libraries no longer reset when upgrading the package. To those using older versions of buf who want to copy their libraries before upgrading, the library files can be accessed in the buf/library directory.
• 1.0.0a8: Bug fixes.
• 1.0.0a7: Improved documentation.
• 1.0.0a6: First release to PyPI proper.
• 1.0.0a1: First release of buf to Test PyPI!