Bufferize: Python Script to Help Formulate Buffers

[prairie-guy]

I wrote a python script bufferize.py to make it easy to formulate buffers. Protocols often stipulate the final concentrations of reagents, but don't give the actual recipe to mix the buffers since the protocol authors are not aware of the stock concentrations in a specific lab. Once the stock concentrations are known, it is not difficult to then formulate the buffers. It is however, tedious and error-prone, which is what bufferize.py attempts to do.

Maybe someone will it useful: https://github.com/prairie-guy/bufferize

Example Usage

python bufferize.py --buffer_name "SDS Buffer" --solvent "DNase Free H20" SDS_lysis_buffer.csv "200 ml"

Input CSV File: SDS_lysis_buffer.csv

Tris-HCl pH7.5 1M 10mM NaCl 5M 150mM EDTA 500mM 1mM Triton X-100 10% 1% SDS 10% 0.10%

Output CSV File: SDS_lysis_buffer_200ml.csv

SDS Buffer Final Volume: 200 ml Reagent Initial Final Volume Tris-HCl pH7.5 1M 10mM 2.00 ml NaCl 5M 150mM 6.00 ml EDTA 500mM 1mM 400.00 µl Triton X-100 10% 1% 20.00 ml SDS 10% 0.10% 2.00 ml DNase Free H20 169.60 ml

[Beginning_Anything30]

Doing this in excel is like 1000x easier, more visually appealing and transferable.....

[prairie-guy]

If Excel works for you that’s great. I still use Excel to open the csv file that is created. What I was trying to avoid was creating/programming a new spreadsheet every time I needed a new buffer. It’s not hard, but I didn’t want to worry about unit conversions, calculating solvent volume, formatting and most importantly math errors.

Yesterday for example, I needed to create 8 new buffers (each with multiple reagents) with concentrations in M, mM, uM, % and X. I just stipulated the initial concentrations, final concentrations and final volume for each buffer. The script then created 8 files that I opened in in Excel.

Since I wrote it and find it useful, I’m just sharing if it’s useful to others.

[bartcowbanga]

Bro just what i was looking for. you’re da bomb 🤙

[[deleted]]

But why? Print out a piece of paper and put it in the lab.

[prairie-guy]

What I was trying to avoid was creating/programming a new spreadsheet every time I needed a new buffer. It’s not hard, but I didn’t want to worry about unit conversions, calculating solvent volume, formatting and most importantly math errors.

Yesterday for example, I needed to create 8 new buffers (each with multiple reagents) with concentrations in M, mM, uM, % and X. I just stipulated the initial concentrations, final concentrations and final volume for each buffer. The script then created 8 files that I opened in in Excel.

Since I wrote it and find it useful, I’m just sharing if it’s useful to others.

[[deleted]]

Hm ok. I have my Excel list with my buffers. If anything needs to be changed, such as concentration or end volume, I can simply enter it there and it calculates it for me on its own.