CDSA-Tools

Tools to make living CDSA easier and faster. This is a work in progress!
Feel free to use them as you see fit. If you found these tools useful, I would be greatful if you could acknowledge this GitHub Repo! =)

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TO INSTALL:

1. Download the latest version of python 3 from here (these codes were written for python 3.10 or higher):
2. Install python. Make sure to select the 'Add python.exe to PATH' in the installer if it is an option.
3. Install the python modules we need:
   1. For windows:
   1. Press the windows key + x and then select 'windows powershell (Admin)
   2. Then, type the following (without quotation marks):
   1. "pip3 install numpy"
   2. "pip3 install matplotlib"
   3. "pip3 install pandas"
   4. "pip3 install seaborn"
   5. "pip3 install scipy"
   6. "pip3 install xlsxwriter"
   7. "pip3 install hplc-py"
   3. wait for each package to install before starting the next. You can use the same "pip3 install X" command to install any package named X.
   4. you can check your python installation works by typing "py -3 --version" in the command prompt / powershell, it should tell you your python version.
   2. For OSX (mac users):
   1. Open a new terminal window (type terminal into the search bar)
   2. In the terminal, type the following commands (without quotation marks):
      1. "python -m pip install numpy"
      2. "python -m pip install matplotlib"
      3. "python -m pip install pandas"
      4. "python -m pip install seaborn"
      5. "python -m pip install scipy"
      6. "python -m pip install xlsxwriter"
      7. "python -m pip install hplc-py"
   3. you can use the same "python -m pip install X" command to install any package named X.
   4. you can check python works by typing "python -V" in a terminal window to see your python version.
   3. Linux users should know what to do!!
4. now you can use the scripts! The scripts are designed to go in the same folder as the data you wish to analyze. More details on this coming soon.

---- Modules needed: ----

You will need the following installed on your system to utilize these codes:

1. Python 3.10 or higher
2. Numpy
3. Matplotlib
4. Pandas
5. Seaborn
6. SciPy
7. xlsxwriter
8. hplc-py

Please Note: Not all scripts need all packages.
---- Current tools: ----

So far, we have:

1. General chemistry tools:
   1. Molecular Weight Calculator
   2. GPC processing and data plotting (supports multiple samples, uses Mw and WF/dLogM data).
      To use this scrpt, just place it in the same folder as your GPC data. Currently this supports Malvern Omnisec instruments and Wyatt/Agilent insturments.
      Examples of the data input format needed can be found in the 'GPC processing' folder.
   3. HPLC processing and data plotting.
      Supports Shimadzu insturments.
   4. UV-Vis processing and data plotting.
      Supports Agilent insturments.
   5. CD processing and data plotting.
      This is a work in progress.
   6. Magritek Benchtop NMR Folder Cleanup.
      This script deletes the shim and standby datasets from a backup folder to save space.


2. Self-assembly tools:
   1. living CDSA calculator (for seeded growth experiments)
   2. Micelle Counting Statistics and Histogram Script (automates the analysis of measured nanoparticle sizes/lengths from Fiji/ImageJ).
      To use this script, just place it in the folder with your measurment data from Fiji and ensure the measurments file is called "Results.csv".
      Then run the batch script!
   3. Continuous-Flow Self-Assembly Experiment Planner.
      This script allows you to quickly and easily plan self-assembly experiemnts in flow. More features and updates are planned.

More ideas coming when I have time! Any feedback is welcome =)