About

Purpose

The BiochemPy (i.e., Biochemistry + Python) web application was created by a group of passionate Computer Science students at Iowa State. The purpose of the app is to provide a suite of figure plotting and data analysis tools that can be easily used on daily basis, especially for researchers in a typical biochemistry or biophysics lab.

The code was initially based on a set of Python scripts developed by Dr. Shae Padrick, which fits protein binding and actin polymerization data. The reasons for creating this website are:
  1. The long-time frustration of using graphs generated by Excel to make publication- quality figures in Adobe Illustrator
  2. The major barrier of learning Python coding for biochemists
This site offers users many built-in features to facilitate daily data analysis and graphing:
  • Flexibility of uploading and editing data sets in plain text or CSV formats
  • Ability to store, retrieve, and share work sessions
  • Full customization of graphs
    • Currently supporting line/scatter and swamp/bar graphs (more coming)
  • Generation of publication-quality graphs that can be directly edited in Adobe Illustrator
  • Transparency of data analysis results
    • All analysis results can be saved with raw data to comply with good practices of lab note taking
The web development team is currently in the process of making further improvements to this site and developing new features. Details on the latest changes will be posted in the 'App Version Information' tab on this page. So, stay tuned.

Credits

Developers
BiochemPy Web App Development Team
  • Leyuan Loh
  • Ganesh Prasad
  • Finlan Rhodes
  • Aubrey Uriel Sijo-Gonzales
Iowa State University-Department of Computer Science
COM S 402 (Undergraduate Senior Design) FA' 2021
Current Developer
  • Andy Foo Guo Zhen

    Undergraduate Student
    Department of Computer Science
    Iowa State University

Acknowledgements
  • Shae Padrick, PhD

    Original Python Script Developer
    Assistant Professor
    Dept. of Biochemistry & Molecular Biology
    Drexel University College of Medicine

    Original Script Citations:

    • Doolittle LK, Rosen MK, Padrick SB. (2013) Measurement and analysis of in vitro actin polymerization. Methods in Molecular Biology 1046:273–293.
    • Shae Padrick, PhD, SBP_data_analyze.py (v0.77) [Source code]. SBP_data_analyze.py file download

  • Baoyu (Stone) Chen, PhD

    Instructor of BiochemPy Development
    Assistant Professor
    Roy J. Carver Dept. of Biochemistry, Biophysics & Molecular Biology
    Iowa State University

  • Miles Aronnax

    Manager Information Technology Systems
    College of Liberal Arts & Sciences Administration
    Iowa State University

  • Iowa State Research IT

    College of Liberal Arts & Sciences
    Iowa State University
    https://researchit.las.iastate.edu/

  • Simanta Mitra, PhD

    Professor | Course Instructor for COM S 402
    Department of Computer Science
    Iowa State University

  • Graham Mobley

    Undergraduate Student
    Department of Computer Science
    Iowa State University

Version 2.1

10/29/2022

What's New?

  • Hotfix: Plotting for negative values
    • Single column plotting for Module 1 accepts negative values
    • Scatter box plot and violin plot now supports negative value plotting
    • NOTE: Negative value plots will not work with log scale option turned on
      •  

Version 2.0

9/18/2022

  • New Linear Regression Module
    • Fits and computes gradient, r^2 value and y-intercept for multiple datasets
    • Users can choose to fit datasets through origin or perform normal linear regression fitting
    • Range settings for individual datasets can be adjusted prior to linear regression fitting
    • Graph's legend shows fitted equation for fitted line
    • Download Result(s) button allows users to download computed results in csv format
      •  

Version 1.3

8/6/2022

  • Secondary Y Axis
    • Dyanamically displays selected dataset on graph while using secondary y-axis options as reference
    • Users can toggle secondary Y axis options for Modules 1, 2 and 3
    • Settings for secondary Y axis such as title, min, max, intervals and log scale can be adjusted
      •  

  • Fix: Button delay issues resolved
    • Mac users no longer have to double click to load example datasets
    • Line options and marker options change instantaneously when clicked
  • Imrpoved reliability for email retrieval functionality
    • Frontend to Backend roundtrip expected to work even after MySql pods are restarted

Version 1.2

5/12/2022

  • Line Graphs
    • Smoother log scale curves for Modules 2 and 3
    • Reorganized columns for 'Customize Graph' table and made them more compact
    • Adjustable X and Y axes
    • Add 'Reference Line' option for Module 4
      • Automatic calculation of max and min inten values for each dataset
      • 'Input Module Parameters' only displays rows for plotted dataset and selected reference line
    • New default settings for line plots
      • Set line width to 1
      • If dataset has more than 20 points, set marker width to 0
      • If dataset has at most 20 points, set marker width to 10
  • Swamp Graphs
    • New option for dynamically resizing bars and graph space
    • New default settings for swamp plots
      • Set bar color to white with black boundary of width .5
      • Set marker color to gray with 50% opacity
      • Set marker size to 10
      • Default to addition of capped error bars for standard deviation

Version 1.1

2/23/2022

  • New website design and improved interfaces
  • Bar widths for scatter box graphs are now customizable
  • New Module 4 Actin Analysis Modes: Max AP Rate, Nucleation Rate
    •  

  • Addition of 'Edit Data' button on 'Results' page
    •  

  • Changes to Task Retrieval Link feature:
    • Form to create a new session is now on the 'Results' page
      •  
    • Enable user to extend session for another seven days
      (Popup for extension option appears after pressing 'Save Session' in a current session)
      •  

Version 1.0

12/28/2021

  • Download Swamp Bar graphs for Module 1 (Plot Data)
  • Merged Scatter Plot and Line Plot options into only one Line Plot option for Module 1 (Plot Data)
    • To remove markers, set marker size to 0
    • To remove lines, set line width to 0