MY CODE

My Code (fun and educative stuff 🦉)

My Code (serious stuff 🔬)

PDF DATA EXTRACTION

This is a personal suite of Python functions that I recently used in a project for a biotech company.

The input was a PDF report containing 1,356 lines of data and descriptions covering:

14 experimental subjects (sbj)
54 different types of observations (obs)
3 possible outcomes (1, 2, 3) per observation
17 experiments or observation times (t)

The expandable figure below illustrates the progress and final output showing only two subjects (SbjA/B) and only two types of observations (Obs1/2).

An HTML/js/css program for BATCH DNA AND PROTEIN SEQUENCE ANALYSIS

Click to use: MolBioWiz

MolBioWizcan process up to thousands of DNA or protein sequences at once, for sequence formatting, translation, reverse-complementing, reverse-transcription, and motif searches. It can also help design peptide immunogens, do multiple antibody V-region sequence alignments and find antibody developability problems as shown in the figure below.

An HTML/js/css program for BATCH TEXT FILE TEXT EXTRACTION TOOL

Click to use: TET

Text Extraction Tool, finds and extracts lines containing a keyword and optionally, additional lines above and/or below it. It can also extract sentences even if they span several lines. The input is either a list of up to hundreds of text files, or text uploaded, pasted, or entered into the INPUT area. You can use a regex expression as a KEYWORD (google "js regex" to learn more). PDF and Microsoft Word files ARE NOT text files (but, see my next two batch file conversion programs). Examples of text files are .txt, .text, .csv, and many programming and data files.

HTML/js/css programs for BATCH PDF TO TEXT AND DOCS TO TEXT CONVERSION

Click to use: PDF→Text and MSWORD→Text

These two programs use the public libraries (pdf.min.js, pdf.worker.min.js, for pdf, jszip.min.js for word and FileSaver.min.js for both), to convert a list of up to hundreds of pdf or word files to text files. The programs will split the original content into "perceived" sentences. While the loss of page formatting and the occasional misinterpretation of characters, will make it difficult to read the converted files, the text will be searchable and can be mined using the TET program. The User interfaces are identical except for the background color.

Click to use: abPlot

An HTML/js/css program for FITTING ANTIBODY BINDING DATA TO LOG LOGISTIC FUNCTIONS AND PLOTTING IT

FITTING ANTIBODY BINDING DATA TO LOG LOGISTIC FUNCTIONS

This program will fit antibody binding data to a log-logistic function of up to 5 parameters, and plot the data and the fit. Ideally, the data should be coppied and pasted from a spreadsheet. The first column contains the antibody or ligand concentrations (x). You can have up to 12 (y1 - y12) columns of readings. You may have repeated x concentrations and omit or duplicate some of the y readings. While I prefer to use Python for plotting pretty charts this program allows me to manually adjust the parametes of any of the 12 data-sets individually. I am in the process of updating the program to make it a bit more user-friendly (Jan 2024).