maciaslab / htsdsf_explorer

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HTSDSF Explorer

DSF data explorer focused in HTS. Used to find binders to proteins which alter Tm.

Description

A program that is agile and allows to analyze a very high number of curves in a very short time. The program finds wells for which dTm with respect the reference is higher than a given threshold. Then allows the user to validate the Tm with the minimum number of clicks. The program has been tested in Mac OSX and Windows, but any modern OS with python3 and a web browser should run it.

Execution

Just download the package and run: python server.py Program will start a webserver and open a browser pointing at http://localhost:5555/index.html

Windows Installation Instructions

There are two options to run the software in windows:

1- The easy way: Download a release

Just download the latest windows release, unpack it and run the exe file. Find the file here : https://github.com/maciaslab/htsdsf_explorer/releases/latest

2- The less easy way: Installing python

  1. Download python 3 64-bits from https://www.python.org/downloads/ and install it, checking the "Add to path"· option.

  2. Follow the rest of the instructions

Requisites

Python 3

Python modules:

scipy pandas xlsxwriter openpyxl numpy matplotlib python-docx

To install modules:

python3 -m pip install scipy pandas xlsxwriter openpyxl numpy matplotlib python-docx

Use

Program in python, interface through web server.

Two different modules:

Tm calculations are done using first derivative, smoothed and supersampled (x5). In case of multple Tms, the one closest to refTm is used. Arbitrary number of reference wells, averaged and with stddev.

data: Put data files in folders at {data_path} Supported file types:

txt:

xlsx:

Plateinfo

The plateinfo folder contains the information that correlates the wells in the plates with the ligands in them. In HTS experiemnts, the sample plate templates are reused for different proteins. You can (optionally) define these templates, and then assign a template to your plates. Format: 5 columns, tab separated. .txt extension. One header line.

Column 1: COMMENT
Column 2: Molecule id
Column 3: Smiles for Molecule
Column 4: Plate template name
Column 5: Well

You can have as many .txt files as needed, program will read all of them. After matching a plate with a Plate tempalte name, the well will be used to find the molecule in the well (Molecule id and Smiles for Molecule) when generating a report.

Settings

settings.ini contains the program settings.

Default file:

[Default]
data_path=data/
cache_path=cache/
persistent_path=persistent/
plateinfo_path=plateinfo/

Citing this software

A paper describing this software is in process of being written.

License

This piece of sotware is under the GPL v3 license (https://www.gnu.org/licenses/gpl-3.0.en.html). Some parts of it are created by third parties and are under a MIT license. These parts have been unmodified and the files contain the headers corresponding to the original license and the original authors are credited below:

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Chart.js

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DataTables

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jQuery

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