1
Launch the executable
Open the StaulliQ .exe file. When you publish the final release, place the executable in the same release bundle as the sample package or in the same folder beside these example inputs.
StaulliQ setup guide
How to start exploring StaulliQ
This page explains the basic startup workflow. When you add the final Windows executable later, keep it together with the sample package so users can launch the software and load the example files immediately.
Package contents
Stalling probability.xlsxamino_tables_Chou_Fasman.xlsxpause_directory/with all.txtfiles for optional MLP modefull_gene_list_short.xlsx- The
.execan be added later into the same release build
Before you begin
StaulliQ opens as a desktop application. The default sequence shown in the current GUI is PDIA3, so users can begin exploring immediately after loading the required data tables.
For the optional MLP workflow, users also need to select the provided pause_directory folder.
2
Load the stalling file
In the field labelled Stalling probabilities (CSV/Excel), browse to the example file Stalling probability.xlsx. This file provides the residue-level stalling probabilities used by the core scoring workflow.
3
Load the amino acid / Chou–Fasman table
In the field labelled Chou–Fasman tables, browse to amino_tables_Chou_Fasman.xlsx. This file supports the α, β, and coil propensity calculations used in the integrated secondary-structure analysis.
4
Use the default PDIA3 sequence or paste your own
The GUI currently opens with PDIA3 loaded by default. Users can keep this sequence to explore the example workflow, or replace it with another gene sequence in the sequence box.
5
Press Run analysis
Click Run analysis to generate the stalling profile, Chou–Fasman moving averages, and sequence-region interpretation panels. From there, users can continue into 3D view, interactive plots, AlphaFold comparison, CoolPolarity clustering, batch analysis, and Gromacs simulations.
6
Optional: use MLP mode with the pause directory
If users want to use the MLP workflow, they should browse to the provided pause_directory folder in the Optional MLP pausing .txt folder field. The folder contains all required pausing .txt files for the motif-based scoring mode shown in the software screenshots.
Main required inputs
Stalling probability.xlsx and amino_tables_Chou_Fasman.xlsx
Default example
PDIA3 is already present in the StaulliQ GUI as the starting sequence.
Optional MLP input
Load the full pause_directory folder containing all pausing text files.
Publishing note
Right now the website download button serves the sample zip. When your final .exe is ready, replace the zip in downloads/StaulliQ_sample_package.zip or publish a new archive under the same filename so the site keeps working without any HTML changes.