This repository contains the resources and documentation to develop and build the TopDownApp. The different components of the app can be found in the respective subfolders.
The app lets you analyse (1. deconvolve, 2. identify, 3. visualise) TopDown data without having to install multiple software, and is available on every platform. In the default GUI setting, for the analysis it is expected as input a TopDown LC-MS/MS (for the time being, Thermo) RAW file and matching FASTA file for sequence based identification. TopDownApp also works without a GUI, e.g. for automated analysis on HPC infrastructure. It is a highly configurable platform intended to share analysis capability fast, through flexible code reuse.
The fastest way to get started with TopDownApp is if you have a container engine already installed (Singularityor Docker). Then, you can simply start the app right away (run with port 5006 mapped), then follow the localhost link in the output, usually http://localhost:5006/topdownvisapp!
For container engine specific commands and step-by-step instructions visit the documentation.
The TopDownApp runs nextflow workflows to effect the analysis of data input. These can be reused for data analysis on local compute infrastructure. See that folder's README.
The workflows use containerised tools and the TopDownApp itself can be containerised. All container recipes (Dockerfile/.sdef) can be found here. See that folder's README.
The TopDownApp handles input and output data with HUPO-PSI standard formats. Development code, dedicated im-/exporters, and documentation can be found here. See that folder's README.
The TopDownApp uses panel to build the browser interface for the app. This is also where the core of the TopDownApp lives. See that folder's README.
This folder contains notebooks illustrating TopDownApp re-use/development and (user-submitted) use-case studies. See that folder's README.
This folder contains documentation on this repository, the code, and its use. Including a glossary for technical jargon used in this project.