Announcement: Alpha version of psos available for public testing
psos, the protein sequence observation service, helps you to run sets of predefined bioinformatics tools on protein sequences and to visualize the results. It provides a simple user interface with several visualizations of the results. Developers can easily integrate psos into their own application via its Rest API.
Currently included analyses are homology search against UniprotKB/Swissprot (ghostx) and PFAM-A (hmmer3), signalpeptide prediction, transmembranehelix prediction and cellular localisation prediction. There are predefined profiles for gram+/- bacteria, eukaryotes and plants. These differ in the used analyses and their configuration.
Check it out at: https://psos.computational.bio
Goals of this alpha test are
- Stability and performance evaluation
- User-interface improvements
- Identification of additional features, tools and visualizations
The idea behind psos
At some point the modern microbiologist - analyzing genome, transcriptome or proteome data - reaches the point where an interesting protein lacks sufficient annotation, usually depicted by being a 'hypothetical protein'. The following steps usually include a deeper characterization of the protein, which involves running several bioinformatics tools (either from the command line or by submitting the sequences to an online tool) and collecting their respective results. This is the moment where psos can support the researcher by offering a uniform interface for many amino acid based analysis tools. In its simplest form the application that displays the annotation has an 'Analyze with psos' button and automatically sends the data to psos. It will analyze the data and display the results of all executed tools in a web frontend. As the tools have different runtimes, psos will display each tool result as soon as it is available.
Design and development of psos were based on three main goals:
- Enable simple integration into any application
- Avoid the requirement of tool specific result parsers
- Be open for extension
These goals were realized by providing a REST API and a helper library (Integration), the conversion of tool results into result-type specific json documents (Avoid different parsers) and making the project open source so that anyone can deploy and develop new features to psos (Open for Extension).
Technologies used in psos
Backend: Java, Vert.x
Frontend: Vue.js, Bio.js
Analysis and database retrieval: Python, Nextflow, Docker, Singularity, Biocontainers, ELK-Stack