Benutzerspezifische Werkzeuge

Information zum Seitenaufbau und Sprungmarken fuer Screenreader-Benutzer: Ganz oben links auf jeder Seite befindet sich das Logo der JLU, verlinkt mit der Startseite. Neben dem Logo kann sich rechts daneben das Bannerbild anschließen. Rechts daneben kann sich ein weiteres Bild/Schriftzug befinden. Es folgt die Suche. Unterhalb dieser oberen Leiste schliesst sich die Hauptnavigation an. Unterhalb der Hauptnavigation befindet sich der Inhaltsbereich. Die Feinnavigation findet sich - sofern vorhanden - in der linken Spalte. In der rechten Spalte finden Sie ueblicherweise Kontaktdaten. Als Abschluss der Seite findet sich die Brotkrumennavigation und im Fussbereich Links zu Barrierefreiheit, Impressum, Hilfe und das Login fuer Redakteure. Barrierefreiheit JLU - Logo, Link zur Startseite der JLU-Gießen Direkt zur Navigation vertikale linke Navigationsleiste vor Sie sind hier Direkt zum Inhalt vor rechter Kolumne mit zusaetzlichen Informationen vor Suche vor Fußbereich mit Impressum


Artikelaktionen

Announcement: Alpha version of psos available for public testing

TL;DR Alpha version of psos is available. Runs multiple tools on protein sequences and visualizes the results. Can be integrated into your own software.

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
  • Bug-finding
  • 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