Implementation of software protocols in computational proteomics

[veitveit]

Abstract

Proteomics is a broad research field embracing a wide range of alternative experimental and computational approaches. This led to the development of a zoo of single- and multi-purpose software tools where documentation of tool usage and applicable pipelines are either scattered over the respective web sites or not available.
This project aims at creating a set of protocols that describe how well defined problems can be solved using a given software. More specifically, we aim to provide user-friendly and immediately applicable protocols for the principal computational tasks in proteomics research. Additionally, we will work on creating software containers that allow performing the tasks in a controlled environment.
The resulting documented workflow containers will be made available in a central repository and published in a well-defined format. The format will establish the layout for future protocol submissions. Herein, we want to promote interactive solutions, interlinking with user support platforms and common training platforms such as proteomics-academy.org and ELIXIR TeSS.

Ultimately, we aim to collect material for publication in a dedicated issue, e.g. in Journal of Proteomics.

Work plan

• Discussion about publication format and areas of interest
• Outline of protocol layout:
  • Specific Docker or bioconda image that holds the full working environment
  • Container available from repository (Biocontainer or alike)
  • Forum for user requests and bug reports
• Implementation of workflow containers and individual protocols
• Testing of reproducibility of the described tasks
• Define final format and discuss way of evaluation for future protocol submissions

Benefits
Individual: Dissemination of your work or your favorite workflows
Community: Lower the bar for using proteomics software

Technical details

Software developers and data analysts with experience in setting up workflows are very welcome.

Experience in html, javascript/php and setup of software containers will be of advantage

Contact information

Johannes Griss
Department of Medicine I,
Medical University of Vienna,
Vienna, Austria
johannes.griss@meduniwien.ac.at

Veit Schwämmle
Department of Biochemistry and Molecular Biology
University of Southern Denmark
Denmark
veits@bmb.sdu.dk

[bittremieux]

Interesting and highly relevant topic!