D6.1: Genomics Workflow Preservation Requirements
Creators: name: Roos, Marco
name: Hettne, Kristina
name: Henneman, Peter
name: Mina, Eleni
name: Leenheer, Dennis
name: Peter-Bram 'T Hoen
Publisher: name: Zenodo
Year: 2011

description: One of the main challenges for biomedical research lies in the integrative study of large and increasingly complex combinations of data in order to understand the mechanisms that explain the onset and progression of human diseases. Computer-assisted methodology is needed to perform increasingly complex integrative analysis, while upholding scientific principles such as reproducibility and the preservation of experimental materials and methods as evidence for our findings. Therefore we develop the concept of a Research Object in this project. From a biological perspective this is a structured container for the materials and methods involved in a computational experiment. They collect and organize the diversity of information needed to support a research finding, and can be exposed to colleagues and peers similar to sharing a notebook or a published methods section. At this time, there is no widely adopted standard for recording and publishing a computational experiment as part of a biological study. Several public resources offer partial solutions, such as the Human Genome project and its many followers. As part of their infrastructure to share data, they provide reliable references to their content and sometimes enforce formatting rules upon submission of data and metadata. Ontologies and Semantic Web tools provide additional means for referencing computational artefacts that will help useful archiving. For methods and code, myExperiment and BioCatalogue are obvious candidates to provide archiving facilities. Case studies at the Human Genetics Department of the Leiden University Medical Centre provide feedback and requirements for Wf4Ever developments, in particular a genotype-phenotype study for unravelling Metabolic Syndrome, and a study to reveal the role of epigenetics in Huntington's Disease. These provide real-life examples of what a Research Object may contain and mockup interfaces structured underneath by the envisioned Research Object model. We defined a step-wise requirement analysis procedure between biologists and technologists via Wf4Ever intermediates. Requirements are extracted from non-technically focussed user scenarios, which in turn are prioritised through feedback from the biologists. We identified three user roles: (i) 'researcher user of workflows', (ii) comparator, (iii) reviewer. Our initial requirements are based on the first. The top ranked user requirements are (1) being able to reuse (parts of) workflows, (2) finding workflows on the web by their content, biological purpose, and outcome, (3) recording notes while designing or running workflows, (4) keeping everything together, and (5) facilitating the publication of research objects. We suggest two main types of research objects: 'Live' Research Objects, for recording and organizing material before publication, and the abridged and clarified copies ready for publication: Publication Research Objects.
description: Wf4Ever Deliverable identifier: oai:repo.wf4ever-project.org:21