Coronado, Sergio

Gu, Wei

Jarosz, Yohan

Satagopam, Venkata

Schneider, Reinhard

Trefois, Christophe

Open Repository and Bibliography - Luxembourg

Luxembourg Centre for Systems Biomedicine REPRODUCIBLE RESEARCH RESULTS - R3Christophe Trefois1, Yohan Jarosz1, Wei Gu1, Venkata Satagopam1, Sergio Coronado1, Reinhard Schneider11Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg (UL)79-A89-R00IntroductionIncrease quality of research with the R3 reproducibility layer Details of the R3 reproducibility layer Conclusions1. Electronic Lab Notebook - Holds protocols and experimental methods - Contents can be locked and are accessible everywhere - Contains metadata of experiments2. Structured Data - CIA triad   - Confidentiality:  Secure and selective access  - Integrity:     Prevent data modifications  - Availability:    Long-term access to raw and processed data - Computerized access to available data3. Source code management - Version control  - Ownership of generated code4. Computational environment - Create workflows / pipelines to standardize data analysis - Regroup all dependencies, programs and computational        environment in one self-contained packageIn this project, we aim to implement the R3 reproducibility layer at the LCSB across the different research groups and define a framework to help different academic institutions in achieving a similar environment. Finally, there is:  - Increasing need for reproducible computational research - Need to establish a reproducibility layer to cover all processes     from experiment to article publishing - Reliable and heterogeneous infrastructure has to be establishedUltimately, the goal of reproducible science is to provide the reader with all the information required to accurately reproduce scientific results.Problem statementThe Luxembourg Centre for Systems Biomedicine (LCSB) has a flagship research area around Parkinson‘s disease (PD). PD is a multi-factorial disease for which the etiology still remains to be elucidated. By the nature of its projects, the LCSB has tightly integrated collaborations between research groups and accurate, shareable reproducible results are required in order to tackle and understand the complex disease mechanisms. In the last decade, this need for increase of standardization has been rising in the whole research community.     With increasing complexity of generated data and associated analysis, there has been raising concerns in the scientific community about the reproducibility of findings and conclusions in many peer-reviewed scientific articles. In the past, experimental procedures and summary statistics were required in the publishing process. However, often, workflows, computational environments and data sets were not, leading to a global problem where many research findings cannot be reproduced based on the contents of a published article. There is a constant increase of errors in published scientific output and it is largely not feasible to reproduce findings based on published material in peer-reviewed articles. We have identified a number of areas contributing to this decrease in scientific quality over time: - Increasing complexity of research environment - Lack of availability of data, algorithms, source code - Standardized operating procedures for data handling & analytics - Decreasing persistence of outdated technological tools Due to these issues, there is an inherent need to harmonize IT infrastructures, data processes, tools, data handling and methods. The penultimate goal of these efforts is to raise research quality for the increasing complexity of research and increase overall reproducibility. Therefore, we propose a R3 reproducibility layer aiming to standardize all elements in the classical research publication workflow.5. Freeze state of project - Protocols, data, source code and environment cannot be changed    anymore - Project state needs to remain accessible / runnable over time LegendReproducibility LayerLab ScientistCarry outexperiments Data Analysis ArticleResultsReader /ReviewerElectronic LabNotebookProtocolsRaw data Source codeWorkflowsR3 standard operatingprocedures Analysed dataFiguresConclusionsBypassStructured Data Source codemanagementComputationalenvironmentFreeze state of projectReproducibleTraditional

Reproducible Research Results R3

http://orbilu.uni.lu/bitstream/10993/27052/1/BBC2014_Poster_v2.pdf

Reproducible Research Results R3

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