Integration of the Single-Cell RNA Sequencing scRNAbox Pipeline in CBRAIN
Poster No:
1830
Submission Type:
Late-Breaking Abstract Submission
Authors:
Natacha Beck1,2, Michael Fiorini3,2, Rhalena Thomas3,2, Pierre Rioux1,2, Serge Boroday1,2, Darcy Quesnel1,2, Xuan Pham1,2, Reza Adalat1,2, Bryan Caron1,2, Sali Farhan3,2, Alan Evans1,2
Institutions:
1McGill Centre for Integrative Neuroscience (MCIN), Montréal, Québec, Canada, 2Montreal Neurological Institute (MNI), McGill University, Montréal, Québec, Canada, 3Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
First Author:
Natacha Beck
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Co-Author(s):
Michael Fiorini
Department of Neurology and Neurosurgery, McGill University|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Department of Neurology and Neurosurgery, McGill University|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Rhalena Thomas
Department of Neurology and Neurosurgery, McGill University|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Department of Neurology and Neurosurgery, McGill University|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Pierre Rioux
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Serge Boroday
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Darcy Quesnel
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Xuan Pham
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Reza Adalat
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Bryan Caron
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Sali Farhan
Department of Neurology and Neurosurgery, McGill University|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Department of Neurology and Neurosurgery, McGill University|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Alan Evans
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
McGill Centre for Integrative Neuroscience (MCIN)|Montreal Neurological Institute (MNI), McGill University
Montréal, Québec, Canada|Montréal, Québec, Canada
Late Breaking Reviewer(s):
Introduction:
CBRAIN (Sherif et al., 2014) (https://cbrain.ca) is an open source, web-based, collaborative research software platform designed to address major challenges in big data research. CBRAIN allows scientists to launch large-scale big data analyses using advanced scientific tools through an easy to use web-based user interface, removing the steep learning curve and pitfalls associated with a complex command-line environment. CBRAIN makes available over 160 pre-configured analysis pipelines for neuroimaging and genetics. This includes scientific tools for single-cell transcriptomics such as scRNAbox (Thomas et al. 2024), a single-cell RNA sequencing (scRNAseq) pipeline.
As new scientific tools and pipelines are being developed, the capability to seamlessly integrate them in CBRAIN is crucial. The process to integrate new tools has been streamlined and uses Boutiques (Glatard et al., 2018) to define the command line and tool parameters in a JSON format. The use of Boutiques offers multiple parameter validation features and enables clearer form validation messages. Based on the descriptor, CBRAIN automatically builds the user interface for each tool allowing users to select application parameters while automatically performing parameter validation. Containers, namely Docker and Apptainer (Kurtzer et al., 2017), are used to encapsulate the tool.
Occasionally, the integration of the tool in CBRAIN via Boutiques descriptor requires additional programming steps to define custom modules that will be used by the CBRAIN framework. To integrate scRNAbox two new custom modules were implemented.
As new scientific tools and pipelines are being developed, the capability to seamlessly integrate them in CBRAIN is crucial. The process to integrate new tools has been streamlined and uses Boutiques (Glatard et al., 2018) to define the command line and tool parameters in a JSON format. The use of Boutiques offers multiple parameter validation features and enables clearer form validation messages. Based on the descriptor, CBRAIN automatically builds the user interface for each tool allowing users to select application parameters while automatically performing parameter validation. Containers, namely Docker and Apptainer (Kurtzer et al., 2017), are used to encapsulate the tool.
Occasionally, the integration of the tool in CBRAIN via Boutiques descriptor requires additional programming steps to define custom modules that will be used by the CBRAIN framework. To integrate scRNAbox two new custom modules were implemented.
Methods:
The scRNAbox pipeline leverages the Seurat framework (Yuhan Hao et al. 2021) and incorporates eight analytical steps into a comprehensive scRNAseq analysis (Fig. 1). With the integration into CBRAIN, users are able to perform all these steps through the CBRAIN web interface.
To integrate the pipeline in CBRAIN, a wrapper was created (https://doi.org/10.5281/zenodo.14945083) to prepare the input files, including the creation of a config file that contains a summary of variables and options needed for the pipeline execution.
The integration of scRNAbox raised two main issues:
- Input management: in scRNAbox the tool mutates the input given to the pipeline by adding the output to the input given by the previous step. This behaviour can lead to issues in CBRAIN if multiple tasks are run on the same input data. It can result in tasks starting with different input or working on data that has been mutated by other tasks in the cache.
- Resource management: each step had different requirements in terms of memory usage and CPU time. For example, Step 2 needs only 16GB of memory, whereas Step 7 needs up to 150GB.
To integrate the pipeline in CBRAIN, a wrapper was created (https://doi.org/10.5281/zenodo.14945083) to prepare the input files, including the creation of a config file that contains a summary of variables and options needed for the pipeline execution.
The integration of scRNAbox raised two main issues:
- Input management: in scRNAbox the tool mutates the input given to the pipeline by adding the output to the input given by the previous step. This behaviour can lead to issues in CBRAIN if multiple tasks are run on the same input data. It can result in tasks starting with different input or working on data that has been mutated by other tasks in the cache.
- Resource management: each step had different requirements in terms of memory usage and CPU time. For example, Step 2 needs only 16GB of memory, whereas Step 7 needs up to 150GB.
·Fig1: Single-cell tool for CBRAIN integration: scRNAbox – scRNAseq Pipeline
Results:
To solve the input management problem a Boutiques custom module called 'BoutiquesInputCopier' was developed. This module allows the creation of a full copy of the input before starting the tool. In the case of scRNAbox, the copy is always performed. However, the creator of the Boutiques descriptor can add an option to make this feature selectable in the form, allowing the user to avoid the extra copy, if desired, for other tool integrations.
To address the resource management problem, the 'BoutiquesScrnaboxResourceManager' was developed. This module allows the creator of the Boutiques descriptor to specify the resource requirements for each step of the pipeline. This approach minimizes the resource requests on HPC systems, ensuring efficient use of memory and CPU time.
To address the resource management problem, the 'BoutiquesScrnaboxResourceManager' was developed. This module allows the creator of the Boutiques descriptor to specify the resource requirements for each step of the pipeline. This approach minimizes the resource requests on HPC systems, ensuring efficient use of memory and CPU time.
·Fig2: scRNAbox pipeline steps as presented through the CBRAIN user interface
Conclusions:
Integration of scRNAbox into CBRAIN demonstrates the flexibility and extensibility of integrating tools using the Boutiques framework. To address the challenges posed by scRNAbox, two modules were created to manage input data and resource allocation, ensuring efficient and reliable execution of the pipeline. Future work can include generalisation of the 'BoutiquesScrnaboxResourceManager' in order to accommodate other pipelines.
Genetics:
Genetic Modeling and Analysis Methods 2
Genetics Other
Neuroinformatics and Data Sharing:
Databasing and Data Sharing 1
Workflows
Informatics Other
Keywords:
Data analysis
Open-Source Code
Open-Source Software
1|2Indicates the priority used for review
Abstract Information
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Provide references using APA citation style.
2. Glatard T, Kiar G, Aumentado-Armstrong T, Beck N, Bellec P, Bernard R, Bonnet A, Brown ST, Camarasu-Pop S, Cervenansky F, Das S, Ferreira da Silva R, Flandin G, Girard P, Gorgolewski KJ, Guttmann CRG, Hayot-Sasson V, Quirion P-O, Rioux P, Rousseau M-E, Evans AC, Boutiques: a flexible framework to integrate command-line applications in computing platforms, GigaScience, Volume 7, Issue 5, May 2018, giy016, https://doi.org/10.1093/gigascience/giy016
3. Thomas, R.A., Fiorini, M.R., Amiri, S. et al. ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems. BMC Bioinformatics 25, 319, 2024. https://doi.org/10.1186/s12859-024-05935-y
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