MOMIC: A Multi-Omics Pipeline for Data Analysis, Integration and Interpretation

Round 1

Reviewer 1 Report

Excellent work featuring reproducibility! Really appreciate all these GitHub links! Here are some questions from a computer system researcher's perspective. It would be great if the authors could address them in a revision or leave them for future work.

1. How does MOMIC scale? Can it support datasets larger than memory?  
2. What is the experimental environment used? What are the sizes of datasets used (in terms of MBs, GBs, or TBs)? What hardware is used, and how fast do the analyses run?
3. I'm worried about the extensibility of this work. Though the authors claim it to be a highly reusable pipeline, everything is organized as Jupyter notebooks. This means changes (if any) need to be made to these notebooks, which are error-prone and challenging to perform version controls. Would it be possible to revise a set of R APIs so that everything can be version-controlled and reused in the future?

Minor:

line 157: link overflows

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

This paper presents MOMIC a comprehensive pipeline to analyze single-omics data by means of meta-analysis. The tool integrated various components and protocols. Although the researchers explained the tool very well, there are many areas of improvement as follows:

• The research problem is not clear to me. The researchers must provide a clear problem statement and explain the problem the tool solved. 
• The researchers did not provide related studies that addressed similar problems.
• Although the researcher discussed existing tools for omic analyses, they do not compare the results of their tool with other tools. 
• The comparison between the existing tools should not be in the discussion section.
• What is the difference between Figure 10 and Table 1? one of them needs to be removed.
• The discussion section needs improvement since the researchers did not discuss the results of their work.
• Research contribution should be introduced.
• Future work should be introduced.

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

The work describes a platform (MOMIC) a comprehensive pipeline capable of analyzing and summarising single-omics data by means of meta-analysis, as well as performing integrative analysis of different molecular levels. 

The work is interesting but I believe that some improvements can be made:

• line 56: "Each of the datasets are then independently analyzed following appropriate protocols." -> this means that these protocols work for all the datasets? should be better explained.
• Section 2.1 should be better introduced. Several techniques are mentioned and they should be explained here or in the introduction, for example, what is limma?
• line 83: "The protocol comprises data pre-processing, differential expression analysis (DE) and annotation steps." Why this phases are always needed? 
• Section 2.2. Format problems need to be solved. The OS should be better described. Which windows? windows 10 or xp?
• Section 3. The results should be discussed for each protocol. Add only the images is not sufficient.  
• Line 183: 1KG project: reference missing
• line 203: I believe this section should be introduced better (also the format should be updated)
• Figure 10 and table 1 present the same information. Figure 10 should be removed
• A section or at least a subsection explaining the jupyter notebooks in a glance should also be added. 

Author Response

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Author Response File: Author Response.pdf

Reviewer 4 Report

Thanks for giving me an opportunity to review this work. 

The authors developed MOMIC, that guides the user through the .
application of different analysis on a wide range of omics data. 

A great work indeed!

The manuscript is well written and the applicability of MOMIC is well-conceptualized. My only concern is conclusion section where author(s) may emphasize on the implications of the study. Also, limitation section needs to be added. 

Good luck and best wishes for this exemplary work!

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The authors have addressed my comments and I am satisfied with the improvements.