jfrelinger
commented
10 years ago - Can you refer readers to where they can find these hyperparameters in your code?
Hyperparameters are instance variables of the various model generating objects. This information is now included in the paper.
- Reference, but no citation for other packages mentioned
a citation for Bioconductor has been added.
- Yes - I'd like more code (or pointers to code) if it's not to much trouble.
More examples can be found in the package documentation at http://packages.python.org/fcm/. The document has been updated to include this information.
Reviewer: Dav Clark Department/Center/Division: D-Lab Institution/University/Company: UC Berkeley Field of interest / expertise: Computational Social Science / Neuroscience Country: USA
Article reviewed: Fcm - A python library for flow cytometry
GENERAL EVALUATION
Please rate the paper using the following criteria (please use the abbreviation to the right of the description)::
below doesn't meet standards for academic publication meets meets or exceeds the standards for academic publication n/a not applicable
SPECIFIC EVALUATION
For the following questions, please respond with 'yes' or 'no'. If you answer 'no', please provide a brief, one- to two-sentence explanation.
Is the code made publicly available and does the article sufficiently describe how to access it?
Yes. But a little more on navigating the code would be nice (along with code for figures in the paper, etc.)
Does the article present the problem in an appropriate context? Specifically, does it:
Yes!
Yes!
Yes!
Yes!
Is the content of the paper accessible to a computational scientist with no specific knowledge in the given field?
I think so. The editors expressed some concern about this, though. Even if you don't fully understand the biology, the methods are quite straightforward (single parameter or quadrant-based "gates" or otherwise commonly used mixture and k-means models).
Does the paper describe a well-formulated scientific or technical achievement?
Yes
Are the technical and scientific decisions well-motivated and clearly explained?
Yes! Commendable in the clear explanation of the scientific problem. Extra points for explaining the importance of improving methodology / automation.
Are the code examples (if any) sound, clear, and well-written?
Yes, though they are pretty thin.
"Sensible defaults for hyperparameters have been chosen that in our experience perform satisfactorily on all FCS data samples we have analyzed." Might aggrivate some readers, but you can only put so much in such a paper... Can you refer readers to where they can find these hyperparameters in your code?
Is the paper factually correct?
As far as I can tell.
Is the language and grammar of sufficient quality?
Yes.
Are the conclusions justified?
Yes.
Is prior work properly and fully cited?
Reference, but no citation for other packages mentioned (proprietary and R bioconductor). Note, however, that mentioning other packages is already above-average for scipy 2012 (based on my limited sample ;)
Should any part of the article be shortened or expanded? Please explain.
Yes - I'd like more code (or pointers to code) if it's not to much trouble.
In your view, is the paper fit for publication in the conference proceedings? Please suggest specific improvements and indicate whether you think the article needs a significant rewrite (rather than a minor revision).
Yes