Review of A Computational Framework for Plasmonic Nanobiosensing

[minrk]

Reviewer: Min Ragan-Kelley

Department/Center/Division: Helen Wills Neuroscience Institute

Institution/University/Company: UC Berkeley

Field of interest / expertise: IPython

Country: USA

Article reviewed: A Computational Framework for Plasmonic Nanobiosensing (Adam Hughes)

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

• Quality of the approach: meets
• Quality of the writing: meets
• Quality of the figures/tables: below

The figures could definitely use some work.

• Fig 1.
  • mixes at least three typefaces
  • the 's' in nanoparticles is clipped
  • text labels in the right diagram are too small to read easily
  • sketchy markings, look to be from MS Paint
• Fig 2.
  • yet another typeface, not seen in Fig 1.
• Fig. 2., 3., 5. all appear to be very low resolution
• Fig. 5. includes several undefined variables
• Fig. 6., 7. have several unlabeled or unit-less axes
• Fig 7. has difficult to read labels, overlapping lines or other labels

  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

• Does the article present the problem in an appropriate context? Specifically, does it:

  • explain why the problem is important,
  • describe in which situations it arises,
  • outline relevant previous work,
  • provide background information for non-experts

  yes

• Is the content of the paper accessible to a computational scientist with no specific knowledge in the given field

  yes

• Does the paper describe a well-formulated scientific or technical achievement?

  yes

• Are the technical and scientific decisions well-motivated and clearly explained?

  yes

• Are the code examples (if any) sound, clear, and well-written?

  yes

• Is the paper factually correct?

  yes (as far as I know, not being an expert in the domain)

• Is the language and grammar of sufficient quality?

  yes, pending some typos and grammar fixes in PR #7.

• Are the conclusions justified?

  yes

• Is prior work properly and fully cited?

  yes

• Should any part of the article be shortened or expanded? Please explain.

  no

• 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, pending minor typo fixes. If there is any significant change warranted, it would be the figures, but I leave that decision to editors.

[ahmadia]

This paper is accepted.