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Hi everyone,

recently my group publish a review paper, and I did the final images in Affinity Designer (which were slightly edited by the journal editor...). 

If you can, have a look and give me your opinion -- I'm seeking constructive criticism, so I can improve :)

Thank you 

 

Edited by lsilva.m
typos

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I may be a (retired) biologist, but certainly not an oncologist, so I looked at the images without any proper context. They look to me to be well-designed and clearly legible. I did wonder if the colours could be a bit more saturated to give more contrast with the embedded white text.

John


Windows 10, Affinity Photo 1.8,3 Designer 1.8.3 and Publisher 1.8.3 (mainly Photo), now ex-Adobe CC

CPU: AMD A6-3670. RAM: 16 GB DDR3 @ 666MHz, Graphics: 2047MB NVIDIA GeForce GT 630

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Yeah, that was one of the things they changed. They changed the size of the font, in the original the font was almost tightly fit within the object and bold for the main proteins. 

But I will explore that idea of more saturated colours :) Thanks

 

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Interesting Figure.

1. You seem to have two (2) figures (upper A and lower B) . Even though the ellipse "CBP/p300" belongs to A it appears to hang in space !

A is referred to as follows :

A: Schematic representation of CITED2, hypoxia-inducible factor (HIF)-1α and CBP/p300.

And B  is referred to as follows:

B: Model for CITED2, HIF-1α and CBP/p300 in hypoxia-responsive gene regulation.

Perhaps these should be Figures 1.a and I.b

Difference between Schematic and Model ... ?

2. For a professional publication the Figure 1 could be better:

The boxes in A have the writing on the outside where as the boxes in B have the writing on the inside.

As the shapes have been filled the writing with in should be of higher contrast.

Diagram A is confusing in that the  three lines all have an input " N" and an Output " C" . The inputs to the " Competition function "  come from the  CR2 output  and the N-TAD ...

I believe that this could be drawn more professionally.

That's my two bobs worth.

Jeremy.

 

 

 

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15 hours ago, Jeremy_Waller said:

it appears to hang in space

I see your point. This is to show that it is that protein that is being represented above -- the size relative to the other it's to give an idea of relative size between the proteins.

15 hours ago, Jeremy_Waller said:

Perhaps these should be Figures 1.a and I.b

 

in scientific papers we use the short (A) and (B) -- it's a standard in the community.

15 hours ago, Jeremy_Waller said:

input " N" and an Output " C"

The way I draw that is to represent the proteins, and by convention they are represented from the N to C, which means that we are representing them from the N-terminal to the C-terminal; that would be the alternative to "N" and "C" --> "H2N----" and "-----COOH"; or, there is another acceptable alternative that is the number of amino acids that make the protein, so that would be from left to right: "1" to "n".

The boxes in the line represent domains of the proteins - that is parts of the protein that have a function. 

15 hours ago, Jeremy_Waller said:

The inputs to the " Competition function "  come from the  CR2 output  and the N-TAD

 

In this case the CR2 domain is competing with N-TAD for the CH1 domain.

15 hours ago, Jeremy_Waller said:

The boxes in A have the writing on the outside where as the boxes in B have the writing on the inside.

 
 
 

I thought about that. Originally, I only had the boxes without text, but then, for scientific rigor all domain of the protein should be represented, even if you just want to focus in one; that's why I left them grayed out. I tried to place the names inside to be more coherent, but it would bring inconsistency in font size to fit the domain box -- how would you solve that? Because I have two constrains here: (1) font size should be at least 10, and (2) the proportion of the line and the boxes needs to be kept since they represent the protein, and parts of the protein, respectively.

15 hours ago, Jeremy_Waller said:

should be of higher contrast

How do you check for this in Designer?

Thank you

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1.

1 hour ago, lsilva.m said:

How do you check for this in Designer?

Drawings like this are better done in MS Powerpoint. Most  journals would use a type setting language like Latex. The format is provided by the journal staff.

 

1 hour ago, lsilva.m said:

in scientific papers we use the short (A) and (B) -- it's a standard in the community.

Really?  Which journals ?   Nature,  BMA,  IEEE, Science Direct ... etc

Rgds,

Jeremy.

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This is the sought of stuff that may be done in MS Powerpoint.

Attached is a *.jpg image of a slide that I made for a presentation. Images like this may be inserted in your publication.

Jeremy.

MS_powerpoint_example.jpg

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18 hours ago, Jeremy_Waller said:

are better done in MS Powerpoint

not for me -- working in MS PowerPoint to make this kind of drawings is a both  interface and  lack-of-fluidity pain to my brain. That is why I followed the advice of a friend I give a try to Designer -- after trying Inkscape, which was also a pain. 

Other than that, for example you can't (at least so easily) export ´.tiff´ or ´.svg´ formats, let alone that you can't opt what dpi use for the export. You can change the HKEYS though.

Plus, there is one more thing about using MS PowerPoint: it compresses microscopy pictures, and that could add noise, and reduce quality of a picture that sometimes its already hard to interpret (biologically speaking).

What I do is to make the drawings in Designer, export to ´.svg´, then add it to a MS PowerPoint slide, make it "flat" so my colleagues can edit.

18 hours ago, Jeremy_Waller said:

Really?  Which journals ?

yes. Many. I don't know one in the life sciences that shows "Figure1.A \\ Figure1.B etc ". Here is one example from Cell (Elsevier).

I think graphic designers and scientists should have coffee more often :)

Best,

L

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1 hour ago, Jeremy_Waller said:

Years ago I published in the Elsevier  journal

Can you share?

1 hour ago, Jeremy_Waller said:

Good luck in your drawings

Thank you.

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Perhaps you may want to look at some of the text and citations:

https://www.semanticscholar.org/paper/An-adaptive-coherence-filter-Waller-Brushe/2fd587353c4a8993e2901493f35d38174ecc16f5?citingPapersSort=relevance&citingPapersLimit=10&citingPapersOffset=0&year%5B0%5D=&year%5B1%5D=&citedPapersSort=relevance&citedPapersLimit=10&citedPapersOffset=10

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16 hours ago, Jeremy_Waller said:

https://www.sciencedirect.com/science/article/abs/pii/S1051200405000540

Thanks for sharing.

Interesting. As you can tell from the figures that started this post, I am not from electronics. But I am doing a collaboration with the electronics department, and oh boy, I have so many doubts/questions on electronics now. 

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