SEA-PHAGES | Starterator UI updates

Link to this post \| posted 21 Jul, 2016 21:58
cdshaffer	I would appreciate any and all suggestions for how to improve starterator graphics output. The latest version has green and yellow indicators on each track for annotation starts instead of the older blue. These marks were updated to indicate annotated starts based on thier provenance. The green annotated starts are based on non-draft status entries in the phamerator database (i.e. based on submitted annotations which have been reviewed). The yellow annotated starts are based on the start called in the "draft" annotations (i.e. based on Glimmer/GeneMark only). Are there other updates that you can think of that would make for a better experience? or things that your students found confusing that could use clarification? Please post your ideas below. For example in the July 20th SMART meeting Lee asked for an indication of the level of conservation of each start. I am looking into this and will post updates here. Other ideas: Is there any other information you would find informative on the first few pages or at the end or each pham? Any input is useful.

Link to this post | posted 21 Jul, 2016 21:58

I would appreciate any and all suggestions for how to improve starterator graphics output.

The latest version has green and yellow indicators on each track for annotation starts instead of the older blue. These marks were updated to indicate annotated starts based on thier provenance. The green annotated starts are based on non-draft status entries in the phamerator database (i.e. based on submitted annotations which have been reviewed). The yellow annotated starts are based on the start called in the "draft" annotations (i.e. based on Glimmer/GeneMark only).

Are there other updates that you can think of that would make for a better experience? or things that your students found confusing that could use clarification?

Please post your ideas below. For example in the July 20th SMART meeting Lee asked for an indication of the level of conservation of each start. I am looking into this and will post updates here.

Other ideas: Is there any other information you would find informative on the first few pages or at the end or each pham?

Any input is useful.

Link to this post \| posted 26 Jul, 2016 17:37
cdshaffer	I have been playing with the graphical output for the gene tracks with the idea of indicating conservation. I have found that it would be very difficult to change the property of the line that indicates the chosen start site but I can easily manipulate the start labels. I have tried several changes that can be mixed and matched: 1. Change color of start label if that start is "highly conserved" 2. Set the labels to be dark or faint based on level of conservation (for example less conserved starts have a light grey label, strongly conserved starts have a dark black label) 3. Change the number of times that the track label appears on the track I have posted two examples with several phams in each. Example 1 increase font size of labels, change color to red if start is "highly conserved" (>95%), set grey level of label from 25% to 100% based on level of conservation. https://wustl.box.com/s/oq7fq654et6v27vyl2qqn6fhq4ode7yd Example 2 increase font size of labels, change color to red if start is "highly conserved", other labels are faint blue to dark blue based on level of conservation, set number of track labels to 1. https://wustl.box.com/s/9rmx88699z9mz34miy9beyyqvvasreom Comments/feedback appreciated

Link to this post | posted 26 Jul, 2016 17:37

cdshaffer

I have been playing with the graphical output for the gene tracks with the idea of indicating conservation.

I have found that it would be very difficult to change the property of the line that indicates the chosen start site but I can easily manipulate the start labels. I have tried several changes that can be mixed and matched:

1. Change color of start label if that start is "highly conserved"
2. Set the labels to be dark or faint based on level of conservation (for example less conserved starts have a light grey label, strongly conserved starts have a dark black label)
3. Change the number of times that the track label appears on the track

I have posted two examples with several phams in each.

Example 1 increase font size of labels, change color to red if start is "highly conserved" (>95%), set grey level of label from 25% to 100% based on level of conservation.

https://wustl.box.com/s/oq7fq654et6v27vyl2qqn6fhq4ode7yd

Example 2 increase font size of labels, change color to red if start is "highly conserved", other labels are faint blue to dark blue based on level of conservation, set number of track labels to 1.

https://wustl.box.com/s/9rmx88699z9mz34miy9beyyqvvasreom
Comments/feedback appreciated

Link to this post \| posted 26 Jul, 2016 18:12
welkin	I love the gray vs red, and the shading to indicate conservation. IT is really nice. pham 10201 is almost impossible to read no matter what the colors look that. Too many starts! I am not sure how to fix that. I am finding myself wishing for a Zoom function. Is there anyway to say " OK, I just want to see the first 50 amino acids, redraw?" I am also having trouble reading the start numbers with the large font– too many of them are on top of each other and on the tracks. Maybe space the tracks farther apart and bump the numbers up outside the tracks? -Welkin Edited 26 Jul, 2016 18:18

Link to this post | posted 26 Jul, 2016 18:12

welkin

I love the gray vs red, and the shading to indicate conservation. IT is really nice.

pham 10201 is almost impossible to read no matter what the colors look that. Too many starts! I am not sure how to fix that. I am finding myself wishing for a Zoom function. Is there anyway to say " OK, I just want to see the first 50 amino acids, redraw?"

I am also having trouble reading the start numbers with the large font– too many of them are on top of each other and on the tracks. Maybe space the tracks farther apart and bump the numbers up outside the tracks?
-Welkin

Edited 26 Jul, 2016 18:18

Link to this post \| posted 27 Jul, 2016 01:20
lhughes	I like the gray scale/red font options. That comes across very easy to see. As Welkin mentioned, when there are too many starts (or too many tracks) it gets really hard to see anything. The font size example doesn't work as well (to me) as the 1st option did. Thanks for working on this! Lee

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