Talk:CH391L/S14/CAD systems


 * --Dennis Mishler (talk) 13:46, 28 January 2014 (CST) Gabo, the Snapgene description needs to be checked for grammar.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Absolutely right, I think I improved it now.
 * --Dennis Mishler (talk) 13:46, 28 January 2014 (CST) Gabo, the "standardizing representation of synthetic biology design" section is a bit confusing. What is the purpose of this section?  Was there a bigger issue within the field that needed addressing?  If so, perhaps the section should start by identifying this issue or need. If this section refers to how certain objects stand for certain parts (like a promoter, RBS, etc...), this should be explicitly stated.


 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Ok, I gave a clearer view of the issue and replaced the the word 'design' with 'parts'.


 * --Ew6977 (talk) 15:48, 30 January 2014 (CST) In introduction, consider capitalizing the first letter of the 3 steps, this is just a formatting suggestion
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Nice, thanks! Just did.
 * --Ew6977 (talk) 16:01, 30 January 2014 (CST) I think that there is some valuable information that you included in your slideshow that I do not see in the Wiki. Your tinkercell information was very detailed in the presentation, but there is very little information in the wiki. I think including that the Tinkercell program can have added downloadable content as well as providing a picture of the tinkercell interface would add some valuable information for future readers.


 * --Ajv684 (talk) 21:58, 30 January 2014 (CST) I found the wiki page very thorough and in general well laid out. I would suggest that depending on the target reader, that might probably be a lay reader with almost no previous knowledge on the topic, it would be great to simplify it quite some. Also, I was personally more interested in tinker cell and I would've liked to see more detailed information about it in here.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) I address this answer to the two previous comments: Thanks for your views. Yes, it's lot's of information.  Lot's of programs to cover.  Tinkercell was a mere example.  I guess best thing is to go to their link where they'll have so much more detail there.  I hope this wiki report serves as a good starting point from where to explore the various CAD tools out there; that was what I had in mind when I was working to improve it as much as I could.


 * --Ashley Kessel (talk) 2:16, 31 January 2014 (CST) The wiki page is very well done. It is informative, seems very thorough, and uses implements images appropriately. There is a sentence in your introduction, which you may want to reword slightly for clarity: "The field of synthetic biology is advancing to the point where high throughput automated design of synthetic biological devices will be necessary to realize the potential of the discipline."
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Thanks mate! I've got that done.

Overall Format and structure: I liked the progress (past the introduction) of laying out the more individualized functions moving down to the full featured tools. This made it confusing when you then went back to pathway-prediction tools. I think it would be more clear if you moved section above the full-featured tools.
 * --Dennis Mishler (talk) 09:07, 31 January 2014 (CST) Liz's Critique


 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) I agree. Fixed that.

(Grammar could be cleaned up throughout)

Introduction and background material: Personal preference, but I like “…are created to help design and engineer new systems” vs “…are created to help in designing…” Your next sentence has the same structure too. For the diagram/ steps: It makes more sense to me to only have two steps, then make some remark about repeating this process until analysis is satisfactory. Also, it would be better to be more specific- “performs some analysis” does not include (for me) the idea of a standard you are trying to reach/ could fail to reach. Methods and main body/concepts: Again, I like the layout here. My main problem is keeping up with the technologies you drop into the descriptions of the tools. Try to read through as a layperson/ haven’t been researching this and define your terms in order.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST)I decided to change that first sentence as you suggested, it does sound better.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST)Yeah, I was planning to do that. It goes better with the image.

I think your introduction paragraph is more confusing than helpful. I understand you want to introduce the overarching quality of CAD but I think you include too much there. I have the most experience with programs in your Basic Design/Alignment section so I thought that was pretty well done. I would have liked to see a definition of “part” or “device” by now- I know it was well-covered in class but would help making this a standalone article. Last sentence in Basic Design could use reorganizing.

Assembly Tools- not sure how your first example doesn’t better fit in Standards section- maybe expand on what you mention towards the end?

Full Feature- Main problem here is that throughout I feel that I’m only getting a snapshot of what each program can do, and same for these. It’s hard for me to distinguish them as something with more broad functionality. (Not sure how to fix this, but maybe you can make that clearer in the first lines? I.e. how is Snapgene much more full-feature than any of the programs mentioned in Basic Design?) Relation to iGEM and future directions: I like this section- good information at layperson level. Did you mean to put a link to the Registry? Figures, Figure legends, and citations: No caption or citation on your arrow diagram Figure 4 can’t be read- enlarging makes it okay- can you fix that?
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Ok, I re-phrased the intro sentence, hopefully it's clearer now, although you are right, there's really no clear line to distinguish more task specific programs from "full featured" ones.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST)Fixed.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Oh, I didn't want people clicking on the image, since it's simple and original, I guess no citation need.  You can actually click on it still and it will say I did it.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Phew!Took me a while, but fixed it. Looks nicer for sure.

Personally, I like to see citation number in the legend. You might want to add those in.
 * --Gabriel Suarez (talk) 04:30, 3 February 2014 (CST) Oh, I'll have to ask how to do this.