Re: [DIYbio] Re: Genome Compiler

I am most looking forward to being able to use the Metabolic pathway search, it looked great in the demo video.

A few small suggestions:

 It'd be great to have a circular overview of a plasmid, just because I think many people are used to seeing them like that, myself included.  Manipulating the genes on the horizontal layout is perfect, but on the "genome" zoomout view it'd be sweet to see them as a circle with all the restriction cut sites and labelled genes.  

It'd also be nice to have a small popout info window when browsing through the materials and pieces, without having to drag and drop the pieces into the main screen.  There are tons of iGem biobrick parts, and I like just surfing through them at random and seeing what is out there, ya never know what you may stumble upon that could inspire some new piece of DNA.  That being said, I'm not going to drag and drop every single one to the center of the screen, and close each window.  Having a brief overview window that updates in real-time with basic info would be fantastic.

Also, I don't know how difficult it would be, but being able to explore all of the BioBricks "in house" would be  good too, without the need for the registry website.  I was wanting to find some Lux genes, but Lux yields no search returns, even though in the description of some of the biobrick parts the words Lux do appear often (does the search only target specific fields, and ignore others?).  So I had to go to the registry website, find some Lux Bba_ ID's then come back and search them out in Genome Compiler.  Not a huge inconvenience by any means but, it'd be nice to stay inside the software.      

Searching "Amp" only yields an E.Coli strain and a bacteriophage, maybe that was by design, but it'd be nice to see all things that have the Amp gene in them.  I know some plasmids have them, and I think it'd be a great way to be exposed to new plasmids you might not normally chose, but that have some of the desired features you want (like Amp resistance).  Something along the lines of, "hey pUC18 is my go-to screening plasmid, but I'd really like another plasmid with more cut sites in the Amp gene, let me search for Amp and find a new plasmid - maybe pBR322 will work.

So in that sense, I think the search function could use a little boost.

Besides that I could see myself using the software in the future, though I havn't used the "check price" now function.  Keep up the interesting work.

-Dakota