Talk:CH391L/S13/CAD

• Kevin Baldridge 03:31, 30 January 2013 (EST):If anyone has any suggestions or links, it's a really new topic to me so I'd be glad of the tips. Thanks!
• Jeffrey E. Barrick 10:43, 1 February 2013 (EST):Here are some ideas to get started:

1. CLOTHO is what I hear the most about, but it seems very buggy when I try to use it on my Mac, so I haven't been able to do anything with it.
2. TinkerCell has a neat interface and some simulation functions, but I don't think it is supported any more.
3. TeselaGen is a company with a Beta of a synthetic biology tool going on right now. You can register and play with it for free, I believe.
4. The iGEM team usually ends up using Geneious to design their constructs, but it doesn't have any real CAD functions except for editing sequences with annotations and drawing nice pictures.
5. Also, check out the software division of iGEM. It has a lot of "Best-X-tool" prizes, which must mean that X is a synthetic biology CAD framework.

• • Kevin Baldridge 14:33, 2 February 2013 (EST):Thanks, these are all great leads and better than most of what I was able to find with a quick google search. I'll flesh this out more today

• • Gabriel Wu 15:13, 4 February 2013 (EST): j5 is a program coming from Nathan Hillson at the Joint Bioenergy Institute at Berkeley (JBEI). It automatically designs oligonucleotides for gene assembly for Gibson and Gibson-like synthesis.
    • Kevin Baldridge 17:35, 4 February 2013 (EST):JBEI is involved in a lot of the open source CAD development. There is a reference listed for their publication. I didn't talk much about it but one of their programs is GD-ICE, which I believe is meant for interfacing with the registry (or a different database, maybe).
    • Jeffrey E. Barrick 00:32, 7 February 2013 (EST):Looks like a custom database that you create.

• • Gabriel Wu 16:56, 4 February 2013 (EST): I think for the Basic Features, things like VectorNTI (commercial), geneious, amplify (virtual PCR), and maybe even sequence aligners like BLAST might be considered CAD at this basic level.

• • Gabriel Wu 17:07, 4 February 2013 (EST): I don't think it belongs here, but there are lots of biological modeling projects going on these days. These systems are too complex to engineer de novo, but I think understanding these things or trying to will aid in engineering simpler systems. Maybe this belongs more in a future directions section. Here's fun list

• • Gabriel Wu: Oh, how about flux balance analysis (FBA)? Does this have a role here at all?
    • Jeffrey E. Barrick 00:32, 7 February 2013 (EST): It seems like FBA falls more in the metabolic engineering / systems biology realm. People use it to predict knockouts or alterations that improve pathways, but they rarely design entire systems of metabolic pathways from the ground up.

• Benjamin Gilman 13:23, 7 February 2013 (EST): For biological CAD programs to be as useful as their engineering counterparts, like SolidWorks or ePlan, they need to be able to predict the output of a system based on some estimated performance of each component. Is anyone attempting to use measurements like PoPS or some relative activity (like we read about last week) in their software to model systems?

• Gabriel Wu 17:26, 4 February 2013 (EST): What are the killer apps for synthetic biology?
  • Max E. Rubinson 23:02, 7 February 2013 (EST): Is there one? It doesn't yet seem like there is a single bioCAD tool that is absolutely indispensable for those in the field of synthetic biology.

• Neil R Gottel 13:58, 7 February 2013 (EST):Some more CAD tools:

1. Gene Designer provided by DNA 2.0
2. Life Technologies's Gene Optimizer
3. Gibthon, an assist tool for gibson assembly by Cambridge 2010.

Aspirin vs vitamins

In the startup world, a common notion is about what type of "pain" your product is addressing. Is it something for which pain relief is almost required, like Aspirin for a bad headache? Or is the pain such that pain relief is merely "nice to have", like taking vitamins when you the have money to spend on them? Are there any true Aspirin pains in synthetic biology today for which software tools could provide the relief? Or does the field need to advance more (i.e. grow more complex) before the real Aspirin pains will be encountered? Dwight Tyler Fields 18:51, 4 February 2013 (EST):

• Jeffrey E. Barrick 00:27, 7 February 2013 (EST):Designing and keeping track of synthetic biology constructs can be done with MS Word. Simulating them can be done with R. However, doing things this way quickly becomes a headache. You need to know where in your freezer to efficiently get parts from, then design a lot of primers and a strategy to assemble them, and then make nice schematic figures for talks and publications. The ability to do these things quickly can save a lot of time.
  • Aurko Dasgupta 20:55, 7 February 2013 (EST):I'm actually learning to use R now in Biostatistics. If/when I get better at it, maybe I could take some of the burden off of you regarding statistics in the MA projects.

iGEM Software Projects of Interest

• Neil R Gottel 12:49, 7 February 2013 (EST):I'll take Gibthon, made by the Cambridge 2010 team to assist their Gibson assemblies.
• Max E. Rubinson 22:09, 7 February 2013 (EST):I'll take Spectacles, designed by the Berkeley 2009 team for "synthetic biological design needs."
• --Alvaro E. Rodriguez M. 00:05, 8 February 2013 (EST)* I'll take iGaME:Synthetic Biology for Gamers, designed by the Chungbuk National University 2010 iGEM team. Although there is also a second page from the same univerity, but from its 2012 team that was trying to come up with a tool for minimal genome designminimal genome design which might be interesting to look at this coming week.
• Thomas Wall 1:07, 9 February 2013 (EST): Do it yourself gene assembly http://gcat.davidson.edu/IGEM06/oligo.html