Talk:CH391L/S13/CAD

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**'''[[User:Gabriel Wu|Gabriel Wu]] 15:13, 4 February 2013 (EST)''': [http://j5.jbei.org 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.
**'''[[User:Gabriel Wu|Gabriel Wu]] 15:13, 4 February 2013 (EST)''': [http://j5.jbei.org 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.
 +
****'''[[User:Kevin Baldridge|Kevin Baldridge]] 12:50, 11 February 2013 (EST)''':I added a section about j5 under full featured tools
***'''[[User:Kevin Baldridge|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 [http://code.google.com/p/gd-ice/ GD-ICE], which I believe is meant for interfacing with the registry (or a different database, maybe).
***'''[[User:Kevin Baldridge|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 [http://code.google.com/p/gd-ice/ GD-ICE], which I believe is meant for interfacing with the registry (or a different database, maybe).
***'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 00:32, 7 February 2013 (EST)''':Looks like a custom database that you create.
***'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 00:32, 7 February 2013 (EST)''':Looks like a custom database that you create.
**'''[[User:Gabriel Wu|Gabriel Wu]] 16:56, 4 February 2013 (EST)''': I think for the Basic Features, things like VectorNTI (commercial), [http://en.wikipedia.org/wiki/Geneious geneious], amplify (virtual PCR), and maybe even sequence aligners like BLAST might be considered CAD at this basic level.
**'''[[User:Gabriel Wu|Gabriel Wu]] 16:56, 4 February 2013 (EST)''': I think for the Basic Features, things like VectorNTI (commercial), [http://en.wikipedia.org/wiki/Geneious geneious], amplify (virtual PCR), and maybe even sequence aligners like BLAST might be considered CAD at this basic level.
 +
****'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:04, 11 February 2013 (EST)''':I added a little bit about BLAST, but I was unable to find anything about amplify. Do you have a link for that one?
**'''[[User:Gabriel Wu|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 [http://www.flickr.com/photos/3dvc/sets list]
**'''[[User:Gabriel Wu|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 [http://www.flickr.com/photos/3dvc/sets list]
 +
***'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:44, 11 February 2013 (EST)''':I added the future directions section, is there anything else here you think I should include for examples?
**'''[[User:Gabriel Wu|Gabriel Wu]]''': Oh, how about flux balance analysis (FBA)? Does this have a role here at all?
**'''[[User:Gabriel Wu|Gabriel Wu]]''': Oh, how about flux balance analysis (FBA)? Does this have a role here at all?
***'''[[User:Jeffrey E. Barrick|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.
***'''[[User:Jeffrey E. Barrick|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.
 +
****'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:08, 11 February 2013 (EST)''':TinkerCell has some capabilities for FBA, and I wouldn't be surprised if synbioSS also does, although I haven't donie any playing with synbioSS
*'''[[User:Benjamin Gilman|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?  
*'''[[User:Benjamin Gilman|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?  
 +
***'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:23, 11 February 2013 (EST)''':Yes, there are at least a couple of programs which take that into account. Those are the parameters that you fill in with TinkerCell, which I was showing some in class last week. I would imagine that some of the others like SynBioSS also would have to account for kinetic parameters of a given part, although I can't say for certain since I haven not played around with that package.
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:26, 4 February 2013 (EST)''': What are the killer apps for synthetic biology?
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:26, 4 February 2013 (EST)''': What are the killer apps for synthetic biology?
 +
**'''[[User:Max E. Rubinson|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.
 +
***'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:23, 11 February 2013 (EST)''':I think Max is right about this, there doesn't seem to be any one program that covers all the needs of the synthetic biology community, or we would all be using it already. I think there are several that have a lot of features in common, and it is primarily a preference of the user at this point to choose which software to use.
*'''[[User:Neil R Gottel|Neil R Gottel]] 13:58, 7 February 2013 (EST)''':Some more CAD tools:
*'''[[User:Neil R Gottel|Neil R Gottel]] 13:58, 7 February 2013 (EST)''':Some more CAD tools:
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# Life Technologies's [http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis/GeneArt-Gene-Synthesis/GeneOptimizer.html Gene Optimizer]
# Life Technologies's [http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis/GeneArt-Gene-Synthesis/GeneOptimizer.html Gene Optimizer]
# [http://django.gibthon.org/ Gibthon], an assist tool for gibson assembly by Cambridge 2010.
# [http://django.gibthon.org/ Gibthon], an assist tool for gibson assembly by Cambridge 2010.
 +
***'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:23, 11 February 2013 (EST)''':Thanks Neil, I added the two that weren't already included (Gene Optimizer and Gibthon)
== Aspirin vs vitamins ==
== Aspirin vs vitamins ==
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*'''[[User:Jeffrey E. Barrick|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.
*'''[[User:Jeffrey E. Barrick|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.
**'''[[User:Aurko Dasgupta|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.
**'''[[User:Aurko Dasgupta|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.
 +
**'''[[User:Kevin Baldridge|Kevin Baldridge]] 13:31, 11 February 2013 (EST)''':I think the pain is there, it is very tedious to do a lot of these things manually, as Dr. Barrick says. I think the part that is lacking is more the implementation. The complexity of biology is still not very well understood, if you compare it to something like electrical circuits (everyone's favorite analogy). So deciding how to write a program which can reliably design the best construct is going to be even harder when a person with experience can't always get it right the first time themselves. There's not enough of a pain to provide the market for a highly successful commercial CAD program, because after a few clones a person with experience can accomplish the design better than an automated code. It's not worth paying for a half-functional program which you will have to manually check anyway, when you have already learned how to design things manually yourself.
== iGEM Software Projects of Interest ==
== iGEM Software Projects of Interest ==
*'''[[User:Neil R Gottel|Neil R Gottel]] 12:49, 7 February 2013 (EST)''':I'll take [http://gibthon.org/ Gibthon], made by the Cambridge 2010 team to assist their Gibson assemblies.
*'''[[User:Neil R Gottel|Neil R Gottel]] 12:49, 7 February 2013 (EST)''':I'll take [http://gibthon.org/ Gibthon], made by the Cambridge 2010 team to assist their Gibson assemblies.
 +
*'''[[User:Max E. Rubinson|Max E. Rubinson]] 22:09, 7 February 2013 (EST)''':I'll take [http://2009.igem.org/Team:Berkeley_Software/Spectacles Spectacles], designed by the Berkeley 2009 team for "synthetic biological design needs."
 +
*'''--[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 00:05, 8 February 2013 (EST)'''* I'll take [http://2011.igem.org/Team:CBNU-Korea/Data/Browser 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 [http://2012.igem.org/Team:CBNU-Korea/Project minimal genome design]minimal genome design which might be interesting to look at this coming week.
 +
*'''[[User:Thomas Wall|Thomas Wall]] 1:07, 9 February 2013 (EST)''': Do it yourself gene assembly http://gcat.davidson.edu/IGEM06/oligo.html
 +
*'''[[User:Dwight Tyler Fields|Dwight Tyler Fields]] 15:34, 8 February 2013 (EST)''': I'm doing Cumulus: a Cloud based modelling and data exchange program [http://2011.igem.org/Team:Groningen/modeling_cumulus http://2011.igem.org/Team:Groningen/modeling_cumulus]
 +
*'''[[User:Yunle Huang|Yunle Huang]] 20:24, 10 February 2013 (EST)''': I'll do Optimus Primer http://2011.igem.org/Team:BU_Wellesley_Software/OptimusPrimer
 +
*'''[[User:Aurko Dasgupta|Aurko Dasgupta]] 13:10, 11 February 2013 (EST)''':I'll be covering  [http://2011.igem.org/Team:CBNU-Korea/Data/Browser God], a program that simplifies artificial genome construction.
 +
*'''[[User:Benjamin Gilman|Benjamin Gilman]] 13:15, 11 February 2013 (EST)''': I'll talk about [http://synbioss.sourceforge.net/ SynBioSS], a program which models reactions inside the cell using existing kinetic parameters.

Current revision

  • 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 12:50, 11 February 2013 (EST):I added a section about j5 under full featured tools
      • 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.
        • Kevin Baldridge 13:04, 11 February 2013 (EST):I added a little bit about BLAST, but I was unable to find anything about amplify. Do you have a link for that one?
    • 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
      • Kevin Baldridge 13:44, 11 February 2013 (EST):I added the future directions section, is there anything else here you think I should include for examples?
    • 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.
        • Kevin Baldridge 13:08, 11 February 2013 (EST):TinkerCell has some capabilities for FBA, and I wouldn't be surprised if synbioSS also does, although I haven't donie any playing with synbioSS
  • 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?
      • Kevin Baldridge 13:23, 11 February 2013 (EST):Yes, there are at least a couple of programs which take that into account. Those are the parameters that you fill in with TinkerCell, which I was showing some in class last week. I would imagine that some of the others like SynBioSS also would have to account for kinetic parameters of a given part, although I can't say for certain since I haven not played around with that package.
  • 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.
      • Kevin Baldridge 13:23, 11 February 2013 (EST):I think Max is right about this, there doesn't seem to be any one program that covers all the needs of the synthetic biology community, or we would all be using it already. I think there are several that have a lot of features in common, and it is primarily a preference of the user at this point to choose which software to use.
  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.
      • Kevin Baldridge 13:23, 11 February 2013 (EST):Thanks Neil, I added the two that weren't already included (Gene Optimizer and Gibthon)

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.
    • Kevin Baldridge 13:31, 11 February 2013 (EST):I think the pain is there, it is very tedious to do a lot of these things manually, as Dr. Barrick says. I think the part that is lacking is more the implementation. The complexity of biology is still not very well understood, if you compare it to something like electrical circuits (everyone's favorite analogy). So deciding how to write a program which can reliably design the best construct is going to be even harder when a person with experience can't always get it right the first time themselves. There's not enough of a pain to provide the market for a highly successful commercial CAD program, because after a few clones a person with experience can accomplish the design better than an automated code. It's not worth paying for a half-functional program which you will have to manually check anyway, when you have already learned how to design things manually yourself.

iGEM Software Projects of Interest

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