Comments on: Python libraries for synthetic biology http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/ Sun, 29 Nov 2009 11:31:39 +0000 http://wordpress.com/ hourly 1 By: http://bioticcomputer.blogspot.com/ http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-135 http://bioticcomputer.blogspot.com/ Sun, 29 Nov 2009 11:31:39 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-135 Greet library,but i hope we can see a more documentation on it some where. I'm working on simple programming algorithm (linear programming) check my blog : http://bioticcomputer.blogspot.com/ that make understanding easy but cost a lot of time so i think using library such biopython should be easier to program. Greet library,but i hope we can see a more documentation on it some where.

I’m working on simple programming algorithm (linear programming) check my blog :

http://bioticcomputer.blogspot.com/

that make understanding easy but cost a lot of time so i think using library such biopython should be easier to program.

]]> By: Brad Chapman http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-106 Brad Chapman Fri, 14 Aug 2009 20:59:27 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-106 Cesar; I am absolutely interested. You are free to utilize whatever code in there that you find useful. If there are specific things it would be useful to generalize, I can help with abstracting those out. It's great to see y'all spearheading this effort. Brad Cesar;
I am absolutely interested. You are free to utilize whatever code in there that you find useful. If there are specific things it would be useful to generalize, I can help with abstracting those out. It’s great to see y’all spearheading this effort.

Brad

]]> By: Cesar A. Rodriguez http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-103 Cesar A. Rodriguez Fri, 14 Aug 2009 08:31:43 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-103 Brad, My name is Cesar Rodriguez, I'm a postdoc in Drew Endy's lab at Stanford. Raik Gruenberg, Drew, and I are developing Python libraries for Synthetic Biology: http://code.google.com/p/synbiopython/ We're interested in working with you on this effort. Please drop me a line if you're interested: cesarr@stanford.edu Cesar Brad,

My name is Cesar Rodriguez, I’m a postdoc in Drew Endy’s lab at Stanford. Raik Gruenberg, Drew, and I are developing Python libraries for Synthetic Biology:

http://code.google.com/p/synbiopython/

We’re interested in working with you on this effort. Please drop me a line if you’re interested:

cesarr@stanford.edu

Cesar

]]> By: Chris Lasher http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-77 Chris Lasher Tue, 02 Jun 2009 03:24:29 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-77 Sorry to hear your company went under, Brad, but this is great you're releasing the code into the wild. Sorry to hear your company went under, Brad, but this is great you’re releasing the code into the wild.

]]> By: Brad Chapman http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-76 Brad Chapman Mon, 01 Jun 2009 15:13:01 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-76 Ricardo; Glad to hear this will be useful for your work. I was hoping to release this in a more ready to go phase, but came to realize that if I waited until everything was refactored nicely I would never get it out. Hopefully you or others will be interested in picking up useful bits. Peter; Yes, the melting temperature code there is a bit more up to date than what Sebastian has in Biopython right now. Many of the parameters overlap, but it incorporates data from a 2004 SantaLucia paper and handles non-exact alignments with stem loops. For identical matches, like finding primer melting temperatures, the results should be identical. If you are looking at potential cross-hybridizations, you need the non-exact additions. Istvan; Agreed completely. I hope to be able to spend time to extract useful parts, generalize and document them. I wanted to make it available in this initial raw state so others could help, or pull things they need right away. Ricardo;
Glad to hear this will be useful for your work. I was hoping to release this in a more ready to go phase, but came to realize that if I waited until everything was refactored nicely I would never get it out. Hopefully you or others will be interested in picking up useful bits.

Peter;
Yes, the melting temperature code there is a bit more up to date than what Sebastian has in Biopython right now. Many of the parameters overlap, but it incorporates data from a 2004 SantaLucia paper and handles non-exact alignments with stem loops. For identical matches, like finding primer melting temperatures, the results should be identical. If you are looking at potential cross-hybridizations, you need the non-exact additions.

Istvan;
Agreed completely. I hope to be able to spend time to extract useful parts, generalize and document them. I wanted to make it available in this initial raw state so others could help, or pull things they need right away.

]]> By: Istvan Albert http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-75 Istvan Albert Mon, 01 Jun 2009 13:35:44 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-75 I applaud the effort. But I wish there was more documentation and lots of examples. For most people time is the most valuable resource and not being able to understand what type of functionality a library offers makes it difficult to really get it. I applaud the effort.

But I wish there was more documentation and lots of examples. For most people time is the most valuable resource and not being able to understand what type of functionality a library offers makes it difficult to really get it.

]]> By: Peter http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-74 Peter Mon, 01 Jun 2009 13:18:57 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-74 Hi Brad, I've only read your blog post, but perhaps some of the "Calculation of melting temperatures" code would fit into Biopython's existing (minimal) Bio.SeqUtils.MeltingTemp module? Peter Hi Brad,

I’ve only read your blog post, but perhaps some of the “Calculation of melting temperatures” code would fit into Biopython’s existing (minimal) Bio.SeqUtils.MeltingTemp module?

Peter

]]> By: Ricardo Vidal http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-73 Ricardo Vidal Mon, 01 Jun 2009 12:54:51 +0000 http://bcbio.wordpress.com/2009/05/31/python-libraries-for-synthetic-biology/#comment-73 Once again, a great post. I'm currently working on a bioinformatics app that is related to synthetic biology and this code will definitely come in handy. I'm not a proficient coder like yourself and have never contributed code to biopython (or any other community, to be honest) but will be glad to help in any way possible. Once again, a great post. I’m currently working on a bioinformatics app that is related to synthetic biology and this code will definitely come in handy.

I’m not a proficient coder like yourself and have never contributed code to biopython (or any other community, to be honest) but will be glad to help in any way possible.

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