Comments for Steve's Systems Biology blog

Comment on project planning(?) by Steve

Steve — Fri, 09 Jul 2010 09:37:54 +0000

I’ve had a look around openwetware.org. I also find the forums on bitesize bio can be useful. My cloning problem was my boss wanting to do directional cloning using a SalI and XhoI combination and refusing to entertain the acknowledged problems of using this combination. I had major problems as my insert was a PCR product which new england biolabs has acknowledged SalI has a problem with. I ended up starting again with different restriction sites and just ignoring the boss. The recent round of cloning worked 1st time (surprise surprise). I will remember to have a route around on openwetware in future though as it can be useful to compare a number of protocols before starting. I haven’t encountered ligation by selection and will investigate this one.

Comment on tools of the trade by Steve

Steve — Fri, 09 Jul 2010 09:19:24 +0000

Hi,

thanks for reading my blog I will add ApE to the list. I had used it last year. There is a really useful feature to search for restriction sites that aren’t present, which I used for inserting custom sites by directed mutagenesis. Our lab has a copy of clone manager which I’ve found to be indispensable and although I don’t normally use commercial software, it’s well worth the money. A colleague of mine swears by serial cloner as well, but I haven’t used it.

Comment on tools of the trade by t

Fri, 09 Jul 2010 07:37:03 +0000

http://www.biology.utah.edu/jorgensen/wayned/ape/

has the ability to color based on a feature list, etc etc.

good tutorial here

http://openwetware.org/wiki/Arking:JCATutorialIntro9

Comment on project planning(?) by t

Fri, 09 Jul 2010 07:34:12 +0000

Check out openwetware.org they have a lot of good protocols. If you don’t mind sharing, what are the cloning steps that you are getting bogged down in? In my experience, things can be sorted out rather quickly if you have the right setup (GFP dropout, proper flanking restriction sites, use of ligation-by-selection)

Comment on mathematized by Steve

Steve — Sat, 24 Apr 2010 19:49:37 +0000

Thanks for the link. much appreciated. i found a copy on Google Books as well. I’ll definitely have a read through it

Comment on mathematized by Rui

Rui — Fri, 23 Apr 2010 16:19:29 +0000

Found it, check it out:

http://avaxhome.ws/ebooks/modelling_metabolism_with_mathematica_isbn_0849314682.html

It’s called modelling metabolismo with mathematica.

Cheers,

Rui B.

Comment on mathematized by Rui

Rui — Fri, 23 Apr 2010 15:53:47 +0000

Hey Steve!

I just got to your blog when I was searching for a book, and this book is precisely what you need!

I think its called “modelling with mathematica” or “systems biology modelling with mathematica”, I think it will help you out a lot!

Whenever I get it I will share it with you.

Keep your posts coming!

Cheers,

Rui B.

Comment on mathematized by Teklu

Teklu — Sat, 06 Mar 2010 02:03:02 +0000

You are not the only one who has drifted away in a strange but exciting world. I am currently auditing a course in systems biology at UofC.
Best of Luck,

Teklu

Comment on can a scientist be “multidisciplinary”? by Abhishek Tiwari

Abhishek Tiwari — Thu, 02 Jul 2009 07:54:26 +0000

Nice and timely post Steve, I have follow up post here http://www.abhishek-tiwari.com/2009/07/bioinformatics-and-systems-biology.html.

Comment on About by Abhishek Tiwari

Abhishek Tiwari — Wed, 06 May 2009 12:13:05 +0000

Hi Steve,
Interesting blog. I am a PhD student at University of Auckland and currently working on Systems Biology especially cell level modelling. I was curious what kind of work you are doing and if you will be interested to work on a systems biology podcast series. let me know your thoughts.
Abhishek