Comments on: Bioinformatics basics and beyond

Question: Bioinformatics basics and beyond

Sublimity — Thu, 25 Sep 2008 12:37:30 -0800

Bioinformatics filter: Suggestions for resources to get up to speed on current approaches in genomics and bioinformatics?

I have a graduate-level biochemistry background, but in a different area, and am interested in getting up-to-date on where this part of the field is developing. I'm hoping there are others in the Hive Mind who are much closer to this cutting edge and can point me to some good resources for an "advanced beginner".

I would appreciate reviews, tutorials, or textbook suggestions on in vitro and in vivo experimental methods, as well as computational/bioinformatics methods and tools to try to make sense of the great flood of information.

I've already got a few easy-to-find resouces to start: this bioinformatics tutorial page, the NCBI Tools for Data Mining page, and the NCBI Science Primers, such as this microarray page.

Any and all other suggestions (journal articles? user groups or listservs? more?) are welcome. Thanks so much!

By: halogen

halogen — Thu, 25 Sep 2008 13:06:12 -0800

Sublimity, where are you located? My school (a research university), for example, sponsor weekly/bi-weekly seminars which are free to attend and open to the public. Oh, and they serve free lunch, by the way. I have found it helpful (and enjoyable) to see the application of computational methods rather than just read about them in a book and do immense yet mind-numbingly dull homework assignments. Also, look around for conferences that are open to the public, such as the Keck Center Annual Research Conference in Houston. Last year, I had to drag my boyfriend (visiting from Seattle, so he was stuck with me), and even he as a computer scientist found some aspects of it interesting (okay, there is a chance that he may have lied about that). They also had free lunch for everyone, by the way.

Sorry if this is of no help at all. I tried my hand at bioinformatics with much enthusiasm, but have found out that it is way too reductionist for me.

By: TheOtherGuy

TheOtherGuy — Thu, 25 Sep 2008 14:29:36 -0800

I am a little biased, as it is my area of research, but these days there is a very large overlap between bioinformatics (as it relates to genetic information) and structural biology (the three-dimensional structure of proteins).

The touchstone for all things structural biology computation is the ccp4 bulletin board. Many of the prominent members of the bulletin board were instrumental in the writing of software used in resolving the crystal structures of protein (which quite often uses data-mining of genomic databases). Indeed CCP4 is the name of an open source software package that many structual biologists use. Might be a little advanced for an 'advanced beginner', and there is a lot of off-topic stuff that gets posted, but everybody who is anybody in structural biology computation hangs out there.

Oh.. and here is a good link on using Python in bioinformatics.

email is in the profile if you would like some more resources more specifically tailored to what you are looking for.