This past weekend I said goodbye to all my hair to support kids with Cancer. I was fortunate enough to exceed my goal of $500 (donations are still welcome and appreciated)! By bundling my hair I also I got to donate to Locks of Love.
As someone who is in academics and benefits from funds raised by this type of event, I felt it was necessary to participate. Not only did I have the opportunity to give back but it also helped to remember why we do the research we do; why we participate in science. I came back to school so I could pursue a career that benefited other people’s well being. Prior to that I was just twiddling my fingers away working for a credit card company. I enjoyed this event very much and encourage anyone else who has the opportunity to participate in various things outside of the lab to remember why we do what we do.
For everyone who donated:
THANK YOU!
My “bridging the gap” posts were intended to help teach other computer scientists biology jargon. If you’ve been here for a while you know I haven’t really been followed through (only two posts) with this concept, but starting today I’ll to give it another run.
Today I attended a seminar and found myself looking up various terms related to stem cell research. I’m sure you all have heard all the buzz going on about stem cell research the past couple of years. But I’m sure you didn’t know that there were two kinds branches of stem cells. More specifically there if a cell can differentiate into a mutre type then it is classified as either a pluripotent stem cells and multipotent stem cells [Stem Cell Research Foundation].
As I have very little knowledge in this field, does anyone care to share what they know about stem cells and the research?
I attended a seminar today where the speaker mentioned a gene whose name or function I’ve never heard of before. I used to use Wikipedia to look up a gene but that source is frowned upon by the scientific communtiy due to its unreliability. Now I use NCBI’s Online Mendelian Inheritance in Man (OMIM) which gives a nice condense summary of common knowledge on a gene.
Another one of the graduate students in my lab suggested iHOP that not only has a cool looking monkey on the front page but is also presents a page describing a gene that is loaded with links to various abstracts contained within PubMed.
What tools does everyone else out there use?
Want to select that list of genes without the pain of closing and reopening the file in Excel? Diana Higgins at Windows Fanatics reminds us to do this using most text editors (it can also be done in Word). Simply hold down the Alt key (or the option key in Macs) when making a selection.
Unfortunately this little trick doesn’t work in Microsoft’s notepad and I wasn’t able to find such a key in Gnome for Linux either. Does anyone else out there know?
Sorry that this wonders off the purpose of the blog but I feel its necessary.
I found an interesting post on today explaining the genetic properties of eye color. The article describes how eye color is a polygenetic trait (i.e. more than one gene involved) and of the genes involved one particular gene, OCA2, has more of an influence than the rest.
Its a brief article but I thought it would be useful as it has some jargon that is commonly used in biology and bioinformatics.
Key Terms: single nucleotide polymorphisms (SNPs), gene expression [Wikipedia]
This actually happened about three months ago but I never got time to share.
Since I came into my lab two years ago I have become involved in an age long battle between biologists and computer scientists (when I say age long I really mean never existing). The biologists and technicians called me “Neo”, asked me regularly if I was hacking into the FBI’s website, and complained when they couldn’t use my computer (I’m running Fedora Core 6). I called their bench work fancy biological hand waving.
An exceptionally good prank of theirs was wrapping my computer, mouse, monitor and keyboard all unplugged in bubble wrap. I actually thought we were moving labs. Pure comedy. I got the tech back by remotely logging into his Mac and having it sing a little tune for him. It seemed like this kind of fun would last forever but alas all good things come to an end and our lab technician was offered a position somewhere else. On his last day as a truce at work I allowed him to go ahead and fool around with my workstation one last time. The following pictures are his depiction of his thoughts on Linux.
It seems like my public ramblings are not a waste. Not only am I talking to myself and former classmates but people from other blogs as well. Even Google’s first search result for “bioinformatics blogs”, nodalpoint, references this site. Although I don’t like the heading “perl hacking”, I shouldn’t complain for being acknowledged by my own peers. Plus its my fault that I don’t post more often.
Who knows maybe this recognition will inspire me to post more when Spring Break ends. You’ll just have to tune in and see =).
This network made digg about a month ago. I thought it was interesting because I actually saw it a year ago. You’ll find that network/graph theory is a big topic in Bioinformatics.
I personally find its use in Bioinformatics to be a little bit of a double edge sword. Their importance has emerged as these networks are used to present a systematic overview of various biological processes (i.e. all the gene interactions at a given time in the cell). Which is one of the overall goals of Systems Biology as I briefly touched on in my previous post.
But at the same time their novelty has also caused their misuse in biological community. You may find biologists who want to include these networks in there study but have no knowledge of how they are constructed. One of the Ph.D. students in my lab terms these networks use as fancy bioinformatic “hand waving”. Which is what they are some of the time. The point is, these theoretical networks should be taken for what they are, a tool that facilitates further interpretation, not a concrete view of how a system works.
Here is an interesting quote form my school’s site that a professor recently pointed out in class:
… systems are more than a sum of the parts, and that nonlinear interactions of components and processes result in emergent properties that can not be predicted from knowledge of the individual components and their behavioral processes.
In lamen’s terms, the study of entire biological systems (i.e. looking at all the genes of a cell at once) provides more insight to properties of the system that could not be seen or identified with the old biological dogma of single gene studies.
This is what Bioinformatics has done to the study of Biology. It has transcended the study from a micro exploration of individual gene function to the macro examination of the system as a whole by observing all the parts simultaneously.
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