St. Baldrick's Day

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!

Bridging the Gap: Stem Cells

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?

Looking Up Genes

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?

Vertical text selection

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?

UPDATE: Here are some tips from the comments

• In editplus (at least in windows) the same can be done with Alt+C.
• In Vim you can use the Ctrl-v combination and then HJKL (or arrow) keys to adjust your selection.
• Alt-mouse drag will select columns in TextPad
• Option Drag works with TextWrangler on Mac too. Cool Tip. I was looking for similar.

Go Rams!

Sorry that this wonders off the purpose of the blog but I feel its necessary.

Congratulations Rams!

Eye Color

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]

"The Iguana"

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.

Hello Me!

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 =).

Network Theory

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.

Systems Biology

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.

Beginner's Guide to Bioinformatics

As a computer scientist coming into Bioinformatics I was faced with the heavy task of catching up on my Biology and Chemistry (I was a Physics minor in undergrad but that wasn't applicable to my Bioinformatics catch up). This meant two semesters of General Chemistry, a semester of Organic Chemistry and a semester of Cell Biology. Though all this course work was very educational and useful for my degree I don't think its all that necessary for a someone who may be interested in fooling around with Bioinformatics problems on the side.

Here is a very general overview of cell biology for Non-Biologists wanting to get involved in Bioinformatics:

1. Proteins are the essential part of all living organisms. Proteins have a variety of functions and are involved in every process within our cells. [Wikipedia]


2. DNA is the blueprint for proteins. Segments of DNA (genes) translate into proteins. For more detail look into the Translation and Transcription of DNA to proteins.


3. Cell function is determined by which proteins are expressed and their quantity. This means that some kind of gene regulation must take place. Also one can argue if you know the amount of genes expressed in a cell you can possibly infer that cells function.

For a more specific overview, the following are some of the essential key points for biology and bioinformatics:

1. Genome - all the DNA in a cell.


2. DNA - a string of nucleic acids (i.e. GATCACTT…ATCG).


3. Gene - a substring of DNA that encodes proteins.


4. Proteins - a string of amino acids (i.e. ACDEF…RSTY).


5. Gene expression is regulated by the product of other genes. It is a network of interactions.


6. Post-translation modifications are an important regulation mechanism for gene expression.

You may notice that the above deals quite a bit with string manipulation, hence the strong emphasis for Perl experience in Bioinformatic job postings. You will find that string manipulation is not the only driving force for computer science in Bioinformatics. I will try to explain other topics in subsequent posts.

As for Biologists wanting to do Bioinformatics I can not provide the best advice since I didn't come into Bioinformatics from that direction but I would imagine that you may want to look into the following:

1. Learn how to program. You want to know how to use a scripting language (preferably Perl) for smaller every day tasks and an object-oriented language such as C, C++, or Java for larger projects.


2. Learn how to use databases. Bioinformatics deals with very large datasets. At some point your are going to have to deal with either retrieving information from databases or building your very own database so you might as well begin playing with them now.


3. Install and run a Unix/Linux OS (Optional). This might be my personal bias but I believe if you are going to be working in Bioinformatics and its large data sets eventually you will find yourself either maintaining a server or SSHing into one so you might as well become familiar with that type of environment. At the very least XP users should install Cygwin.

Useful Links:

• Bioinformatics intro offered at my university.
  
• Graduate level of the Bioinformatics intro course.


• Library of videos that cover a wide range of biological topics (theoretical and practical).


• RT-PCR a common molecular biology method practiced in the lab.


• Virtual lab which provides a virtual lab for non-biologists to actually work through basic molecular biologist techniques.

Finally I must say that I am far from an expert so any constructive suggestions to help clarify or expand the above is welcomed and appreciated.

MIA...

Sorry I've been missing in action. I'm completing my last semester of classes.

Since I'm on Spring Break (AKA catch up with all my work break) there will be quite a bit of posts popping up on information I've gained throughout the semester but have not had the time to post on.