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Bioinformatics in The Economist
Erich Schwarz writes "Bioinformatics has gone from being an esoteric sub-field to being a business. The Economist gives a useful overview, while warning 'Bioinformatics is not for the faint of heart...'"
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If I had to do it again, I'd definitely choose biology or bioengineering or something related.
It seems as most everything in computer has "been done", and biology/chemisty/biochemical engineering seems to be where all the fun & excitement is these days.
Anyone else agree? Just curious.
Is it really what we want/need as humans? I'm not sure. But I for one won't wager a guess until there's more research done in the area, so I say let's explore it more before we defame it conclusively or support it as a technological breakthrough.
Some other recent news items:
... Development Agency (NABDA) and the United Nations Education Scientific and Cultural ...
Nabda, Unesco Collaborate in Bioinformatics Training
AllAfrica.com,Africa-05 Dec 2002
Organisation (UNESCO), penultimate Tuesday held a two-day Bioinformatics
Bioinformatics ahead for Danville
... Developing these plants will involve both horticulture and bioinformatics and will ...
Danville Register and Bee,VA-30 Nov 2002
be one major focus of Danville's Institute for Advanced Learning and Research
The race to computerise biology ...
Economist (subscription),UK-12 Dec 2002
Welcome to the world of bioinformatics--a branch of computing concerned
with the acquisition, storage and analysis of biological data.
Observing Proteins And Cells In The Wild: Quantum Dots May ...
... Today it is internationally renowned for research and graduate education ...
Science Daily-13 Dec 2002
in the biomedical sciences, chemistry, bioinformatics and physics.
Run, don't walk to bioinformatics.org and contribute!
The first O'Reilly bioinformatics conference rocked. Shame I wont make the next one in San Diego - I get to go to Adelaide for the ISMB in June instead
I don't read your sig, why do you read mine?
Hmmm. Seems like it would be easier to say that everything which has been done in computer science has 'been done', whereas everything that hasn't been done in computer science, 'hasn't'.
Seriously, though, you may be mis-categorizing your subjects. Look at computers as computational entities, rather than disk drives, monitors, and so forth. In that case, an optical computer or a biocomputer operates on many of the same systems priciple as a 'digital computer', and there is therefore much to be done in the field of computer science.
Absolutely. Optical computing is getting some great advances in Holographic Video at the MIT Spatial Imaging Group. And chemical computing is advancing nicely in Carbohydrate Chips at the University of Chicago.
For my money, I'd bet on optical video cubes, 3D television, and biochips in the future... which are all applications of computer technology. Remember, 'computer' use to refer to the job title of a person.
For my money, I think that the future has got SnowCrash, Cryptonomicon, Neuromancer, Count Zero, Mona Lisa Overdrive, and Johnny Mnemonic written all over it (and maybe a bit of Jurassic Park.
What you can do, however, is apply computer science and engineering skills to biological problems: work as a developer or engineer for a biotech company or lab.
now people are overhyping bio-informatics. Yes, it's an important field. It's been an important field for decades. And it's going to continue to make steady progress, not because of, but in spite of the attention and hype, and the stupid patents and opportunism that come along with it.
Actually, bioinformatics is just starting out and the hype has not even begun. Just wait a few years. Additionally, bioinformatics is not decades old. It really started to come together about 15 years ago, and is still an emerging field at the nexus of computer science, chemistry, genetics, physiology, anatomy, pharmacology, epidemiology, medicine, engineering, virology, microbiology, pathology, mathematics, statistics, information management and molecular biology. All of these fields are contributing rapidly exploding amounts of information and making sense of all of this information and communicating the results is what bioinformatics is all about. In fact, because of the advent of bioinformatics, new fields like pharmacogenetics, or the tailoring of drug treatments to specific individuals are being created.
For a number of reasons, the major contributor of information to the field right now is genetics. This is because genetic and protein sequences lend themselves to large-scale analysis in a much easier to encode manner and thus are easier to interpret than other types of data such as tertiary or quaternary protein structure, histology or biochemical pathways. This ease of management is because genetic sequences can be easily represented by letters which represent base pairs, and what one sees when examining a genetic sequence from DNA for example is an endless stream of the letters A, G, C, and T representing adenine, guanine, cytosine, and thiamine, the four nucleotides that make up DNA.
You are probably familiar with the relatively recent announcement of the human genome being sequenced. What has been accomplished here is that all of the A's, T's, G's and C's in the human genome have been placed in roughly the appropriate places by a consortium of both private and public research groups. What all of these base pairs mean is another set of problems that needs to be unraveled. For instance, where do genes begin and end in these sequences of letters? What regions encode proteins and which do not? These are only two of literally millions of questions that can now be asked illustrating that this rough draft is only the beginning and it is only one genome out of many that has been sequenced which will lead to a more complete understanding of organismal biology. And this is just the mammalian stuff. The real money will be on advances made in agribusiness.
Visit Jonesblog and say hello.
I graduated from Rutgers U. (decent NJ state school) in May 2000 with a bachelor's in biology. Back when I decided to major in bio, I really enjoyed studying the field, and (high school) teachers were telling me that molecular biology was the fastest growing job sector. So by the time senior year came around I began looking for a "real" job. I checked all the papers, company websites, monster, etc. and realized that there really are NO good jobs out there for biologists. There are a few bioinformatics jobs, but guess what, you need a CS degree for them, not biology. I ended up getting a lousy job as a lab technician paying around $14 an hour (which took several months to find, btw, and this was when the economy was booming), and I'm extremely unhappy. I've completely lost any love I had for this field. Say what you want about money not being the most important thing, but when you can't afford to do anything you want, your life gets miserable very fast, I don't care how great your job is. Biology jobs typically have zero mobility and are extremely underpaid. You think there's a flood of people graduating from CS? Biology is far worse. My CS classes have about 20-30 people in them. My bio classes had hundreds.
Just recently I decided to go back to Rutgers for a second bachelor's in computer science. Not only are the job prospects better and higher-paying (even considering the dot-com collapse), I've always enjoyed working with computers and my grades are actually far better (although I was never a bad student). I'm actually having fun in my CS classes, I never had fun in bio. The classes were more like a chore. Another horrible thing about biology is that you really don't learn anything practical in college, you just memorize facts. At least with computer science you learn many useful tools to make you a competant programmer, which is actually a marketable skill. Nothing about biology is marketable. I highly discourage anyone from majoring in Bio unless they seriously, seriously love it and intend to get a PhD and devote their lives to research without regards to trivial things like money and job prospects.
Karma: Excellent (In Soviet Russia, karma pimps YOU)
Bioinformatics is a fun interesting field. I worry however, that it may be a little overhyped. People who are interested in bioinformatics need to realize it is a very (albeit cool) specialized field. There aren't going to be a million more bioinformatics researchers in the world. The demand for these researchers just isn't there (and won't be there in the near future). For example, a search on hotjobs reveals only 51 listings for the keyword bioinformatics and nearly 900 listings for programmer.
That said, bioinformatics is exciting. If a computer savy person is interested in getting into it, they should intern or work for a researcher/professor on a research project. You might be surprised, however, when you find that working as a programmer elsewhere pays 2-4 times more.
-Sean (sdm@stanford.edu)
I don't think protein protien interaction is
trivial either. Lets assume that both proteins say the same shape. Take one protein
rotate it and move it around the other protein
in all possible positions and orientations the
relavent group action is R(3) tensor O(3), (the group transitions of one body in 3d, times the
group of rotations in 3d:
six dimensions. proteins are big molecules,
for each of the possible orientations and positions you need to calculate the electrical and
pauli forces between each atom on the surfaces of
one protein with those on the the surface of the
other protein to see if the there can be any chemical interaction between the two. This is a
heavy ammount of computation. But its worse than
that one protein can change the shape of another
one making the calculations even more complex.
Proteomics needs the folding problem solved.
Protein Protein interaction solved.
The inverse folding problem solved (for drug/DNA design).
Then DNA-protein interaction, and the interactions
with macro sugar molecules. Once you've done all
that and have it tabulated in vest lookup tables
for common problems
and with computation on demand for rarer problems, then you can simulate a single cell.
An interesting overview about CI can be found at Nature.
Still, you need dedication for this job: A Ph.D. in chemistry plus solid computer science knowledge is still the norm. But those few who qualify are really sought after.
Disclosure: I am the Director of Chemoinformatics at start-up ChemCodes (www.chemcodes.com), so I know what I am talking about.
goto www.lanl.gov and click on the 'jobs' tab then the postdoc link.
here is one example:
Summary: Postdoctoral Positions in Protein Bioinformatics and Structural Genomics: The Bioscience Division (B-2 Group) is seeking 2-3 highly motivated researchers for immediate openings to work with our interdisciplinary team of Bioinformatics and Structural Biology. Research activities will focus on the development and application of methods in Functional and Structural Genomics, including: 1) inference of function in proteins based upon structural and sequence information; 2) prediction of protein structure, protein binding, ligands, and active sites using both ab initio approaches and experimental information; 3) identification of signatures of pathenogenosis; 4) annotation and analysis of selected genomes; and 5) creation and curation of annotated protein databases.
Required Skills:Experience in at least 2 of the following areas is required (more than two areas of experience is highly desirable):
- Protein structure modeling or protein-ligand analysis or other related modeling
- Background in molecular biology, or microbial pathogenesis, or related fields
- Experience with the common sequence analysis tools for Blast search, sequence alignment, phylogenetic analysis, etc.
- Drug design, or protein design or protein structure predictions or docking
- Functional annotation of putative genes based on literature analysis
- Curation of biological databases and web programming
Desired Skills:Knowledge of one computer programming language (e.g., Perl, Python, FORTRAN, C++). Use of common molecular graphics tools such as Pymol, Xtal. Research in genomic sequence analysis or protein structure. Familiarity with SQL databases, unix, and XML is useful. Education:A Ph.D completed within the last 5 years or soon to be completed is required. Notes to Applicants:Starting salaries range from $59,300 to $67,300. For further technical information about the position and the project, contact Charlie Strauss at cems@lanl.gov (505-665-5838), or Murray Wolinsky at murray@lanl.gov (505-665-0952).Candidates may be considered for a Director's Fellowship and outstanding candidates may be considered for the prestigious J. Robert Oppenheimer, Richard P. Feynman or Frederick Reines Fellowships. Please see Special Postdoctoral Fellowships for further details.
For general information refer to the Postdoctoral Program page.
Some drink at the fountain of knowledge. Others just gargle.