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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.
Biological processing units!
Imagine being able to create a creature which is basicly a living supercomputer! It will break teh limitations of current cpus
We already created a polio virus from scratch, and we are trying to create a organism from scratch.
(bad joke ahead)
Imagine living beowulf clusters, we could create a cell with cpu like properties, they would reproduce by splitting, and your biocomputers computing capacity would double every few minutes!
Now if each cell could perform 1 megaflop then a petaflop computer would need 1,000,000,000 cells. 2^30 is appox 1,000,000,000. So if it took 10 minutes for cells to split, then a petaflop biocomputer could be grown in about 5 hours!
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.
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.
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.
Wow, your story parallels mine eerily. I graduated in 1996 with my B.Sc., microbiology major. Jobs that paid enough to live off were just about non-existent (this is what happens when several hundred people graduate with your degree EVERY YEAR in a city of half a million people).
:)
Now, I'm 3/4 of the way through a CS degree, and enjoying school like I never have before. Sure, part of it is a little more maturity/experience, but I find now that I'm in something that I ENJOY, I couldn't care less if I'm learning about NP-Completeness today, or Java Beans tomorrow. Regardless, I'm about to enter a co-op work term that will pay $18/hr - and this is one hell of a lot above average salary around these parts (think closer to $12), even for people with university degrees (maybe $15 if you're lucky).
Good money, really fun work, this is the life. It's certainly NOT what I experienced in the bio field. Ironically enough though, I'll be graduating with my CS degree just as 'bioinformatics' (they've changed the buzzword for this a few times since I was in high school) is supposed to hit the big time. Would be kinda neat to have that microbio degree be worth somethign after all
Endless arguments over trivial contradictions in books written by ignorant savages to explain thunder in the dark.
Interesting you should say that, since the foundation of molecular biology owes a lot to noted physicist Erwin Schrodinger, and his little book, "What Is Life?" Most of his speculations were incorrect- he believed that proteins, not nucleic acids, were the information carriers of the cell, for example, but as is often the case, sometimes asking the right questions can be even more important than finding answers. However, it's more than a case of a genius coming in with a bold new idea- by the late 1940s, molecular biology was an idea whose time had come. If "What is Life?" had been written in say, 1890, it would have probably been quickly forgotten- in order to make molecular biology a reality, a critical mass of organic and physical chemistry knowledge was needed, and a variety of chemical and biological techniques like X-ray diffraction, mass spec, chromatography, and cell fractionation needed to be developed.
In my opinion, the "What Is Life?" of the bioinformatics age is J. Craig Venter's whole genome shotgun sequencing method. Once again, a totally different way of doing things, and once again, from an outsider- not as much from the field of study as from every one else engaged in that field. I've had the honor of meeting Dr. Venter and listening to him lecture- he's staggeringly brilliant. He also may be the most arrogant man I've ever met. (And I've also met Stephen Wolfram.) I think often a maverick or an outsider is needed to shake things up and move things forward- either an ingenue who doesn't know the "conventional wisdom" or the hardnosed type who simply doesn't care what everyone else thinks.
Of course, once again, the new idea would have gone nowhere without thre requisite advances, this time in computing, not just in technology, but in computer science (fast algorithms so very important), and also in the development of the miracle that is the Polymerase Chain Reaction. Oh, and with regard to the title of this thread, noted biochemistry student reverseengineer is decidedly more upbeat about the idea of a bunch of "damn biologists drving Ferraris." He wants a 360 Modena, a red one.
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
I'm not certain I follow the reasoning as to why 64-bit computing is ideal for genomics. I mean, it's generally going to be faster and more efficient than 32-bit computing, but that really has little to do with codons. I don't know why you would need to assign a 64-bit number to an element in a set of 64 elements- as other posters have pointed out, you'd only need a 6-bit set of numbers to label 64 things. Besides, saying there are 64 codons is a tad naive, since it doesn't account for things like post-translational modifications to amino acids and nonstandard tRNA anticodons. I hope no one has tried to study the translation of something like collagen (full of modified amino acid hydroxyproline) thinking that the codons were the last word in the formation of the protein. I don't see why 64 bits is optimal as far as the crunching is concerned- are you saying that a 128-bit computer program would for some reason not be as suitable to the task?
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."