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CSE 527, Au '03: Reading #1: What Students Found |
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I asked for brief reports on good primers on course-related topics. Here's what you found:
The book offered just enough biology background for a non-bio person to understand and appreciate whatever he was discussing yet without ever feeling like a textbook.
Review 2 As it mentions at the beginning, it's an article prepared for scientists without strong biology background. It covers a lot of stuff, but also digs a lot of holes. I think it's a little too brief even at an introductory level. Some important concepts, like eukaryote vs prokaryote, are explained but not emphysized. That is, if you are also clear about them, you'll find those descriptions, but if you are not, you might just miss them.
One nice thing about this article is, it gives a lot of links to rich resources. And it also talks about microarray, a good reference for the class. I think it's basically a good article to read for biology beginners, but it's better if the reader already has some knowledge.
Review 3 I'm a computer guy trying to get oriented to the biology side of comp bio.
The first few sections on organisms, cells, and DNA background duplicated the material we covered in the first couple of lectures. I've done enough background reading as well to be familiar with most of this basic material. The section on functional genomics provided a good idea of where some of the interesting research is occurring in the field and how regulation fits in. The microarrays sections also mostly duplicated the lectures we've had to date.
Overall this primer was a nice review of the course lectures along with some good background on gene regulation and expression.
Review 4 It was a good introduction to biology and genetics for someone like myself, who hasn't taken a biology course in several years. It also contained links to more detailed information about some of the concepts, and a number of references for further reading at the end.
Review 2 Although this chapter came form a book that is already 10 years old, it appeared to me both informative and sufficiently broad while still accessible. It starts with some very basic stuff such as attempts to define life itself followed by a broad characterization of the major classes of living creatures. The it introduces basic issues related to evolution and dives into describing components of typical cells. Then it goes into more detail first about important basic molecules (energy carriers, proteins, etc) and then about DNA (with replication and transcription). Finally, it talks about the common model organisms and most relevant experimental techniques and the kinds of data they can provide.
Last year I also took Dr. Sibley's intro class (GS 551) and I find the latest edition of Alberts, et al. textbook to be a perfect resource for answering any questions I might have about cellular components or processes. It's only drawback is its price.
So far I've read only the overview which gives a nice summery of the field of computational biology, and explains simply the two different branches of computational biology: "knowledge discovery" which is used within bioinformatics for prediction of exon-intron and protein structures from sequence, and "simulation based analysis" which attempts to predict the dynamics of systems by using computer models.
It includes the following articles:
Overview: Computational systems biology
Review articles:
Plus FAQs on the website http://bioinformatics.org .
I already have had a reasonable exposure to computational biology in that I spent a summer in David Baker's lab looking at protein folding, and a summer as an intern at Rosetta Inparmatics doing computational analysis of alternative splices. One subdivision of bioinformatics which I found in this nature paper which I had not yet learned of is Laboratory Management Information Systems (LIMS). LIMS track all the information about a certain progect including what chemicals were used, where they came from, what the status of the experiment is, and a multitude of other pieces of information. This paper calls LIMS "electronic lab notebooks." My problem with computationaly biology will be the hard core programming aspects. I'm in applied math, and therefore have done some code writing; but I still feel very weak in this area since my formal computer science training is very limited. Therefore, both of the sources I came upon didn't exactly meet my particular needs although they could be very useful for others (probably someone in CS OR Biology who has never heard of bioinformatics). What I need is something that goes through the machinery (algorithms, search engines) at a lower level. If you have any suggestions for this, that would be great.
This was the text book for Genetics 371 and 372 in early 2002.
The most relevant chapters, from a computer scientist's point of view, are:
Chapter 14, Genomics, feels a bit dated, and maybe that's one reason the textbook for 371 is now "Genetics From Genes to Genomes, 2nd edition" by Lee Hartwell, Lee Hood, et al. It appears to have more details on current techniques/technologies.
This is presented as a tutorial covering 10 different areas of Molecular Bio that are relevant to Computational Biology. It contained several links to other sites complete with pictures, examples and exercises.
Given that I already had a basic foundation in Molecular Biology, I found this tutorial very helpful in reviewing topics and refreshing the details. I also particularly appreciated the emphasis on pointing out the relevance of each of the concepts (a pathway, reaction, particular protein/enzyme, etc.). There were always examples to go with any abstract concepts, never leaving one guessing about where it fits in and why it is important.
I found that this site was reasonably thorough, and allowed me to explore as much or little detail as I felt comfortable. It starts from a reasonable simple level, though for someone with less familiarity with the topics it may have been slower reading and a bit too complicated.
I would recommend this tutorial to a computer scientist who has had a little background in molecular biology, or has had enough biology and chemistry to understand the basics of cell biology and genetics. Its good for recalling details and building on previous knowledge. I would also recommend this as a reference to look up details as needed when one requires mores detail or depth than initially explored.
Good overview of concepts in biology and genetics well written for anyone to understand. The only problem is the accessibility, since this book is part of the Kaplan review course and usually not available otherwise.
The best consise introduction I've found to genetics. Despite its name it does not sacrifice accuracy for "cuteness", and provides a rapid introduction to both classical genetics and molecular genetics for the non-biologist. In particular it does a great job of describing the processes of transcription and translation.