This is an assignment for you.  You will do the exersise alone and write the answers by yourself.  I don't want group projects for answers.  If you each do them the answers will be similar but not the same; I understand that.  You will spend more time trying to make them different than if you just worked on this assignment on your own.

Have fun, this is a neat assignment.

Introduction The internet can be on of the most influential information sources known, Think of how it has changed the way we learn and think versus 7 or 8 years ago. Unfortunately with the good comes the bad, the web can be the greatest absorbent of time and generator of misinformation if one isn't informed. While clicking hyperlinks often leads to very useful and fun web sites, discipline is necessary. The internet is very useful for scientific information. We will look at several of the ways one can use the internet as a source of technical scientific knowledge.

The internet originally began as the U. S. Defense Department's answer to a nuclear attack on the US. The electromagnetic pulse that is believed to follow a large tonnage nuclear air burst would disrupt most of the communication available during the cold war. To allow the military to continue to communicate in defense of the nation, a network called ARPAnet was designed. This early network allowed communication between computers. Later other organizations devised their own network (NSFnet). The interconnection of these networks comprised the internet. This network of computers on various campuses around the US was eventually taken over by the academic personal who maintained it. The protocol governing the Internet, TCP/IP (transmission control protocol/internet protocol), determines who the computers communicate with one another. Thankfully the web browsers we use today do not require that we have any knowledge of these protocols.

Science and the internet - Several kinds of scientific information can be found on the internet. Straight forward information that may or may not have scientific merit. (this is the type of information you can find by poking around using one of the search engines such as Yahoo or Excite. The problem is that this kind of a search won't get you far if you are looking for specific information. Typically one can start at one of a few sites many of them are maintained by the federal government. These sites typically are very large and intimidating due to the massive amount of information but are still excellent sources of information.

One very important key in searching the 'net is knowing what kind of information you are looking for. If you are looking for general information such as advise or an opinion on something such as breast cancer, using your favorite search engine is fine However the volume can be overwhelming. Limiting the searches can be key in this type. The terms used are also important.  I generally like to start using a gneeric term then see what types of specific subjects are found.  If this is the kind of information I want then the search can be refined if not start over with a better set of terms.  Also different search engines use different algorithms to look for the search hits so it is important to use more than one type and become familiar with several engines.

There are several non-government web sites that can be used for both general and specific purposes. One f them is http://www.fastsearch.com/med/index.html. This is a med search engine that has use for both public health information and scientific information.  But becareful, while it is a good web site it is awful slow. Another is biomed.net at ( http://www.biomednet.com/ ). I recommend thisone for a more scientific based search. It has several informational articles and opinion pieces on biomedical science. As well as some very interesting links. One problem with this site is that you need to register for it. It is a free site and if you have the inclination I would recommend you get, keep and REMEMBER the password. Later when we discuss literature searches, this site is very useful. It will keep a history of the literature searches you've made. I personally use it for most of my searches.

 Literature searches. Now lets get specific - The backbone of what we do as scientists is to read papers. Text books are nice to use as a background but (particularly in the biomedical sciences) they are usually out of date and not as in depth as one needs for research. In fact as scientists, you will progressively use text books less and less and use publications more and more.

What journals are the best? That is a good question. The answer is controversial and depends on what discipline you are looking for. For the most part the journals Science and Nature are two of the most prestigious publications. A career can often be defined by the number of publications you have in these journals. The publications in these two journals have a very high impact and are usually cited more than any other journals. From there the journals Cell, Proceedings of the National Academy of Sciences, USA are also very important Journals. For biochemistry, the Journal of Biological Chemistry (JBC) is one of the leading publications. Opinion can vary but these are considered the top journals and a publication in these are considered very good.  An older more traditional manner to assess the use of a specific  publication has been to find out how many other publications have cited a specific paper.  That has been a way many Journals have been selected by scientists for being important.  The Science Citation Index is a publication corporation that measures the impact of journal and scientific publications from over 3700 peer reviewed journals.  See below for links to the journals themselves.

There are several different databases that are usually discipline directed. There are different databases for journals on chemistry (this usually contains some biochemistry journals), plant biology and field biology and for biomedical journals. Most biochemistry, molecular biology, physiology and structural biology journals (those that deal with eukaryotes and prokaryotes) are usually found on a database called MEDLINE.

The true power of the internet is that you can search a huge data base with your computer without leaving home or the office. Even the most complete libraries do not have all of the journals you may require. More and more these publications are on the internet. At least the titles and abstracts are. Later I will list several very important biochemistry journals and there web sites but for now lets discuss searching all of the literature. One of the free government web sites is maintained by the National Center for Biotechnology Information (NCBI). This site is run through the National Institutes of Health (NIH). As mentioned above, there are several databases which you can access. For biomedical literature (biochemistry, molecular biology, cell biology physiology and such) you will need to access the MEDLINE database

So where can you search for a paper? If you have registered for the biomednet site that’s one place but there are several others. Once you get used to these sites they are the most powerful means of looking for information on specific topics. I will focus on the PubMed search engine that uses MEDLINE but there are others including one called grateful med. There a few differences between the two.  GratefulMed is a very broad based search engine while PubMEd access MedLine only but can link to several other tools and has some additional mechanisms for helping your searches.
 
 
 

PubMed

Internet Grateful Med

Provides free access to MEDLINE.  Sets of related articles pre-computed for each article cited in MEDLINE   Can use Loansome Doc Document Delivery service  Medical Subject Heading (MeSH) Browser.   Citation Matcher  Choice of Web search interfaces from simple keywords to advanced Boolean expressions. Field restrictions and MeSH index terms (main topics and subheadings) supported.  Linkages to publishers' sites for full-text journals. Approximately,250 journals available, some by subscription only.  Clinical query form with built-in search filters for diagnosis, etiology, therapy, and prognosis.  Links to molecular biology databases of DNA/protein sequences and 3-D structure data.

Provides free access to MEDLINE, AIDSLINE, AIDSDRUGS, AIDSTRIALS, BIOETHICSLINE, ChemID, DIRLINE, HealthSTAR, HISTLINE, HSRPROJ, OLDMEDLINE, POPLINE, SDILINE, SPACELINE, and TOXLINE.  Effective September 1998 searches MEDLINE via PubMed's retrieval system.  Sets of related articles pre-computed for each article cited in MEDLINE  Linkages to publishers' sites for full-text journals. Approximately 250 journals available, some by subscription only.  Can use Loansome Doc Document Delivery service  Offers full range of Medical Subject Heading (MeSH) search features via UMLS Metathesaurus.  Ability to limit searches by language, publication type, age groups, etc., using pull-down menus.

Go to http://www.nlm.nih.gov. This is the MEDLINEplus web site. You should immediately see that there are several options here and that there are lots kinds of information you can get here including several general information sites on health. These are some of the best sites if you want to learn about diseases, consumer related organizations, clinical trials of new drugs and treatments and other health related subjects. Take a little time to poke around the site and see what kind of information you can. You can search the MEDLINE from this site or a number of others.

Now go to the National Library of Medicine Web Site -(Pub Med). From this site you can access DNA and, protein sequences translate DNA to protein sequences using the Entrez, Blast and GenBank sites.  There are over 11 milliion references in this data base!  However - you must realize that this is based on biomedical and some life science information.  Searching here for animal behavior or most plant information will be very limited.  Once you get to the site you can search a number of different types of databases, be certain you are on MEDLINE. Once you get a search started, you can see the abstracts by clicking on the author's name. This window will give you several other links to related documents and presentation formats, as well as the actual journal that the paper came from. Loansome Doc requires registration and application fees. If you want to see the journal, then save the journal citation and go to the library to get a copy. Often times there will be a link to either science direct or the actual journal that publishes the article.  Click on these and you may find you can get the whole arMost of these journals are not available the MSUM library but you can request one through interlibrary loan.

Searching Journals:

• MSU Moorhead has subscribed to a search database called Science Direct.  This is a smaller set of journals than found with pubmed, but many of them are directly accessible from the site.  That means you can easily read more then just the abstracts!  And that's a good thing.  In addition you can search other biology and chemistry databases from here that are not covered in pubmed.
• Another way to find full publications is to review the Pub Med Central Database (PMC).  This data base  is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to PMC is free and unrestricted.
• Finally more and more scientific societies are putting some if not all of thier journal publications on the web to bed access free.  For our purposes, one of the top journals is the Journal of Biological Chemistry (JBC).  If you are a member of the American Society of Biochemistry and Molecular Biology, you have full free access, if not you can still have access to all but the most recent set of journal articles.  Highwire press is the company that hosts the JBC and many other publications on line.  Many of these are partially or fully free!
• A practicle aspect of searching the journal articles are if you should read the HTML or the PDF versions.  For printing out and reading a paper, use the PDF version.  The HTML version will not print well and is organized differently.  To view the paper online, read the HTML.  Reading the HTML version will allow you access to the figures, enlarge the figures and many of the HTML articles will have hyperlinks to other papers or databases.

Other interesting sites. There are several sites which are very useful to biochemists. I have created a very short list of them on a link from my home page.  This page has a link to pub med, science direct and other good links to help you start your search for your Nobel Prize.