Lab11: WWW Resources and Genome Projects
The WWW offers a plethora of resources to molecular biologists, biochemists, geneticists, bioinformaticians, and baseball fans.
I would like to draw your attention to some of those resources and how you
might use them efficiently to your advantage. One can spend all day searching the
Internet and looking at very valueless sites. Some resources and my personal guides
to their uses include:
-
Biotechnological
Computer Tools
There are online newsgroups on almost any topic, running from alt.alien.vampire.flonk.flonk.flonk to uky.classes.bio520 (ridiculous to sublime). Generally, a newsgroup is just an electronic bulletin board to which e-mails with the appropriate subjects are posted. In theory, informed people will post to the group important questions or brilliant thoughts, and other informed readers of similar interests but different experience will e-mail answers or their own erudite musings. Without pointing any fingers, I suspect that some of these groups are of greater value than others.
Some newsgroups likely to be useful include:
- MODERATED newsgroups in an area of interest
- active bionet groups
- manufacturers "help" newsgroups
Netscape Navigator and Internet Explorer both have NewsReaders, necessary to read and reply to newsgroups. The Biology Microlab, for reasons completely unknown to me, use a different reader. Please determine, with microlab help if needed, how you can read news. This area can be fraught with the dreaded "browser configuration" questions, which you should sort out for yourself.
Peruse the listings for an active bionet group, like the yeast biology group (bionet.molbio.yeast). For the last 20 postings, note how many seem relevant to the interest of the group. Many postings are questions followed by answers. Note the percentage of questions answered and the speed with which an answer was received. Now, look over postings for less active groups like bionet.cellbio. I think you will see a larger percentage of irrelevant postings and alot of dead threads.
Now, visit the Microsoft site supporting a product like Powerpoint (microsoft.public.powerpoint )
Note the extraordinary activity, ease of search, applicability, etc.
When do you use a newsgroup?
- When you can't find the answer yourself, but you suspect that a group may have a readership with that answer.
- When you will be able to verify the answer from the newsgroup once you have the info from the newsgroup. (You would not ask a stranger for directions on the street, would you? Really?)
Some representative questions I have successfully asked are:
- We can not find microtiter dishes with 1.2 ml wells in a 96-well format that can be sterilized for reuse and that have sealable caps. I got 3 responses in about 3 hours when posted to the molbio.methods groups.
- I cannot find out how to convert my Eudora mailbox to Outlook Express format. Answered in about 30 minutes over an old Microsoft forum.
There are obvious net etiquette rules that it may profit you to follow. Don't post questions like, " Tell me what you know about fungi" to the bionet.mycology group. Don't respond by prefacing your comments with, "You ignorant...". Used judiciously, these groups are very interesting. I no longer screen these groups often because of all the junk, but I think I remain convinced that newsgroups represent a unique collaborative learning and research environment enabled by the WWW!
There are an extraordinary number of pages that are not much more than lists of URLs. Some are very useful, though many are also very repetitive. Some favorites are:
- General Bioinformatics Lists
- Pedro's Biomolecular Tools (Now very dated, but still useful, list of analysis services, etc.)
- Swiss List (ExPASy)
- (check out Amos Bairoch's personal links-exhaustive, mostly databases, projects, information)
- the Swissprot proteomics tools list has more than just protein tools!
- NCBI-a must link
- Genome Centers and Genome Projects
Electronic Journals/Newsletters
The relative roles of print and online media are in flux. Many scientific journals offer online sites, and some journals are available ONLY online (eg. some physics journals.) Online journals are in transition from a "free-use" to "subscription-only" policy. This is extremely frustrating for most users, who would like to have desktop access, but cannot afford all possible subscriptions.
Just because people make money does not mean that they are ignorant.
Biotechnology companies, biologicals, etc. have extraordinary information stockpiled on their sites. There are many lists of such sites. Try Amos' list!
Many of the biological professional societies, such as FASEB, have compiled lots of information about their professions, particularly career information.
Many biologists seem to think that the primary function of patents is to hide information. In fact, the purpose of patents is to PUBLICIZE information to encourage industrial development based on technological innovation. Patents protect inventors by granting them license fees. Greedy industries keep traade secrets, not patents.
Check out the US patent office.
Okay, I know this is a bit hokey, but I want you to prowl some websites and find these. There is no intrinsic value to most of these questions.
- Please send me the first word in the title of Kitten Kate's posting to bionet.cellbio?
- Which company is listed immediately after Promega in Amos Bairoch's list of WWW links?
- Does UK subscribe to Molecular and General Genetics online?
- Does the PubMed link to this journal work from your computer? (If not, are you on campus or off (uky.edu or not?))
- Name one eukaryotic parasite genome being sequenced.
- Please paste to me the URL of Stratagene.
- Is the Fungal Genetics Society a member of FASEB?
- What is the name of the city in which the next meeting of the Fungal Genetics Society will be held?
- How many patents were assigned to inventors from Lexington, KY in 1997-98?
- Do any of these patents obviously concern genes?
Please put each answer on a separate line and either e-mail this to Tom or print it out. Due DECEMBER 4, 1998.
IF YOU HAVE NO IDEAS, GET TOGETHER WITH THE FRIENDLIEST PERSON IN THE CLASS AND GIVE IT SOME THOUGHT!
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