BIOTECHNOLOGY TECHNIQUES Vohne 10 No.6 (Jme 1996) p.387-390 Received 21st March.

INTERNET UPDATE

LABORATORYPROTOCOLSONTHEINTERNET

Hugh Griffr

Institute of Food Research, Norwich Research Park, Colney, Norwich. SR4 7uA. U.K.

The World Wide Web (WWW) is of major significance to the Biotechnologist. One of the fastest growing and most

useful areas of the internet, the WWW contains information sites, genome and sequence databases, newsgroups and

forums, search and comparison too& and electronic journals. To many scientists, the WWW has become an

indispensable research tool. This paper lists some of the sites provjdjng a wide range of relevant protocols and

techniques and describes how to acces> this information

INTRODUCTION

I;i\re years ago Wa’ter Gilbert urged scient&s Lo develop computer literacy and to “hook our individual computers into

the worldwide network that gives us access to daily changes in the databases and also makes immediate cur

communications with each other” (Gilbert, 1991). Today scientists make use of many aspects of the internet

including email, newsgroups, electronic databases, and the Wcrld Wide Web ,~V?‘W) (Swindell et al., 1996). One of

the fastest growing and most usefJ areas of the internet, the WWW represents a major resource for biologists

(Swindell et al ., 1996; Harper, 1995). A plethora of useful sites are available for the scientist, including information

sites, rewsgroups and forums, genome and sequence databases, search and comparison tools, and electronic

journals. Some of the nx~t usefnl sites are those t!xn describe relevant protocols and techniques !?&ny such dtcs xc

available providing a large number ofvaried protocols for biochemisu~, molecular biology, microb:olog~. generics, :IIX!

cell biclo~~-. Because of lhi: size of the WWW it is becoming ina-easingI! diff?Jt to find uxful and relc~int sites. This

anic!e describes a number of the sites that detail methods ;nd protocols :)f us: to the bicltecnnologist.

387

PROTOCOLSONTHEWWW

The World Wide Web is probably one of the best ways to obtain information on the Internet (Swindell et al ., 1396).

This fast growing resource consists of multimedia hypertext pages that are accessed by Web browsers such as

Netscape or Mosaic. The main advantages of the WWW are its ease of use, its ability to present graphics, and its use

of hypertext links (Swindell et al., 1996). To use the WWW you need a browser such as Mosaic. Mosaic was

developed at the %ational Center for Supercomputing Applications (NCSA) at the University of Illinois in Urbana-

Champaign. One of the most popuiar browsers is Netscape, produced by Belscape Communications Corporation,

501 East Middlefield Road, Mountain View, California, 94043. MacWeb and WinWeb browsers are from TradeWave

Corporation (formerly EINet) 3636 Fxecutive Center Drive, Suite 100, Austin, TX 78731. There are literally dozens of

other browsers available. The documents that the browsers display are hypertext documents. Hypertext is text with

embedded links to olher documents. The links are highlighted text (or graphics) and clicking on the link will select

the document specified. You are then presented with the linked text regardless of where that document is located,

whether on the same server or on another computer on the far side of the world. It is then possible to select links in

the new document or returnback to the original page (Swindell et al., 1996).

l’he !ocation of wwvii pages is specified by the Uniform Resource Locator (URL), Every single web page has its own

unique URI.. These take the form http://www.ebi.ac.uk. The first part of this address specifies the type of protocol

used, for example http means hypertext transfer protocol. The next part, www stands for World Wide Web, and the

following section specifies the host computer and country (uk ) United Kingdom). Often there are additional parts

specifying the actual files to be accessed. Most browsers enable the saving of URIS as “bookmarks” or “hotlists” so

there is no necessity to type in the URL every time you wish to visit a site (Swindell et al., 1996).

There are many excellent sites on the WWW containing biological techniques, protocols, and other information. Over

the last year there has been an explosion in the number of web sites, partly because it is very easy to set up a WWW

page. The WWW doubles in size approximately every four months. This makes it increasingly difficult to find useful

and relevant sites, The list presented here (Table 1) is not intended to be complete but is rather a starting point. As

time progresses more and more vital information is finding its way onto the WWW. A point has now been reached

where no scientist can afford to ignore the internet.

388

Tabl

e 1.

Lab

orat

ory

prot

ocol

on

the

W

orld

W

ide

Web

WW

W

Site

UR

L Pr

otoc

ols

“” th

e ww

w ht

tp:f/

wwwv

.ifm

.bbs

ro

ac.u

k/R

~abl

docs

lpro

toco

Is.b

tml

Des

crip

tion

A m

ajor

Ju

mp

Stat

ion

(dire

ctor

y)

of a

larg

e nu

mbe

r of

site

s pr

ovid

ing

on-li

ne

prot

ocol

s an

d

tech

niqu

es

in b

ioch

emist

ry,

mol

ecul

ar

biol

ogy,

m

icrob

iolo

gy,

gene

tics,

an

d ce

ll bi

olog

y.

Mar

k St

rom

’s M

olec

ular

Bm

logy

Pr

otoc

ols

http

://re

sear

ch,n

wfs

c.oo

aa.g

ov/p

roto

cols

hrm

l

Jim

Brow

n’s

Mol

ecul

ar

Biol

ogy

Mat

e&s

ZUKI

M

etho

ds

Bruc

e A.

R

oe’s

M

olec

ular

Bt

olog

y M

etho

ds

Dm

rd

Bow

tcll’s

Br

oche

rmst

i~.

Mol

ecul

ar

Biol

ogy

and

Cel

l Bm

logy

Pr

otoc

ols

Bren

dan

Rnb

b’s

Col

lect

ion

of P

roto

cols

an

d R

ecip

es

http

://m

edix.

mm

i uc

t.ac.

zam

bhel

p/ca

n2.h

tml

Whi

tehe

ad

Insn

tute

Rap

id

Cyc

lrsr

http

//128

11

0 19

s 11

5

Ambr

os

Lab

Prot

ocol

C

olle

ctio

n ht

tp://

www

dartm

outh

ed

ular

tsci~

iola

mbr

osIp

roto

cols.

htm

l

Uruv

w~ty

of M

aryla

nd

Apph

cd

Mol

ecul

ar

Rio

logy

ht

tp:llu

mbc

7.um

bc

cd&j

wol

f/met

hodl

.h

tml

http

//1

29.2

2.81

13

iPro

to~o

lslPr

otoc

ols.

htm

l

Mol

ccul

x Bt

olog

y Tc

chm

ques

&om

ega

http

:llwww

pr

omeg

a.co

mlte

chdo

c.hl

ml

NW

En&m

l Bt

oiab

s ht

tp:/iw

ww

neb

com

/neb

/ftpt

ech_

supp

ht

ml

Glh

XlHK

L ht

tp:l/

www.

lifete

ch

com

Jonl

ine/

tech

.htm

l

bttp

:llwww

.ifrn

.bbs

rc

ac.u

Wg~

abld

ocs/

iftm

b.ht

ml

An

exce

llent

co

llect

ion

of m

olec

ular

bi

olog

y pr

otoc

ols.

Al

so

a us

eful

M

olec

ular

Bi

olog

y Te

chm

ques

Fo

rum

wh

ere

you

can

subm

it tip

s,

tech

niqu

es,

ques

tions

an

d co

mm

ents

. Th

e m

etho

ds

arc

nice

ly or

gani

sed

into

se

ctio

ns,

inclu

ding

a

sect

ion

on c

ompu

ter

anal

ysis

of d

ata.

Th

is is

the

gop

her

vers

ion

of J

im

Brow

n’s

exce

llent

Hy

perC

ard

stac

k of

com

mon

m

olec

ular

bi

olog

y la

bora

tory

pr

otoc

ols.

A us

eful

m

anua

l of

man

y of

the

eve

ryda

y m

etho

ds

used

in

the

av

erag

e m

olec

ular

bi

olog

y la

bora

tory

, wi

th

emph

asis

on t

he

tech

niqu

es

for

larg

e sc

ale

DNA

sequ

encin

g pr

otoc

ols

and

DNA

sequ

encin

g au

tom

atio

n te

chni

ques

. An

othe

r gr

eat

colle

ctio

n of

pro

toco

ls

on t

he w

eb.

Cont

ains

pr

otoc

ols

in b

ioch

emist

ry,

mol

ecul

ar

biol

ogy

and

cell

biol

ogy.

This

is a

com

preh

ensiv

e co

llect

ion

of

mol

ecul

ar

biol

ogy

tech

niqu

es,

reci

pes

and

prot

ocal

s ar

rang

ed

in a

lpha

betic

al

orde

r.

DNA

purif

icatio

n an

d se

quen

cing

prot

ocol

s

Met

hods

an

d pr

otoc

ols

for

rapi

d PC

R.

for

m&c

&r

biol

ogis

ts

usin

g th

e Id

aho

Tech

noto

gy

Air

Thet

moc

ycle

r

Mol

ecul

ar

biol

ogy

and

nem

atod

e-re

late

d pr

otoc

ols

Gen

erat

m

olec

ular

bi

olog

y pr

otoc

ols

Mol

ecul

ar

biol

ogy

tech

niqu

es.

Exce

llent

so

urce

of

Pro

meg

a’s

tech

nica

l in

form

atio

n,

vect

or

sequ

ence

s,

litera

ture

, et

c.

Tech

mca

l bu

lletin

s an

d pr

oduc

t m

anua

ls fro

m

New

Engt

and

Biol

abs.

A lib

rary

of

tec

hnica

l m

form

atio

n on

Gib

co

BRL

prod

ucts

fro

m

Life

Te

chno

logi

es,

inclu

ding

tro

uble

shoo

ting,

pr

otoc

ols,

bu

lletin

s,

tabl

es,

and

FAQ

’s.

A go

od

intro

duct

ion

to t

he

inte

met

fo

r th

e m

olec

ular

br

olog

ist.

Browser

Web Site

Link

URL

Server

HTML

Jump Station

GLOSSARY

This is the computer program that is used to view documents on the World Wide Web. Many

different browsers are currently available. Examples are Mosaic and Netscape.

A site is a place on the WWW Each site is specified by its unique URL. A site usually contains links

to other sites,

A hypertext link is the simplest method of moving from one site to another. Clicking on the

highlighted text or graphic automatically produces the WWW page specified by the link. The new

page can be on the same server or on another computer on the far side of the world.

The Uniform Resource Locator. The unique address of a web site or page. This is all the

information to move to a new WWW site.

Any computer that holds HTML documents which are accessable to the internet.

HTML stands for HyperText Markup Language. This is the language in which documents are

written so that they can be read by browsers. Really HTML documents are text files with

embedded codes.

A web page containing a list or directory of related WWW sites. For example the

Molecular Biology Jump Station at the LJRL:

http://www.ifrn.bbsrc.ac.ukigm/lab/docs/molbiol.htmi

contains a catagorized list of a large number of sites ofrelevance to molecular biology.

REFERENCES

Gilbert, W. (1991) Nature. 349,99.

Harper, R. (1995) Trends in Genetics 11,223-228.

Swindell, S.R., Miller, R.R., and Myers, GSA. (1996) Internet for the Molecular Biologist. ISBN 1898486026.

Wymondham, UK, Horizon Scientific Press.

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