[I have no idea what ever became of parts 16 and 17...] Date: Fri, 04 Feb 94 08:07:59 +0100 From: eggenber@comp.bioz.unibas.CH Subject: WWW INTRODUCTION: Parts 1-15 WWW INTRODUCTION ================ PART 1: Overview ---------------- This is an overview of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. PART 2: What is the World-Wide Web PART 3: What is available on the Web PART 4: How to get to World-Wide Web PART 5: Overview of WWW client software PART 6: Installing the CERN LineMode browser PART 7: Installing Lynx under UNIX PART 8: Installing Lynx under VMS PART 9: Installing Mosaic under X/UNIX PART 10: Installing Mosaic on the Mac PART 11: Installing Mosaic under DOS/Windows PART 12: What are URL's PART 13: Exploring the Web PART 14: What is HTML PART 15: Customizing WWW PART 16: Troubleshooting (by Reinhard Doelz) PART 17: Glossary Florian Eggenberger EMBnet Switzerland ACKNOWLEDGEMENTS ---------------- EMBnet Switzerland is a project funded by the University of Basel, the Swiss National Science Foundation, and industrial contributions from Digital Equipment and Silicon Graphics (in alphabetical order). WWW INTRODUCTION ================ PART 2: What is the World-Wide Web ---------------------------------- This is the second part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. There are now over two million registered computers on the Internet providing a huge amount of information. Fortunately, the access to these often widely dispersed data has been facilitated by the development of network information delivery systems such as Gopher and the World-Wide Web (WWW, W3). These interactively working network tools are based on the client-server model: The user runs locally a client program that can communicate with a server program on a (remote) host computer. In order to access the information, the client sends the user's request to the server (using a standardized format called a protocol). The server handles the request and sends the response to the user. The Gopher project was developed at the University of Minnesota and has now evolved in a powerful system for offering information across the net. The information appears to the user as a series of nested menus, resembling the organization of a file system. The World-Wide Web has been described as a "wide-area hypermedia information retrieval initiative aiming to give universal access to a large universe of documents". It was invented at the European Centre of Particle Physics (CERN), Switzerland. Basically WWW and Gopher are similar: Both systems allow the user to browse information across the Internet without the necessity to login. However, WWW is much more powerful and flexible than Gopher. Whereas a Gopher menu is a list of items, WWW appears to the user as a text document and can take - provided that the user runs a graphical interfaces such as NCSA Mosaic - full advantage of text formatting. WWW documents are written in hypertext (text that contains links to other text). Selecting certain words within a WWW document via mouse or keyboard causes other documents to be opened, no matter where on the Internet these documents are. In addition, WWW documents can contain links not only to other text, but also to images, sounds and movies. The WWW world is growing very fast. There are already more than 200 WWW servers on the Internet providing a large amount of information, not accessible by other network tools. Moreover, WWW provides a single consistent user-interface to access information of other services such as Gopher, FTP, and News. Not surprisingly, the programs (called WWW clients) that allow to access these data are in use at hundreds, if not thousands, of sites on the Internet today. An overview of currently available WWW client software will be given in part 5 of this series of postings. Florian Eggenberger EMBnet Switzerland REFERENCES ---------- EARN Association (1993) Guide to Network Resource Tools. Foster, J., Brett, G. and Deutsch, P. (1993) A Status Report on Networked Information Retrieval: Tools and Groups. Hughes, K. (1993) Entering the World-Wide Web: A Guide to Cyberspace. Torkington, N. (1993) Frequently asked questions on W3. Smith, U.R. (1993) A Biologist's Guide to Internet Resources. THESE DOCUMENTS ARE AVAILABLE ON THE WEB. WWW INTRODUCTION ================ PART 3: What is available on the Web ------------------------------------ This is the third part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. The Web provides a vast array of information covering almost any biological research area but, unfortunately, these data are widely dispersed and it is therefore often difficult to find something of interest. To solve this problem, a number of people have begun to catalogue the data into lists organized by subject, provider, or access method. Resources of interest for biologists include: * Abstracts of articles in press * Biology news and documents * Graphics and general software * Guides and tutorials * Job offers * Journal indexes and databases * Sequence databases * Software for biology A comprehensive list of locations of biological information archives can be found in Una Smith's "A Biologist's Guide to Internet Resources". Services that provide on-line help to find useful information available on the Web include the Meta-Index of NCSA, CERN's Virtual Library, the Nova-Links created by Rob Kabacoff, and Joel's Hierarchical Subject Index. Keith Robinson at Harvard University maintains a list of WWW servers providing information of interest for biologists. These on-line services are accessible by any WWW client. Written in hypertext they provide a convenient and quick route to everything on the Web. A number of other sites provide similar services using Gopher servers. These sites are accessible by WWW clients as well but lack the hypertext functionality of WWW. Biology-relevant Gopher sites include Don Gilbert's IUBio service, Rob Harper's Finnish EMBnet BioBox, and Reinhard Doelz's list of the European Biology Gopher tree. A list of some WWW starting points for an exploration of Web resources that might be useful for biologists will be given in part 13 of this series of postings. The rules that computers use to exchange messages are called protocols. Most network retrieval systems use their own protocol with limited access to other protocols. In contrast, the HTTP protocols used by WWW servers and clients allows to communicate to other systems including Gopher, WAIS, and FTP. Thus, WWW clients provide access to anything on: * WWW sites (>200) * Gopher sites (>1000) * WAIS sites (>100) * anonymous FTP sites (>1000) * Usenet News, etc. This feature makes the WWW system one of the most comprehensive network retrieval tool. In addition, WWW clients are easy to use and - depending on the user's operating system - there are character based as well as graphical interfaces available. An overview of currently available browser software will be given in part 5 of this series of postings. Florian Eggenberger EMBnet Switzerland REFERENCES ---------- Smith, Una R. (1993) A Biologist's Guide to Internet Resources. Usenet sci.answers. Available on the Web. For a free copy via email, send the text "send pub/usenet/sci.answers/biology/guide/*" to the email address mail-server@rtfm.mit.edu. OTHER USEFUL REFERENCES MAY BE FOUND THEREIN OR ON THE WEB. WWW INTRODUCTION ================ PART 4: How to get to the World-Wide Web ---------------------------------------- This is the fourth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. To access the information provided by remote WWW sites you need a program (called WWW client or browser) that allows to communicate with the remote WWW server. The browser may either be locally installed or on a remote computer. If you are directly connected to the Internet it is recommended to install the client software locally. The disadvantage of accessing the Web by a remotely running client is a lack of full functionality and poorer performance. The audience of this series of postings is assumed to have no WWW client locally installed. Nevertheless you may want to try out what WWW looks like before installing a browser yourself. Fortunately, there are some sites that let you access the Web by remote login. Such services are provided by: The University of Kansas: (requires a vt100 terminal) 1) enter the command you need to open a "telnet" session 2) connect to "ukanaix.cc.ukans.edu" 3) at the login prompt enter "kufacts" 4) use the arrow keys to select an item of interest 5) press to follow the link 6) for help press "?", enter "q" to quit The Finnish University and Research Network (FUNET): (requires a vt100 terminal) 1) enter the command you need to open a "telnet" session 2) connect to "info.funet.fi" 3) at the login prompt enter "www" 4) select "www" as service 5) select "lynx" as interface 6) use the arrow keys to select an item of interest 7) press to follow the link 8) for help press "?", enter "q" to quit The European Centre for Particle Physics (CERN) Switzerland: 1) enter the command you need to open a "telnet" session 2) connect to "info.cern.ch" 3) enter a number to follow the corresponding link 4) enter "Help" for help, or "Quit" to quit Both CERNS's LineMode browser and the fullscreen browser "Lynx" are available as C source code or in executable forms for several platforms. An overview of features of currently available browsers will be given in the next part of this series of postings. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 5: Overview of WWW client software --------------------------------------- This is the fifth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. If your computer is directly connected to the Internet and you want to use WWW, you should install a browser. The advantages of a locally running browser are full functionality and better performance. WWW browsers are available for most environments including: * AIX * HP-UX * IRIX * MacOS 7.x * MS Windows 3.x * NeXTStep * OSF/1 * Ultrix * VMS * X11/Motif WWW browser software is copyrighted but usually free for academic use. The programs can be downloaded by anonymous FTP as C source code or in executable forms. WWW browsers currently available include (there may be other software products that do the same job): * CERN's LineMode browser: This is the basic text-only interface that works on nearly any platforms. Binaries for HP, Mac, NeXT, PC with PC-NFS socket library, IBM RS/6000, SGI, Sun, and VM can be obtained from the European Laboratory for Particle Physics (CERN), Switzerland. * Lynx: This is a character-based browser that provides a full-screen interface for UNIX and VMS platforms and is very easy to use. Binaries for IBM RS/6000, DEC Alpha VMS (Multinet), DEC Alpha OSF1, Sun 4, DEC Mips, DEC VAX (Multinet) can be obtained from the University of Kansas. * NCSA's Mosaic: This is a graphical interfaces for users on X-Windows, MacOS 7.x, and MS-Windows 3.x. Binaries for DEC Alpha, DEC Mips, HP 9000/730, IBM RS/6000, Mac, PC Windows, SGI, Sun Solaris, Sun SunOS can be obtained from the National Centre of Supercomputing Applications (NCSA), Illinois. How to obtain and install the software will be described in the following parts of this series of postings. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 6: Installing the CERN LineMode browser -------------------------------------------- This is the sixth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. CERN's LineMode browser is the basic text-only interface that works on nearly any platforms. The files required to run this WWW browser on your computer can be retrieved by anonymous FTP from sites including (it is quite likely that this may change over time): Hostname Location Type Sweden ftp.sunet.se /pub/www/bin binary /pub/www/src source Switzerland info.cern.ch /pub/www/bin binary /pub/www/src source Important: in order to prevent unnecessary network traffic it is recommended to download the files from a server as close as possible to your location. To get a complete list of sites providing the CERN software use "archie" (ask a local expert). Transfer the browser software from the host to your computer: (Note: hit the key at the end of each command.) 1) enter the command you need to open a "FTP" session 2) type "open" at the ftp prompt and enter the Hostname (see above) 3) at the login prompt type "anonymous" 4) enter your email address 5) type "cd " and enter the Location of the binary (see above) 6) type "ls", you will get a directory listing 7) check whether a name of a directory corresponds to your machine type 8) if so, type "cd " and enter the name of the directory 9) type "ls", you will get a file listing 10) check whether the binary www_*** is available If the binary is available: 11) type "binary" 12) type "get www_***" (replace *** with the appropriate version number, this will load the binary to your local disk and may take some time 13) type "bye" at the ftp prompt 14) make the binary executable (on UNIX systems type "chmod ugo+x " followed by the filename) That's it! Go ahead and execute it. If you need on-line help: type "Help" at the command line. The customization of WWW clients will be described in part 15 of this series of postings. If the binary is not available: (Note: requires "Make" and programs to process tar.Z-files.) 11) type "cd " and enter the Location of the C source (see above) 12) type "ls" and check whether the archives "WWWLibrary_***.tar.Z" and "WWWLineMode_***.tar.Z" are available 13) type "binary" 14) type "get WWWLibrary_***.tar.Z" (replace *** with the appropriate version number) 15) type "get WWWLineMode_***.tar.Z" 16) type "bye" at the ftp prompt The following descriptions apply to UNIX systems. On other systems, the commands may be different. Uncompress and unwrap the two archive files: 1) type "uncompress" followed by the filename 2) type "tar xvf" followed by the filename 3) change to the directory "WWW" that has been generated 4) read the "*.txt" files 5) change to the directory "LineMode", type "ls" The subdirectories listed, reflect the machine types to which the browser has already been ported. Change to the subdirectory for your type of machine. Edit the "Makefile" (ask a local expert). Change to the directory "WWW" and type "BUILD". You should then get a executable file www_*** in the subdirectory for your type of machine. To try it out, change to this subdirectory and type "www". If you need on-line help: type "Help" at the command line. For more information, consult the "User Guide for the WWW Line Mode Browser" in the directory "WWW/LineMode/Default". Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 7: Installing Lynx under UNIX ---------------------------------- This is the seventh part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. Lynx is a character-based browser that provides a full-screen interface for UNIX and VMS platforms. There is widespread agreement that Lynx is currently the best text-based browser. The files required to run this browser on your computer can be retrieved by anonymous FTP from sites including (it is quite likely that this may change over time): Hostname Location Type Netherlands ftp.twi.tudelft.nl /pub/www/lynx binary/source Sweden ftp.sunet.se /pub/www/lynx binary/source USA ftp2.cc.ukans.edu /pub/lynx binary/source Important: in order to prevent unnecessary network traffic it is recommended to download the files from a server as close as possible to your location. To get a complete list of sites providing the Lynx software, use "archie" (ask a local expert). Transfer the browser software from the host to your computer: (Note: hit the key at the end of each command.) 1) type "ftp" and enter the Hostname (see above) 2) at the login prompt type "anonymous" 3) enter your email address 4) type "cd " and enter the Location of the binary 5) type "ls", you will get a file listing (the filenames reflect the supported machine types) 6) check whether the "*.exe.Z" binary (version 2-1 or later) for your system is available If the binary is available: 7) type "binary" 8) type "get" and enter the filename of the binary 9) type "ascii" 10) type "get lynx.cfg" 11) type "bye" To uncompress the downloaded archive file, type "uncompress" and enter the filename of the binary. Then make it executable: type "chmod ugo+x " followed by the filename of the uncompressed binary. Now, change the configuration of your browser. Edit the file "lynx.cfg" (as explained in the file) and put it in the directory specified (ask your system administrator if you don't have "super user" privileges). That's it! Go ahead and try your browser out. If the binary is not available: 7) type "ls" and check whether the archive "lynx*.tar.Z" (version 2-1 or later) is available 8) type "binary" 9) type "get lynx*.tar.Z" (replace * by the appropriate version number) 10) type "bye" Uncompress and unwrap the archive file: 1) type "uncompress lynx*.tar.Z" 2) type "tar xvf lynx*.tar" 3) change to the directory "lynx*" that has been generated 4) read the "INSTALLATION" file 5) edit the files "lynx.cfg" and "userdefs.h" according to your system configuration (changes to be done are explained in the files) 6) edit the "Makefile": specify the local path of the executable 7) type "make" and you will get a list of supported systems 8) type "make" and enter the type of your system, this will generate the executable "lynx" Now, you should be ready to access the Web. Go ahead and start your browser. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 8: Installing Lynx under VMS --------------------------------- This is the eighth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. Lynx is a character-based browser that provides a full-screen interface for UNIX and VMS platforms. There is widespread agreement that Lynx is currently the best text-based browser. The files required to run this browser on your computer can be retrieved by anonymous FTP from sites including (it is quite likely that this may change over time): Hostname Location Type Netherlands ftp.twi.tudelft.nl /pub/www/lynx binary/source Sweden ftp.sunet.se /pub/www/lynx binary/source /pub/library/hytelnet/vms unzip.exe USA ftp2.cc.ukans.edu /pub/lynx binary/source Important: in order to prevent unnecessary network traffic it is recommended to download the files from a server as close as possible to your location. To get a complete list of sites providing the Lynx software, use "archie" (ask a local expert). Transfer the browser software from the host to your machine: (Note: hit the key at the end of each command.) 1) type "ftp" and enter the Hostname (see above) 2) at the login prompt type "anonymous" 3) enter your email address 4) type "cd " and enter the Location of the binary 5) type "ls", you will get a file listing (the filenames reflect the supported machine types) 6) check whether the "*.exe" binary (version 2-1 or later) for your system is available If the binary is available: 7) type "binary" 8) type "get" and enter the filename of the binary 9) type "ascii" 10) type "get lynx.cfg" 11) type "bye" Now, configure your browser. Modify the file "lynx.cfg" (make changes as explained in the file) and put it in the directory specified. Then, set up lynx as a command. Create the file "lynx.com", fill in the local path of "lynx.exe" (e.g. "$ lynx:==$mydevice:[user.lynx]lynx.exe") and add a line with your news server (e.g. "$ define "NNTPSERVER" "myserver""). That's it, type "@lynx" and you should be on the Web. If the binary is not available: 7) type "ls" and check whether the archive "lynx*.zip" (version 2-1 or later) is available 8) type "binary" 9) type "get lynx*.zip" (replace * by the appropriate version number)" 10) type "bye" If there is no program available on your machine that allows to process "*.zip" files, you can retrieve "unzip.exe" by anonymous FTP (see above). If "unzip.exe" is available: 1) type "unzip lynx*.zip" (replace * by the appropriate version number) 2) change to the directory "lynx*" that has been generated 3) read the "INSTALLATION" file 4) edit the files "lynx.cfg" and "userdefs.h" according to your system configuration (changes to be done are explained in the files) 5) type "@build", you will be asked whether you have MultiNet, UCX, or WIN_TCP 6) enter the appropriate number, this will compile the lynx sources and may take some time. Then, set up lynx as a command. Edit the file "lynx.com": fill in the local path of "lynx.exe" and the name of your news server. That's it! Go ahead and try your browser out. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 9: Installing Mosaic under X/UNIX -------------------------------------- This is the ninth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. NCSA's Mosaic for X Windows provides a mouse-driven graphical interface for systems running X11/Motif. The files required to run this WWW browser on your computer can be retrieved by anonymous FTP from sites including (it is quite likely that this may change over time): Hostname Location Type Netherlands ftp.nic.sufnet.nl /mirror-archive/software/ www/mosaic/X/Mosaic-binaries binary /mirror-archive/software/ www/mosaic/X/Mosaic-source source Germany ftp.ask.uni-karlsruhe.de /pub/infosystems/mosaic/ Mosaic-binaries binary /pub/infosystems/mosaic/ Mosaic-source source USA ftp.ncsa.uiuc.edu /Mosaic/Mosaic-binaries binary /Mosaic/Mosaic-source source Important: in order to prevent unnecessary network traffic it is recommended to download the files from a server as close as possible to your location. To get a complete list of sites providing the NCSA software, use "archie" (ask a local expert). Mosaic assumes the presence of programs that allow you to view images and Postscript files. Thus, check whether such so called "external viewers" have already been installed on your machine. The following descriptions apply to UNIX systems. On other systems, the commands may be different. Transfer the browser software from the host to your computer: (Note: hit the key at the end of each command.) 1) type "ftp" and enter the Hostname (see above) 2) at the login prompt type "anonymous" 3) enter your email address 4) type "cd " and enter the Location of the binary (see above) 5) type "ls", you will get a file listing (the filenames reflect the supported machine types) 6) check whether the binary "Mosaic-*.Z" (version 2.0 or later) for your system is available If the binary is available: 7) type "binary" 8) type "get" and enter the filename of the binary 9) type "bye" In order to unpack the binary, type "uncompress" and enter the filename of the binary. Then make it executable: type "chmod ugo+x " followed by the filename. That's it, go ahead and execute your browser. If the binary is not available: 7) type "cd" followed by the Location of the C source (see above) 8) type "binary" 9) type "ls" to check whether the archive "Mosaic-*.tar.Z is available 10) type "get" and enter the filename of the archive 11) type "bye" 12) type "uncompress" followed by the filename of the archive 13) type "tar xvf" followed by the filename of the uncompressed archive 14) change to the directory "Mosaic-*" that has been generated 15) read the "README" file 16) modify the "MAKEFILE" according to your system configuration 17) type "make", this will (hopefully) generate the executable "Mosaic" in the "src" directory. Now, go ahead and try it out. The customization of WWW clients will be described in part 15 of this series of postings. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 10: Installing Mosaic on the Mac ------------------------------------- This is the tenth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. NCSA's Mosaic for the Apple Macintosh provides a WWW interface for Macs running System 7.x/MacTCP 2.0.2 (or later). The files required to run this WWW browser on your machine, can be received by anonymous FTP from sites including (it is quite likely that this may change over time): Hostname Location Type Germany ftp.ask.uni-karlsruhe.de /pub/infosystems/ mosaic/Mac Mosaic Netherlands ftp.nic.surfnet.nl /mirror-archive/ software/www/mosaic/Mac Mosaic USA ftp.ncsa.uiuc.edu /Mac/Mosaic/ Mosaic USA cs.orst.edu /pub/mac/topsTerm StuffIt Important: in order to prevent unnecessary network traffic it is recommended to download the files from a server as close as possible to your location. To get a complete list of sites providing the Mosaic software, use "archie" (ask a local expert). How to download Mosaic: 1) open a ftp session 2) connect to the Host (see above) 3) enter "anonymous" as username and your email address as password 4) change to the Location of the "Mosaic" archive 5) check whether the archive "NCSAMosaicMac.***.sit.hqx" is available 6) select the appropriate button(s) to download the archive 7) download the help files "*.README" and "*.Txt" 8) disconnect from the host and close the ftp session How to process the downloaded "Mosaic" archive: To unbinhex and uncompress the archive, you require "StuffIt" or an equivalent program. "StuffIt" is shareware and can be obtained by anonymous FTP (see above). To execute "StuffIt", double-click the program icon. Then select "Decode BinHex File..." from the "Other" Menu and choose the Mosaic archive to be decoded. Select "Open" and then "Save". This will unbinhex the archive. After that, select "Open Archive..." from the file menu and choose the unbinhexed archive to be uncompressed. Click the "Open" button and select the archive, then click the "Extract" icon and select "Save". That's it, go ahead and double-click "NCSAMosaic***". The customization of WWW clients will be described in part 15 of this series of postings. Note: Mosaic assumes the presence of external viewers. For more information on how to get and install such programs, refer to the help files "*.README" and "*.Txt". Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 11: Installing Mosaic under DOS/Windows -------------------------------------------- This is the eleventh part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. This document is based on Dean Pentcheff's "The DOS Internet Kit". NCSA's Mosaic for Microsoft Windows provides a graphical interface for IBM compatible PC's running Microsoft Windows 3.1 in 386 Enhanced Mode. The files required to run this WWW browser on your machine can be retrieved by anonymous FTP from sites including (this may change over time): Hostname Location Type Germany ftp.ask.uni-karlsruhe.de /pub/infosystems/ mosaic/PC Mosaic /pub/infosysems/ mosaic/PC/sockets Trumpet USA ftp.ncsa.uiuc.edu /Mosaic/Windows/ Mosaic /Mosaic/Windows/sockets Trumpet USA tbone.biol.scarolina.edu /pub/kit Kit Important: in order to prevent unnecessary network traffic it is recommended to download the files from a server as close as possible to your location. To get a complete list of sites providing these software products, use "archie" (ask a local expert). NCSA's Mosaic for Windows assumes the presence of "external viewers" (programs to display images, Postscript files, etc.) and a Winsock- compliant driver such as "Trumpet Winsock" that provides a connection layer between Windows and the underlying DOS packet driver for your network board. Obtaining and installing the software: 1) check what software is required to run Mosaic on your PC: case 1: you only need Mosaic case 2: you need Mosaic and a Winsock-driver case 3: you need a complete package of Internet applications (including NCSA Mosaic for Windows, the LView Gif viewer, NCSA Telnet for DOS, PC Gopher for DOS, the Trumpet Winsock driver, a set of DOS package drivers) and easy to understand instructions on how to install and configure the software on your PC. 2) open a "FTP" session, enter the Hostname of: case 1: a site providing Mosaic (see above) case 2: a site providing Mosaic and the Trumpet driver case 3: a site providing the DOS Internet Kit 3) type "anonymous" at the login prompt and enter your email address 4) type "cd " followed by the appropriate Location (see above) 5) type "ls" and check whether the required archive files are present: case 1: "winmos*.zip" case 2: "winmos*.zip" and "winsock*.zip" case 3: "disk1.exe" and "disk2.exe" 6) type "binary" 7) type "get" followed by appropriate filename, this will load the archive file to your local disk and may take some time 8) type bye 9) install the software on your machine: case 1: unpack the *.zip file (use "pkunzip" or an equivalent program), proceed with STEP 3 case 2: unpack the *.zip file (use "pkunzip" or an equivalent program), proceed with STEP 2 case 3: proceed with STEP 1 STEP 1: Installing the DOS Internet Kit: 1) format two 1.44 MB floppy disks 2) insert disk 1 and switch to the floppy drive 3) execute "disk1.exe", this will unpack "disk1.exe" on disk1 4) insert disk 2, and execute "disk2.exe" 5) insert disk 1 (your current drive should still be the floppy drive) 6) type "install" and select the software products you want to install, this will load the software to your harddisk 7) if you want to install DOS Internet applications such as NCSA telnet, see the "README.DOC" on disk 1 for instructions Important: the following steps assumes that: 1) the DOS packet driver for your network board has been properly installed 2) you know your machine's IP number 3) you know the IP domain name, local netmask, IP number for the local gateway, and IP number for the local nameserver STEP 2: Installing the Trumpet Winsock driver: Note that this Winsock driver is NOT freeware but is distributed under the shareware philosophy. 1) add the Winsock directory to your path list in the "autoexec.bat" 2) if you are going to use SLIP, then reboot and proceed with 5) 3) add a line in your autoexec.bat that will load the Winsock driver immediately after your DOS packet driver, e.g.: c:\winsock\winpkt.com 0x62 (make sure to supply the same software interrupt number that you gave to the DOS packet driver) 4) reboot and check whether both drivers load successfully 5) start Windows and add "tcpman.exe" as a new program item 6) double click "Tcpman" and enter the information you are asked for (given the assumption above, the "packet vector" would be "62") STEP 3: Installing NCSA's Mosaic: 1) make sure that you have a Windows image viewer program installed 2) add the Mosaic directory to your path list in the "autoexec.bat" 3) copy the "mosaic.ini" file in your Windows directory and modify it according to your system configuration 4) start Windows and add "mosaic.exe" as a new program item That's it! Double click "Mosaic" and you should be on the Web. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION ================ PART 12: What are URLs ---------------------- This is the twelfth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. One of the most powerful aspects of the World-Wide Web is that it allows to access nearly any kind of data and network service. In order to locate such object on the Internet, the Web uses Uniform Resource Locators (URLs). URLs specify the access method, the address of the host computer, the port to connect to, and the path and name of the object. The format is: access method://host.domain[:port]/path/objectname Examples may look like this: http://test.unibas.ch:80/ provides access to a WWW server on port 80 ftp://guru.cern.ch/ provides access to an anonymous ftp server gopher://gopher.beta.test.unibas.ch/ provides access to a gopher server news:embnet.net-dev provides access to a news server (Note the absence of "//") telnet://test.unibas.ch opens an interactive telnet session file://test.unibas.ch/file.txt retrieves a text file from a remote machine file://localhost/device1/document.txt opens a text file or WWW document on device1 of a local UNIX or VMS system (Note that some browsers require the file suffix "html" to recognize a WWW document) file:///disk1/document opens a text file or a WWW document on disk1 of a local Mac (Note the use of "///") file:///C|/document.txt opens a text file or a WWW document on drive C: of a local DOS machine (Note the use of "///" and "|" WWW browsers let you specify URLs either directly or by selecting hypertext in the WWW document you are presented with. This will cause the browser to send a request to open the URL specified. Selecting hypertext in a WWW document will take you to related information, which may also have pointers to related information. So don't worry if you don't know the URL of the information you want, simply follow the logical chain of hypertext links to get the information. Some URLs of starting points for an exploration of Web resources that might be of interest for biologists, will be included in the following part of this series of postings. Florian Eggenberger EMBnet Switzerland WWW INTRODUCTION: Part 13

WWW INTRODUCTION

PART 13: Exploring the Web

This is the thirteenth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. Previous parts of this series of postings are available on embnet.net-dev and (for a short period) also here.

The Web provides a vast array of information. But there is no easy way to access this information if you don't know where to search for. This document is intended to give you some starting points for an exploration of Web resources currently accessible.

Services that provide pointers to Internet resources of general interest include the World-Wide Web Virtual Library , the Internet Resources Meta-Index , Joel's Hierachical Subject Index , and the Nova-Links.

A List of WWW services for biologists is maintained by Keith Robinson at Harvard University. Reinhard Doelz 's Europeen Biology Gopher tree and Don Gilbert's IUBio Archive provide links to biology-specific gopher services.

Molecular Biologists might be interested in the information available from the Johns Hopkins University Bioinformatics Web server , the ExPASy WWW server in Geneva, and the WWW services of the European Molecular Biology Network, EMBnet. Further useful services can be accessed via the WWW server of EMBnet Switzerland in Basel.

  • Guides and Tutorials available on the Web include:

    The Web is expanding quite rapidly. So, read the articles in the newsgroups comp.infosystems.www and bionet.announce to find further useful sites.

    Florian Eggenberger

    EMBnet Switzerland WWW INTRODUCTION ================ PART 14: What is HTML --------------------- This is the fourteenth part of a series of postings describing the concept of the World-Wide Web and guiding anyone who is interested in obtaining and setting up the software required to access the Web. HTML stands for Hypertext Markup Language and is the standard language of the World-Wide Web. HTML files usually end with the suffix "html" and are in ASCII (plain text) format though the access protocol of WWW allows 8 bit transfer. HTML documents are composed of elements that start with a tag, followed by the content of the element, followed by the ending tag. The tags contain information about properties of the whole document, about the format of the document, and about hypertext links to other objects. Some elements have neither content nor ending tags. They are called empty. The format of non-empty elements is: content HTML is case-insensitive. "" is equivalent to "" or "". Spaces, tabs, and carriage returns are not significant in HTML. WWW browser ignore any carriage return and multiple spaces are collapsed into a single space unless the 

     tag has previously been used (see 
below).

Elements used in HTML include:

 text 
  specifies the title of a document
 text 
  specifies the nth level of heading
  (where n is a number between 1 and 6)

    
  specifies the end of a paragraph

       
    •  first item 
    •  second item 
    
  specifies an unnumbered list of two items

       
    1.  first item 
    2.  second item 
    
  specifies an numbered list of two items

     text 
    
  specifies preformatted text
  (causes spaces, new lines, and tabs to be significant)
 linkname 
  specifies a link to a document,
  makes the "linkname" the hyperlink to the document to be linked

  specifies an image to be included in the document
  (this is an HTML extension)

HTML documents can be created by any text editors, but if you are going 
to create a lot of WWW documents, then a HTML editor is recommended. An 
example of a simple HTML document has been provided in the previous part 
of this series of postings. You may want to modify this document. So, go 
ahead and open the document using a WWW browser. View the source code, 
make changes according to your preferences, save the changes and reload 
the document to make your changes effective (how to do this, depends on 
the browser software you have installed on your machine).

More information on HTML is available through
 
this hyperlink. 


Florian Eggenberger
EMBnet Switzerland



WWW INTRODUCTION
================

PART 15: Customizing WWW
------------------------

This is the fifteenth part of a series of postings describing the 
concept of the World-Wide Web and guiding anyone who is interested in 
obtaining and setting up the software required to access the Web.

Most browsers come with a hardcoded address of the document to start 
with (called Home Page). This is often a document that does not provide 
direct links to the information you want. Accessing the information by 
following the hyperlinks provided, consequently, may take some time. A 
much quicker route to the World-Wide Web is to start at your own Home 
Page. This will speed up data retrieval and let you work much more 
efficiently.

Like any WWW document, Home Pages are written in HTML. Consult the 
previous part of this introduction to see what HTML is. The HTML 
elements described therein are completely sufficient to write a simple 
Home Page. So, go ahead and create your own Home Page. Specify title and 
heading of the document and include a list of links to sites that 
provide the information you want. (Some links that might be of interest 
for biologist have been provided in part 13 of this series of postings.) 
Save your document as "text only", open it with your WWW browser and 
reedit the source, if desired. 

How to start WWW with your own Home Page depends on the browser software 
and operation system running on your machine. The following description 
apply to those browsers for which installation hints have been provided 
in previous parts of this introduction. 

CERN's LineMode browser, Lynx, Mosaic for XWindows
1) Under UNIX
Use the shell variable WWW_HOME to specify the URL of your Home Page. 
Add a line in the appropriate start-up file:
  when running ksh:  export WWW_HOME=URL
  when running csh:  sentenv WWW_HOME URL
2) Under VMS
Use the logical name WWW_HOME to specify the URL of your Home Page. Add 
a line in your startup file or in the command file that invokes WWW:
  $ define "WWW_HOME" "URL"

Mosaic for Macintosh
Start Mosaic. Select "Preferences..." from the "Options" menu. Replace 
the default Home Page settings by the URL of your Home Page.

Mosaic for Microsoft Windows
Quit Mosaic. Open the "mosaic.ini" file in the "Windows" directory. 
Replace the URL of the default Home Page by the URL of your Home Page.

Most browser software products provide various other parameters that can 
be configured. To change the default settings of these parameters:

* using Lynx: type "o"
* using MacMosaic: select "Preferences..." in the "Options" menu
* using WinMosaic: open the "mosaic.ini" file in the "Windows" directory
* using XMosaic: select the "Options" menu

Go ahead and make changes according to your preferences.


Florian Eggenberger
EMBnet Switzerland


+------------------------------+--------------------------------+
|  Florian Eggenberger, Ph.D.  |  eggenber@comp.bioz.unibas.ch  |
|  Biocomputing                |  eggenberger1@urz.unibas.ch    |        
|  University of Basel         |  Fax  +41 / 61 267 20 78       | 
|  Switzerland                 |  Tel  +41 / 61 267 22 47       | 
+------------------------------+--------------------------------+




Date: Wed, 16 Feb 94 15:19:28 +0100
From: eggenber@comp.bioz.unibas.CH
Subject: WWW INTRODUCTION: Part 17

WWW INTRODUCTION
================

PART 17: Glossary
-----------------

This is the seventeenth and final part of a series of postings 
describing the concept of the World-Wide Web and guiding anyone who is 
interested in obtaining and setting up the software required to access 
the Web.

The whole series is available on the newsgroup  
embnet.net-dev  and (for a short period) also  here. 
 
    

The World-Wide Web has its own terminology. Here is a brief explanation 
of terms used in previous parts of this WWW introduction:

AIX - UNIX based operation system developed by IBM

Anonymous FTP - FTP that allows to retrieve files from public sites

Archie - a network tool that searches anonymous FTP sites for files

ASCII - American Standard Code for Information Interchange

BITNET - "Because It's Time Network", an academic collective of networks

Browser - a client that allows to access the World-Wide Web

CERN - European Centre for Particle Physics, Switzerland

Client - a program that can request services from a server

EARN - European Academic Research Network

EMBnet - European Molecular Biology Network

Ethernet - network standard for hardware and data links levels

FTP - File Transfer Protocol, Internet standard for transferring files

Gopher - network tool that allows to access various types of data

Host - a computer that is directly connected to the network

HTML - Hypertext Markup Language, standard language of WWW

HTTP - Hypertext Transfer Protocol, standard protocol of WWW

Hypermedia - multimedia hypertext

Hyperlink - relationship between two objects on the Web

Hypertext - text that contains pointers to other text

Internet - international collective of networks running TCP/IP

IRIX - UNIX-based operation system developed by SGI

NNTP - News Network Transfer Protocol, method to transfer News articles

Protocol - the rules two computers must follow to exchange messages

Server - a program that provides a service to a client

SLIP - Serial Line Internet Protocol

SMTP - Simple Mail Transfer Protocol

TCP/IP - Transmission Control Protocol / Internet Protocol

TELNET - Internet standard protocol for remote terminal connection

ULTRIX - UNIX-based operating system developed by DEC

UNIX - operating system developed by Bell Laboratories

URL - Uniform Resource Locator

VM - operating system developed by IBM

VMS - operating system developed by DEC

WAIS - Wide Area Information Server


Florian Eggenberger
EMBnet Switzerland


ACKNOWLEDGEMENTS
----------------

EMBnet Switzerland is a project funded by the University of Basel, the 
Swiss National Science Foundation, and industrial contributions from 
Digital Equipment and Silicon Graphics (in alphabetical order).

+------------------------------+--------------------------------+
|  Florian Eggenberger, Ph.D.  |  eggenber@comp.bioz.unibas.ch  |
|  Biocomputing                |  eggenberger1@urz.unibas.ch    |        
|  University of Basel         |  Fax  +41 / 61 267 20 78       | 
|  Switzerland                 |  Tel  +41 / 61 267 22 47       | 
+------------------------------+--------------------------------+

END-----------------cut here------------------