RETURN to the CHEM 498C Home Page

Chemistry on the Internet

Prof. Thomas C. O'Haver
Department of Chemistry and Biochemistry
University of Maryland
College Park, MD 20742
Phone: (301) 4051831
http://www.wam.umd.edu/~toh/
to2@umail.umd.edu

This document describes the main Internet information access tools and lists some of the sites that have chemistry and other science-related material.

Listserv discussion lists
If you have an e-mail account, you can participate in e-mail discussion groups called "listserv lists". There are several in the chemistry area:

CHEMED-L@UWF.CC.UWF.EDU  Chemistry Education
CHMINF-L@iubvm.BITNET    Chemical information sources
CHEMCORD@UMDD.UMD.EDU    General Chem. Coordinators Discussion
CHEMCONF@UMDD.UMD.EDU    Scheduled online chemistry conferences
CHEMCOM@UBVM.BITNET      Chemistry in the Community Discussion
CHEME-L@PSUVM.BITNET     Chemical Engineering
ICS-L@UMDD.UMD.EDU       International Chemometrics Society

(The part before the @ sign is the list name and the part after the @ sign is the host address). The general method for subscribing to most listserv lists is to send a message to LISTSERV@hostaddress in which the first line of the message body is "SUB listname yourname", where listname is the name of the list and yourname is your full name. For example, if you want to subscribe to the chemical education list and your name is John Doe, send a one-line email message to LISTSERV@UWF.CC.UWF.EDU, with a blank subject line, containing the message "sub CHEMED-L John Doe". Once your subscription is procsessed, you would send messages to the list by sending them to the list address (e.g. to CHEMED-L@UWF.CC.UWF.EDU. To unsubscribe (cancel your subscription), send the message "signoff CHEMED-L" to LISTSERV@UWF.CC.UWF.EDU.

Most listserv lists save all their past messages and allow you to search for messages that mention a specific keyword. For example, if you want to know if anyone in the CHEMED-L list has ever mentioned, say, benzene, send the following 6-line message to LISTSERV@UWF.CC.UWF.EDU:

//
Database Search DD=Rules
//Rules DD *
Search benzene in CHEMED-L
Print all
/*

The LISTSERV host will send to you by return e-mail all messages that contain the word benzene. You don't need to actually type this gibberish each time - keep a copy in your computer's "Note Pad" and just edit it for your keyword and Copy and Paste it into the outgoing mail message. (Note: you may not even have to subscribe to a discussion list in order to be able to search it in this manner).

The other listservs operate in the same manner; just substitute the name of the list for CHEMED-L and the host name for UWF.CC.UWF.EDU in the above example.

Usenet Newsgroups
Newsgroups are topic-specific discussion groups, also called netnews or just news.

To access newsgroups from a networked computer (e.g. in a WAM or Open lab), look for a Newsreader client such as InterNews. These local client newsreaders have a point-and-click interface that you can generally figure out by playing around. To access newsgroups when you are dialing in with a conventional terminal program, type "tin" at the Unix system prompt and press return. Press return until you get to the main screen that says Group Selection at the top. If you know the name of a newsgroup you wish to look at (e.g. sci.chem, which deals with chemistry), type "g sci.chem" and press return. If you wish to find whether there is a newsgroup whose name contains a certain keyword, press "y" to "yank" in all newsgroups, then type a "/" followed by the keyword and the computer will search for any newsgroups whose names contain that keyword. (Newsgroup names are usually abbreviated: e.g. sci for science, bio for biology, edu for education; chem for chem istry, comp for computer, etc.) Press / and return again to go to the next match. Press "s" to subscribe to that group (i.e., add it to your Group Selection screen), "u" to unsubscribe. To read a newsgroup, use the arrow keys to move in, out, up and down. Press Q to quit. (Hint: "news.answers" has a good collection of "frequently asked questions" documents).

Here is a list of some chemistry and science-related groups.

sci.chem                         Chemistry and related sciences
sci.chem.organomet               Organometallic chemistry
sci.chem.electrochem             Electrochemistry
sci.chem.labware                 Chemical labware
sci.edu                          Science education
bionet.                          Biological sciences (many sub-groups)
sci.physics.                     Physics (several sub-groups)
sci.med.physics                  Medical physics
alt.sci.physics.                 Physics (several sub-groups)
sci.engr.biomed                  Biomedical engineering
sci.engr.chem                    Chemical engineering
alt.internet.services            Information about services available
news.announce.newusers           Explanatory postings for new users
news.answers                     Repository for periodic USENET FAQs

Journal article search (UnCover).
At the Unix system prompt type "telnet victor", then "PAC", then "8", press enter until you see the VICTOR main menu. Select

Journal Indexes/Article Delivery
UnCover (table of contents/article delivery).

Then enter the 14-digit barcode or OCR number from your library ID card and follow the further on-screen instructions. UnCover searches operate just like U. of Md. card catalog searches. These searches return bibliographic citations but also offer to FAX articles to you at a cost of typically $8 -12 per article (paid via credit card).

World Wide Web
World Wide Web is a global network of linked multimedia "hypertext" documents. Each docu ment contains highlighted (underlined or color) words that serve as "hot links" to other documents. You navigate through the documents simply by selecting the links that interest you. The best way to explore it is to use Netscape, a multimedia WWW brouser that supports embedded graphics and sounds.

What is Netscape?
Netscape is currently the most popular graphical World Wide Web (WWW) browser that is used to view, save, and print multimedia documents that are resident on Web servers anywhere in the world. Netscape is free for academic users; it can be downloaded from the Internet, or you can get a copy on diskette from one of the book/disk combos on Internet and WWW found in the computer sections of better bookstores.

How can I access Netscape?
Netscape is a "local client", a program that runs on your local desktop computer and that accesses the Internet through some sort of network connection. Netscape is easiest to use if your desktop computer is already connected to a local area network (LAN) that has a "gateway" to the Internet. If you are already using other "TCP/IP" clients, such as NCSA Telnet or or Eudora, then it is likely that your are already connected in this way. In that case, all you have to do is to put a copy of Netscape on your hard disk and double-click on it.

Can I access the World Wide Web when I dial in to my UNIX shell account?
Probably. The most popular host-based text-mode Web client is "lynx". Just type lynx at the host system prompt. If that does not work, ask your host system administrator to install lynx or some other WWW client.

Can I access Netscape when I dial in to my UNIX shell account?
Not directly. But it can be done, with the right software. This process is more complex that setting up Netscape on a LAN-connected computer, but it does give you a way to use Netscape at home, where you (probably) do not have a LAN gateway. Basically you'll need a "SLIP" or "PPP" account from your Internet service provider, plus a couple of other pieces of software for your desktop computer: e.g. Trumpet Winsock for Windows 3.1, Dialup Networking for Windows 95, or MacTCP and InterSLIP or MacPPP for Macintosh.

How do I use Netscape ?
Just click! Active "links" are shown as underlined blue text or icons with blue outlines. Just click once on the link to follow it. Click the Back button to go back to the previous page and Forward to move forward again. Internet sites are described by an address in a standard form called a Universal Resource Locator (URL). Web page URLs begin with "http://". For example, http://www.wam.umd.edu/~toh/toh.html is a typical Web URL. To go to a specific URL, use the Open Location... menu item in the File menu and type or paste the URL into the resulting box. Saving and printing a Web page works just like a word processor (Save and Print are in the File menu). When you save you have the choice of "text" or "source". Use text if you plan to import the text into a word processor; use source if you plan to open up the file from within Netscape, using the Open File command.

Bookmarks
Bookmarks allow you to return easily to a previously-visited Web page. To create a bookmark to the page you are on, select Add bookmark from the Bookmark menu. This adds it to the Bookmarks menu (which gets longer and longer). To go to a previous bookmark, just select it from the Bookmarks menu. You can edit the bookmarks, delete them and change their names, by using the Edit bookmarks item. Bookmarks are stored on that machine only; if you access the Web from another computer, you will see a different set of bookmarks.

Downloading graphics
Downloading graphics is much easier if you are using version 1.1 or later of Netscape. In that case, just place the mouse pointer on the graphic, hold down the mouse button, and select Save the Image as... from the menu that pops up. This results in a standard "Save" dialog box. Alternatively, you can Copy Image, and Paste it into another application. Saved graphics are normally in GIF format, sometimes in JPG format. You can use a shareware graphics program such as Graphic Converter (Mac) or LView (Windows) to convert between formats.

Sounds and Video clips
Links to sound files (which usually have an ".au" or ".aiff" extension) can be played through your computer's speakers if you have a "sound player" application in the same folder as Netscape. A popular one for the Mac is SoundMachine, which can be downloaded from various sources. Sound files are often big. Links to digital video (movie) files, which usually have a ".mov" or ".mpg" extension, can be viewed if you have a "movie player" application. Popular ones for the Mac are Simple Player (for Quicktime movie) and Sparkle (for MPEG movies), both of which can be downloaded from various sources. Movie files are usually very large. An alternative to the use of separate helper applications is the use of Netscape plug-ins, which are downloadable (or commercial) software add-ons to Netscape 2.0 that allow multimedia content to be displayed directly on Web pages.

Extending Netscape for chemistry data types
Netscape has the ability to detect hypertext links to specialized data types and to launch a specified helper program or plug-in to view that data. Henry Rzepa of Imperial College (London) has exploited this idea in his online conferences and presentations and has extend the list of recognized special data types to include Adobe Acrobat files, molecular coordinates in ".pdb" (Protein Data Bank) format, structure drawings in ISIS/Draw format, etc. After installing the required helper programs or plug-ins (which for the above data types are freeware programs that can be downloaded from the Internet), and configuring Netscape accordingly, the user need only click on the hypertext link and the data are automatically downloaded and visualized. This allows the user to remain focused on the chemistry and not be distracted by the complexity of downloading. Once you have Netscape installed and running, you can use it to download helper applications and plug-ins for sound, video, molecular visualization, chemical structures, etc. See http://home.netscape.com/comprod/products/navigator/version_2.0/plugins/index.html for the latest plug-ins for Netscape. A great plug-in for chemistry is ChemScape Chime from MDL Information Systems (see http://www.mdli.com/).

How can I create my own home page on the Web?
It's easier than it looks! Web pages are just text files that are "tagged" with "HTML" symbols to represent structure and function. You can prepare Web pages in any text editor or word processor. The system of tags is very logical and easy to learn. Perhaps the easiest way to learn is to look at the "source text" of existing pages - you can do this for any page on the Web just by selecting Source from the View menu, which displays the source text with all its tags in a separate window. Compare this to the rendered page in the main Netscape window, copy the parts you want to, and you will begin to learn in a practical way how it all works. For graphics, use a shareware graphics program such as Graphic Converter (Mac) or LVIEW (Windows) to convert your graphics into GIF or JPG format, then save them in the same directory as your HTML text. Finally, you need to upload all your HTML and graphic files to a Web server so they will be accessible worldwide. For more info see http://www.wam.umd.edu/~toh/Handouts.html.

Using Netscape in Local mode
Netscape can open files stored on your hard disk or on a LAN file server, even if it is not connected to the Internet, by using the Open File command. Text files that contain "HTML" tags will be rendered just like an on-line Web page. In this way you can test the formatting of Web pages that you or your students are creating before they are submitted to the server. This works even on a machine that is not actually hooked up to the 'net. In fact, Netscape can be used an a simple but economical multi-platform multimedia delivery system - it's free, available for Macs and PCs, uses the exact same file formats on all platforms, and has the added benefit that the files are ready to go on-line when you get space on a Web server.

Some useful URLs to get you started
The WWW is growing and changing so rapidly that it is impossible for a print publication such as this newsletter to keep up to date. The following URLs were checked for accuracy and were all operational on May 1, 1996. By the time you read this, some of them may have changed and many new ones will certainly exist. Although the Web is still very new, many chemists are already beginning to exploit its capabilities for chemistry information and education.

Use the Open Location... menu item in the File menu and type or paste these URLs into the resulting box:

Chemistry and chemistry education

Internet Resources for Chemistry
http://www.wam.umd.edu/~toh/Chemistry.html

Sites "approved" by the Journal of Chemical Education
http://jchemed.chem.wisc.edu/JCEWWW/WWWReview.html

General collections of links

Very large collection of links, organized by subject
http://www.yahoo.com/

Large Collection of Science and Math Internet Resources http://www.wam.umd.edu/~toh/MathScience.html

Software and instructions for Web construction and application

HTML Developers Reference Page http://oneworld.wa.com/htmldev/devpage/dev-page.html

"How to Make a Web Page", a hypermedia tutorial
http://www.wam.umd.edu/~toh/HowToMakeAWebPage.html

Macintosh software to access the Web http://forum.swarthmore.edu/workshops/workshop.software.html

PC software to access the Web
http://forum.swarthmore.edu/workshops/pc.html http://ac.dal.ca/~dong/table.htm

Graphics programs for both platforms http://www.public.iastate.edu/~stark/gutil_sv.html

Sound players and related programs http://www.wavenet.com/~axgrindr/quimby4.html

Converting various file formats for use on various platforms http://www.mps.org/~ebennett/

Educational application of the Web http://hakatai.mcli.dist.maricopa.edu/authoring/index.html http://ccat.sas.upenn.edu/teachdemo http://www.covis.nwu.edu/Papers/k12web.html

Notes:
1. You can have multiple TCP/IP local clients running simultaneously; e.g. you can be running Telnet and Netscape at the same time, if your machine has enough RAM memory available.

2. Netscape can have more than one window open at a time, each one accessing a different Web site. Select New from the File menu to generate another window.

3. Netscape has built-in help files and even a User's Manual; see the Help menu.

File Transfer Protocol (FTP)
FTP is a method of downloading (receiving) files from remote computers to your local machine and for uploading (sending) files your local machine to a remote computers over the Internet. You can perform FTP using either a host-based client program (e.g. the "ftp" command in Unix) or a local client such as Fetch for the Mac or WS_FTP.EXE for the PC. There is an important difference between using a host-based and a local FTP client: using a host-based program transfers files to and from the file space on your Unix account, whereas using a local client transfers files to and from the file space on your desktop PC's hard disk.

Many host system run by academic and government organizations run FTP servers that allow "anonymous" access to certain files, allowing anyone to download them. You don't actually have to have an FTP client program just to download files from anonymous FTP servers; it can also be done quite conveniently from Netscape. On the other hand, uploading files (e.g. from your desktop PC to your WAM account space) requires either an FTP client program or the use of "zmodem" or "kermit" (file transfer protocols that work over ordinary dial-up connections). See http://www.inform.umd.edu/UMS+State/UMD-Projects/MCTP/Technology/software.html for a collection of links to downloadable science and chemistry software.

Software Sources
Local clients for gopher, WWW (e.g. Netscape), FTP, Netnews, and e-mail are available commercially, as freeware and shareware (which can be downloaded from the Internet without charge), and on floppy disks and CD-ROMs that come with some books about the Internet. Check out the computer section of your local bookstore.

This page is maintained by Tom O'Haver , Department of Chemistry and Biochemistry, The University of Maryland at College Park. Comments, suggestions and questions should be directed to Prof. O'Haver at to2@umail.umd.edu.