From owner-www@net.bio.net Tue Aug 16 23:00:00 1994 Path: biosci!biosci!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software.www Subject: test of bionet.software.www moderation Date: 16 Aug 1994 23:47:22 -0700 Organization: BIOSCI International Newsgroups for Biology Lines: 9 Approved: bio-www@comp.bioz.unibas.ch Distribution: world Message-ID: <32sbpq$6gg@net.bio.net> NNTP-Posting-Host: net.bio.net test of bionet.software.www moderation; please await the formal opening announcement before attempting to use this newsgroup. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-www@net.bio.net Thu Aug 18 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: doelz (Reinhard Doelz) Subject: WWW: INSTRUCTIONS Message-ID: <1994Aug19.152731.14854@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 19 Aug 1994 15:27:31 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 87 The Newsgroup bionet.software.www is archived, as all newsgroups, at the net.bio.net site, and available to be browsed like any other newsgroup archive (see previous posting). This newsgroup, additionally, keys contributions in 'html' documents so that links are resolved in the 'hypertext' system, and may point to the contribution of the originators, or the subject of the message, respectively. This server runs at the Biocomputing Facility of Basel University. The URL for this server is ============================================ http://www.ch.embnet.org/bio-www/info.html ============================================ and has the following structure: o Contributions to the Group [this is a chronological, marked-up page] o Servers [for services affecting retrieval or search engines, both announcements and updates] o Archives [for archives of data and any kind of massive information] o Descriptions [for site descriptions who update or announce a site running a server] o Discussion [any discussion on topics above, as well as implementation or systematic issues. ] o Keith Robison's WWW Server Index page [Link to the site where all bio-www servers are registered]. To access the information provided by this and 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. 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. Specifically, WWW browser software is available from FTP.NCSA.UIUC.EDU in the /Mosaic directory, or VMS versions possibly on info.cern.ch. Regards Reinhard Doelz -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ | Klingelbergstrasse 70 | EMBnet embnet@ch.embnet.org | |CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch | +---------------------------+------------- http://beta.embnet.unibas.ch/ From owner-www@net.bio.net Thu Aug 18 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: moderate (Bio-WWW moderator @ EMBnet Switzerland) Subject: BIOSCI:EMAIL/USENET INSTRUCTIONS Message-ID: <331mqt$6pk@mserv1.dl.ac.uk> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 19 Aug 1994 07:26:21 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 191 The BIO-WWW/bionet.software.www newsgroup is ready for operation. PLEASE NOTE that many USENET sites do not allow automatic creation of new USENET groups!!! If you do not see bionet.software.www in your newsreader within another day or two, ask your news system administrator to act on our "newgroup" message to enable the group at your site. We have already done several tests and are certain that the group is currently propagating around the network. If he/she can not find the newsgroup message, have them retrieve the bionet checkgroups message from the anonymous FTP area on net.bio.net in pub/BIOSCI/doc/bionet-checkgroups-msg. This file contains the latest list of bionet USENET newsgroups and can be used to update your bionet distribution. If the newgroup did not arrive at your site, it may also be necessary for your news administrator to contact the upstream computer site providing you with your newsfeed and determine if they acted on the newgroup message. Subscribing to this group: -------------------------- IF YOU USE USENET NEWS: you need do nothing other than participate in bionet.software.www when it appears in your newsreader. Depending upon your news software, this may entail you having to answer a prompt indicating that you want to subscribe. You might also try the command "g bionet.software.www" in rn-like newsreaders. IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: please send the word help in the body of your message to MXT@dl.ac.uk to retrieve general server usage instructions. To subscribe to the BIO-WWW list, first be sure that you are sending mail from the address at which you wish to receive news postings, and then send the command SUB bionet-news.bionet.software.www to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and added to the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: log in to the computer account in which you would like to receive mail (not an account that you use infrequently) and send a mail message to the Internet address biosci-server@net.bio.net Leave the Subject: line of the message blank and enter the following line into the body of the mail message: subscribe bio-www This message will be automatically read by our computer and your e-mail address will be extracted from the mail header and added to the list. Canceling your subscription: ---------------------------- IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: first be sure that you are sending mail from the address at which you signed up to receive news postings, and then send the command (in the body of your mail message) UNSUB bionet-news.bionet.software.www to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and removed from the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: send a message to biosci-server@net.bio.net exactly as described above for subscribing except include the text unsubscribe bio-www in the body of the message. Please be sure to send the message from the account whose address matches the one on the list. If your address differs, we will be notified automatically and will remove you manually from the list if we can determine what was your old address. Please contact biosci-help@net.bio.net if you have problems. IF YOU HAVE A PROBLEM: ---------------------- Please send a message to one of the following addresses depending upon your location Address Location ------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim and someone on the staff will help you. PLEASE DO NOT send mail to our personal e-mail addresses as this will delay a response to your request for help. How to post a message to the group: ----------------------------------- If you use news, simply post a message into bionet.software.www. Be sure to set your "distribution" to either bionet or world or else the message might not leave your site!! NOTE - this group is moderated and posts will not appear automatically until the moderator receives and approves them. To post by e-mail, mail your message to one of the following addresses depending upon your location: Posting Address Location --------------- -------- bio-www@daresbury.ac.uk Europe, Africa, and Central Asia bio-www@net.bio.net Americas and the Pacific Rim PLEASE DO NOT SEND SUBSCRIPTION REQUESTS TO THE POSTING ADDRESSES as you will bother everyone on the newsgroup!!! How to reply to a message on the group: --------------------------------------- If you are using a newsreader, simply use the reply or follow-up command on your newsreader (these vary from program to program) to send either private or public replies. If you are using e-mail, replies to messages that you receive will *NOT* be automatically returned to the group. This is the standard for Internet mailing lists as opposed to BITNET LISTSERVs which often send all replies back to everyone. You must be certain that your reply contains either of the two newsgroup posting addresses above in your message header if you want to share it with everyone on the group. Otherwise in most cases your reply may go back to only the original poster of the message to which you are replying. ALWAYS be certain that you examine the address on your messages before you send them!!! Once a message is sent there is no way to cancel it or bring it back!!! Some non-Internet compliant mail systems may attempt to send replies to our error-trapping address called BIOSCI-REQUEST. If yours does this, please be sure to readdress your message to bio-www@net.bio.net or bio-www@daresbury.ac.uk if you want to send it to the newsgroup. How to look at archives of the list: ------------------------------------ Archives for BIO-WWW/bionet.software.www are kept in the anonymous FTP account at net.bio.net [134.172.2.69]. Look in the directory pub/BIOSCI/BIO-WWW for posting archives. Each file is assigned a date such as 9312 for December 1993. Please note that ours is a UNIX system and all file and directory names are case-sensitive, i.e., upper case file names are different from lower case names. You can also access these same files via Gopher if you start a gopher session using net.bio.net as your gopher server. Gopher also allows you to view the individual messages within each monthly archive file. The files are in the BIO-WWW directory. Postings to bionet.software.www are also WAIS indexed and can be searched via either gopher or WAIS at our site. In gopher the option at net.bio.net is "Search Bionet USENET Articles" and in WAIS one should use the WAIS source biosci.src. This is a WAIS index of all BIOSCI/bionet messages including this newsgroup. Please see the BIOSCI FAQ for details. The FAQ can be requested from biosci-help@net.bio.net. Finally, you can also access the archives via WWW/Mosaic. The URL is gopher://net.bio.net/. Once again, if you have any administrative questions that require personal assistance, please address them to biosci-help@net.bio.net in the U.S. or biosci@daresbury.ac.uk in the UK. Best wishes for a successful newsgroup! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-www@net.bio.net Fri Aug 19 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: doelz (Reinhard Doelz) Subject: Welcome to bionet.software.www Message-ID: <1994Aug20.074456.4282@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Sat, 20 Aug 1994 07:44:56 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 62 As nothing is more temporal then the availability of free, highly-valued, massive and seamless data access, this newsgroup to announce changes, updates, developments and questions in the area of networked information access and retrieval has been established. The Newsgroup bionet.software.www is archived, as all newsgroups, at the net.bio.net site, and available to be browsed like any other newsgroup archive (see previous posting). This newsgroup, additionally, keys contributions in 'html' documents so that links are resolved in the 'hypertext' system, and may point to the contribution of the originator, or the subject of the message, respectively. This server runs at the Biocomputing Facility of Basel University. The URL for this server is http://www.ch.embnet.org/bio-www/info.html and has the following structure: Contributions to the Group [this is a chronological, marked-up page] - same, sorted by four sub-areas Keith Robison's WWW Server Index page [Link to the site where all bio-www servers are registered]. bionet.software.www encourages all interested parties to communicate their information on this subject. Its purpose is to announce, and inform on, new achievements on information servers, archives and resources which offer data and/or services in the biology/medicine/related area which can be accessed via electronic networked information retrieval software. Proposals and discussions of these with respect to new strategies and tools, as well as links to contributions dealing with issues of performance and quality of networked information in Biology shall inform and invite to participate. The newsgroup is moderated in order to allow noise reduction and mark-up for the hypertext version. If you submit an article and would like to include links, keep in mind that these are possible for www, gopher, ftp and any other gateway you might have built on these protocols yourself. We will try to incoporate links into the posted text on the W3 server wherever possible. If you need help to set up these links in your posting let us know. (Address info@ch.embnet.org). The 'chronological' listings will get out of date sooner or later. We currently anticipate to keep montly grouped html pages (volume permitting), and possibly introduce subareas to the four main areas of topics if required. As our resources are possibly limited, we will validate html links on a periodic basis but will not be able to ensure that all links are always operable. Go ahead - let's make communication a success! Reinhard Doelz (Moderator) From owner-www@net.bio.net Fri Aug 19 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: steveh@howard.fhcrc.org (SteveHenikoff) Subject: New Blocks Database and Web server Message-ID: <9408181617.AA11548@howard.fhcrc.org> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Thu, 18 Aug 1994 16:17:37 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 30 ___________ ___________ ___________ |\ __________\ |___________| /__________ /| | | | | | | | | | | **********| |***********| |********** | | | | * BLOCKS | | W W W | | SERVER * | | | | **********| |***********| |********** | | \|___________|___________|___________|___________|___________|/ |\ __________\ /__________ /| | | | | | | | | Fred | | Research | | | | Hutchinson| | Center | | | | Cancer | | 1994 | | \|___________| |___________|/ We are pleased to announce that Blocks v. 8.0 is available for searching. This version is based on Prosite v. 12.0 which is keyed to Swiss-Prot 29. The new database consists of 2884 blocks representing 770 protein groups. Homology searches and block retrievals are carried out either by e-mail or by using Bill Alford's new Web server at http://www.blocks.fhcrc.org. Mosaic 2.x users now can search the Blocks Database, retrieve blocks and Prosite information or run Block Maker using the Web, with hypertext links from search results to Swiss-Prot, EMBL/GenBank and Medline via the ExPASy Web server in Geneva. For e-mail users, the current help file is available from blocks@howard.fhcrc.org by sending the word 'help' in the subject line. To search a protein (or DNA) sequence, send it in a standard format to the same address. Individual blocks and the corresponding Prosite entries are available using the 'get' utility or by keyword browsing using the gopher host, gopher.fhcrc.org. The full database may be obtained by anonymous ftp from ncbi.nlm.nih.gov in the repository/blocks/unix directory. From owner-www@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: slfink@netcom.com (Steven Finkelman) Subject: [Q] Newbie Question Message-ID: Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: NETCOM On-line Communication Services (408 261-4700 guest) Date: Sun, 21 Aug 1994 21:20:38 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 13 I am using a remote server. I have a pc, I dial into a pop as a terminal, and communicate with netcom. netcom communicates with the world. What software is there use html format pages? Is there a better terminal type I can set my emulator to than vt-100? (communication package is procomm plus v2.0 for windows) -- Steven Finkelman DATA/Massage slfink@netcom.com From owner-www@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: rsmith@DOT.IMGEN.BCM.TMC.EDU (Randall Smith) Subject: BCM Sequence Annotation Web Server Message-ID: <199408222147.QAA03041@DOT.IMGEN.BCM.TMC.EDU> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 22 Aug 1994 21:47:23 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 65 Announcing a new WWW Server: The BCM Sequence Annotation Server URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html Developed by Kanwal Gill, Brent Wiese, and Randall Smith Human Genome Center, Baylor College of Medicine, Houston TX USA We have created a "Sequence Annotation" WWW Server that allows researchers to add their own annotations to Entrez (NCBI) DNA and protein sequence reports. Our Annotation Server is intended as a method for investigators to easily share new information about sequences, e.g., new features, interesting sequence matches, domain identifications, etc. A user who wishes to make an annotation for an Entrez sequence will be given the chance to select an annotation type (eg coding region, variant, etc.). The user is then requested to enter a short annotation that will appear as an embedded link in an Entrez report. The annotator will then be prompted to enter an extended commentary which gives the further details about the annotation. The annotator may also enter some keywords that can be searched on and URL's that will lead to more information (eg, an entry in another database, a file of data on the annotator's home computer, etc). Only the annotations themselves are stored on our local server. When a user wishes to view an annotated record, our server requests a sequence report from the NCBI Entrez Server. The local annotations are then embedded within the returned report. As an initial entry, we have added several hundred annotations based on data kindly provided by Keith Robison. The annotations list probable coding regions within bacterial sequences that are not annotated as such in GenBank (see Table 2 of K. Robison, W. Gilbert and G.M. Church, "Large scale bacterial gene discovery by similarity search", Nature Genetics 7:205, 1994). We invite the biological community to use the server to view this data as well as to add data of their own. Users wishing to view the data need only the URL listed above and a graphical WWW browser such as Mosaic or Chimera. Users wishing to add data would be well-advised to also prepare the text of their annotation and extended commentary as well as to have their URL's (if any) in mind before beginning. Extensive on-line help is provided for both types of users. Suggestions and comments regarding how the server can best meet the needs of the biological community are welcome. There is a comments form provided in the server for typing in your comments. Comments may also be emailed to Randall Smith at rsmith@bcm.tmc.edu. ------------------------------------------------------------------------ Randall F. Smith Human Genome Center Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine Houston, TX 77030 USA rsmith@bcm.tmc.edu 713-798-4735; FAX: 713-798-5386 ------------------------------------------------------------------------ From owner-www@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: doelz (Reinhard Doelz) Subject: Re: [Q] Newbie Question Message-ID: <1994Aug23.095811.28825@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 23 Aug 1994 09:58:11 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 73 Steven Finkelman (slfink@netcom.com) wrote: : I am using a remote server. I have a pc, I dial into a pop as a terminal, : and communicate with netcom. netcom communicates with the world. Rephrasing, "I can use electronic mail and a VT100 terminal type. Can I use WWW? " Answer 1 - electronic mail: The option to receive HTML files by electronic mail requires that you run a program which allows for 'local' loads of HTML files. This means that any file which is in html can be loaded from disk, and displayed nicely. This is a _formatting_ process. As soon as you access a link which is pointing to a http or any other resource which is unavailable to your station interpreting the file locally, you will fail. Consequence: Yes you can read HTML files if received from electronic mail. However, the 'surfing on the net' requires that you have interactive access to the internet with a suitable client program called 'WWW browser'. Answer 2 - VT100: Despite the fact that 'Mosaic' is much nicer to use and allows the display of in-line images and various goodies associated with graphics, the < a href=http://info.cern.ch/hypertext/WWW/Lynx/Status.html> LYNX browser allows you to utilize plain VT100 type of communications. The display of graphics *in-line* is not possible and you have to hope that people used something as a replacement (e.g., the 'ALT' directive like the following: + This will have displayed the graphics 'gif' as in-lined image but on LYNX it will be visible only as '+' character. If it were an image then this would be a hypertext link to a external image, and, depending on how LYNX is configured, it can possibly handle this by archiving the file on disk and allowing a conversion into a printable format. Consequence: You can possibly run WWW in very convenient way on VT100 if you do not require clickable images (type ISMAP) or in-line images (those pages which come with graphics) that do not have a textual representation. LYNX is used my many people out there and it runs on many platforms. : What software is there use html format pages? If you run a WWW browser locally, there is the page at Cern which lists all possible clients, including those for Mac and PC. : Is there a better terminal type I can set my emulator to than vt-100? : (communication package is procomm plus v2.0 for windows) There is no ultimate need to do so - VT100 is fine for LYNX, and Mosaic is graphics-driven anyway. regards Reinhard -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ From owner-www@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: lloyd@bruce.cs.monash.edu.au (Lloyd Allison) Subject: Aspects of Sequence Alignment Message-ID: <9408220004.AA00493@dec31> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Mon, 22 Aug 1994 00:04:23 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 13 Is this of interest for bionet.software.www? I have a page on some aspects of sequence alignment, multiple alignment, evolutionary trees, mapping and related algorithms and theory at: CS and MolBio There is also a bibliography of misc' references and www sites at: LA bibliography Lloyd ALLISON Central Inductive Agency, Dept. of Computer Science, Monash University, Clayton, Victoria 3168, AUSTRALIA tel: 61 3 905 5205 fax: 61 3 905 5146 email: lloyd@cs.monash.edu.au world wide web: LA home From owner-www@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: doelz (Reinhard Doelz) Subject: A suggestion for writing links in bionet.software.www (Re: How to Message-ID: <33cqp9$5r6@mserv1.dl.ac.uk> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Tue, 23 Aug 1994 12:41:13 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 48 > I DO need help though Ok, here is how it goes. You write a normal text document as you would write an eMail contribution. Then, we suggest that you use a new line for each hypertext line you insert, in order to have it readable as well in a non-html'ed environment.

(the insertion of 'p' tags blows up the text as it is useful to html'ization but might be confusing to ASCII type readers. We will insert these on the announcement or contribution of yours.)

The use of blank lines (here was one) is recommended to structure the text for non-HTML environments. As an example, if you refer to the NCBI file server this line is fairly readable. Similarly, a link to Don Gilbert's Gopher would make a link to a Gopher easily readable. Last, normal hypertext is Keith's server as an example for a meta index. If you would like to write a document which is suitable to be large enough that you can use internal pointers, those do not need the http prefix (in fact, they would hurt, as they avoid to approach the local document as they point outside rather than to internal notes. To point to the name 'note' as above, it were sufficient to se a simple internal pointer like this one. One last note; depending on your environment the link to news bionet might or might not work, depending on your news configuration.

Regards Reinhard (PS: There is a good primer at NCSA on setup of HTML pages and sophisticated details. ) +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ | Klingelbergstrasse 70 | EMBnet embnet@ch.embnet.org | |CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch | +---------------------------+------------- http://beta.embnet.unibas.ch/ From owner-www@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: guilford@salus.med.uvm.edu (William H. Guilford) Subject: HELP CREATE A MUSCLE/NON-MUSCLE WWW SITE!!! Message-ID: <1994Aug22.130920.23811@emba.uvm.edu> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: University of Vermont Date: Mon, 22 Aug 1994 13:09:20 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 62 HELP CONSTRUCT A MUSCLE / NON-MUSCLE CONTRACTILITY & MOTILITY SITE!!! ----------- Bionet folks: A new WWW and Gopher site is being constructed at the University of Vermont Department of Molecular Physiology and Biophysics. This site will house information related to the contractility and motility of muscle and non-muscle cells. WE NEED YOUR HELP! Links to existing information are *nice*, but what the web REALLY needs is information on-line. If you study some aspect of cell motility or muscle physiology, please consider volunteering to author a tutorial on some topic in this exciting field! Recommendations for links to existing sites are also appreciated. Pertinent information may include (but certainly not be limited to): * Exercise physiology (related to muscle) * General physiology and anatomy of muscle * Cellular physiology and anatomy of muscle * Excitation-contraction coupling * Comparative physiology of muscle * Muscle types (smooth, skeletal, cardiac) * Movement in non-muscle cells * Myosin - skeletal - smooth - cardiac V1 & V3 - non-muscle - light chains * Actin & actin binding proteins * Microtubules and microtubule-based motors * Energetics * Methodology - molecular biology - cell lines - new techniques - classic techniques If you know of an existing site housing these data, please pass it along. If you would like to contribute an article on one of these topics, this would be especially appreciated. GRAPHICS are greatly appreciated, and will be displayed "in line" in the WWW pages. WHAT'S IN IT FOR YOU? - Fame, fortune... that is, a by line, and a link to your WWW home page (if you have one). Other bio-netters will appreciate your contributions! I look forward to your replies and questions! - Bill Guilford Department of Molecular Physiology and Biophysics University of Vermont Burlington, Vermont guilford@salus.med.uvm.edu From owner-www@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!yogi!bioftp.unibas.ch!moderate Newsgroups: bionet.software.www Subject: Re: WWW: INSTRUCTIONS [Part 1] Message-ID: <01HG91UV4C1U00037C@SCI.WFEB.EDU> From: Foteos Macrides Date: Tue, 23 Aug 1994 17:58:35 GMT Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Approved: bio-www@comp.bioz.unibas.ch Lines: 41 [this is the original reply, part 2 is the reply referring to this post.] In article <1994Aug19.152731.14854@comp.bioz.unibas.ch>, doelz (Reinhard Doelz) writes: > > The Newsgroup bionet.software.www is archived, as all newsgroups, > at the net.bio.net site, and available to be browsed like any other > newsgroup archive (see previous posting). > > This newsgroup, additionally, keys contributions in 'html' documents > so that links are resolved in the 'hypertext' system, and may point > to the contribution of the originators, or the subject of the message, > respectively. > > This server runs at the Biocomputing Facility of Basel University. The URL > for this server is > > ============================================ > http://www.ch.embnet.org/bio-www/info.html > ============================================ >[...] Could the posting of URL's in this group be formatted as links: This server runs at the Biocomputing Facility of Basel University the link for this server is: WWW in Biology We could then access the messages via a WWW client, check out the link right then and there, and add it to our hotlists/bookmark_files with maximum efficiency and no strain on our failing memories. Fote ========================================================================= Foteos Macrides Worcester Foundation for Experimental Biology MACRIDES@SCI.WFEB.EDU 222 Maple Avenue, Shrewsbury, MA 01545 ========================================================================= From owner-www@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!yogi!bioftp.unibas.ch!moderate Newsgroups: bionet.software.www Subject: Re: A suggestion for writing links in bionet.software.www (Re: How to Message-ID: From: markw@unixg.ubc.ca (Mark Wilkinson) Date: Tue, 23 Aug 1994 16:47:23 GMT Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: The University of British Columbia Approved: bio-www@comp.bioz.unibas.ch Lines: 21 ... deleted stuff ... >(PS: There is a good primer at > NCSA >on setup of HTML pages and sophisticated details. ) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ It strikes me that enough people write their postings in this way (especially to the group comp.infosystems.www.users) that SOMEONE must be able to view these links as hypertext... That someone isn't me! When I use WinMosaic to browse the newsgroups These 'links' come up as regular text. Does anyone see these as hypertext using a WWW client? If so, what did you do to configure your browser that way? thanks, Mark Wilkinson >WWW in Biology > >and the one I posted before as > > Keith's server > >- do the quotes or the line break matter? The HTML docs at CERN indicate that href's should be quoted. It does not appear to matter for any client I've used, but I do the quoting anyway. The news gateway in our clients bounds the messages in PRE tags so my format will indent the link one tab stop in the display. Yours will appear at the left margin. Something is wrong with our access. I initially set up posts/followups from here to go to the decwrl gateway for moderated newsgroups, but the message bounced from there. Have the bionet folks distributed the info about bionet.software.www to all of the moderated newsgroup relays? I modified our MAILPATHS. to send the messages to bio-www@net.bio.net, and that apparently worked, since you go my post. We got the first set of messages to that group, but nothing since, for 2-3 days now (so I haven't seen the message to which you refer above). Fote ========================================================================= Foteos Macrides Worcester Foundation for Experimental Biology MACRIDES@SCI.WFEB.EDU 222 Maple Avenue, Shrewsbury, MA 01545 ========================================================================= From owner-www@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!yogi!bioftp.unibas.ch!moderate Newsgroups: bionet.software.www Subject: [Q] WWW list + help Message-ID: <33jjr2$h1c@usenet.rpi.edu> From: bulkem@rpi.edu (Mark Andrew Bulkeley) Date: Fri, 26 Aug 1994 02:25:38 GMT Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: Rensselaer Polytechnic Institute, Troy, NY. Approved: bio-www@comp.bioz.unibas.ch Lines: 7 I was wondering if there is a list of what exactly is out there on the WWW. Also how does one go about creating there own WWW site , I have some great ideas. Many thanks in advance bulkem@rpi.edu From owner-www@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!yogi!bioftp.unibas.ch!moderate Newsgroups: bionet.software.www Subject: On-line Directory of P450-containing Systems Message-ID: <33hpl7$hum@mserv1.dl.ac.uk> From: Kirill Degtiarenko Date: Thu, 25 Aug 1994 09:52:39 GMT Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Approved: bio-www@comp.bioz.unibas.ch Lines: 22 We would like to announce the new experimental www-page called On-line Directory of P450-containing Systems , developed at International Centre for Genetic Engineering and Biotechnology , Trieste . The goal of this www Directory is to facilitate access to electronic resources for all researchers working in the field of P450 proteins and P450 containing systems. Currently it contains accession numbers for sequences of both P450 superfamily and variety of proteins mediating electron transfer to P450 (NADPH:P450 reductases, specific Fe-S proteins and NADH:ferredoxin reductases, cytochrome b5 reductases and cytochromes b5).

From owner-www@net.bio.net Sun Aug 28 23:00:00 1994 Newsgroups: bionet.software.www Path: biosci!daresbury!bioftp.unibas.ch!moderate From: doelz (Reinhard Doelz) Subject: Re: A suggestion for writing links in bionet.software.www (Re: How to Message-ID: <1994Aug26.135413.6768@comp.bioz.unibas.ch> Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland) Organization: EMBnet Switzerland [Basel] Date: Fri, 26 Aug 1994 13:54:13 GMT Approved: bio-www@comp.bioz.unibas.ch Lines: 25 Mark Wilkinson (markw@unixg.ubc.ca) wrote: : Does anyone see these as hypertext using a WWW client? If so, what : did you do to configure your browser that way? I have seen the links on XMosaic, but fail getting it work on Winmosaic and Mac. Reason seems to be that the 
 tag embracing the news article
prevents or affects the recognition in the link. The only option you have 
is save it to disk ane reopen 'local' if you insist on reading it via 
news. However, you could point your browser to the  
 bio-www WWW server 
and read the news from there - we try to reedit the articles readily 
so the contents of the bionet newsgroup and the server should be identical. 

Regards
Reinhard 



-- 
 R.Doelz         Klingelbergstr.70| Tel. x41 61 267 2247  Fax x41 61 267 2078|
 Biocomputing        CH 4056 Basel| electronic Mail    doelz@ubaclu.unibas.ch|
 Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
EMBnet Switzerland:info@ch.embnet.org 


From owner-www@net.bio.net Sun Aug 28 23:00:00 1994
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Foteos Macrides 
Subject: Re: [Q] WWW list + help
Message-ID: <01HGEJJ8S3ZM0005MJ@SCI.WFEB.EDU>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Sat, 27 Aug 1994 16:18:34 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 21


In article <33jjr2$h1c@usenet.rpi.edu>, bulkem@rpi.edu (Mark Andrew Bulkeley) writes:
> I was wondering if there is a list of what exactly is out there on the WWW.
> Also how does one go about creating there own WWW site , I have some great
> ideas.

	CERN maintains a comprehensive list of server, client, gateway, and
various support software for the Web, organized by operating system, with
summary descriptions and links to the sources and documentation.  You can
access CERN's list via:

	WWW Software products.

				Fote

=========================================================================
 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES@SCI.WFEB.EDU     222 Maple Avenue, Shrewsbury, MA 01545
=========================================================================


From owner-www@net.bio.net Sun Aug 28 23:00:00 1994
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: mue@gsf.de (Bernhard Muenzer)
Subject: Re: A suggestion for writing links in bionet.software.www (Re:  How to
Message-ID: <33kved$92p@cony.gsf.de>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: GSF Forschungszentrum fuer Umwelt und Gesundheit - But I speak only for myself
Date: Fri, 26 Aug 1994 14:49:49 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 19

In article , markw@unixg.ubc.ca (Mark Wilkinson) writes:

|It strikes me that enough people write their postings in this way (especially 
|to the group comp.infosystems.www.users) that SOMEONE must be able to view 
|these links as hypertext...  That someone isn't me!  When I use WinMosaic to 
|browse the newsgroups These 'links' come up as regular text.
| 
|Does anyone see these as hypertext using a WWW client?  If so, what did you 
|do to configure your browser that way?

I don't, but it's useful for me, anyway:
using cut-and-paste, I can copy it into a html file in a vi window.
Opening the file with Mosaic, I have instant access to that link, complete with
a short description.
-- 
int m,u,e=0;float l,_,I;main(){for(;e<1863;putchar((++e>923&&952>
e?60-m:u)["\n)ed.fsg@eum(rezneuM drahnreB"]))for(u=_=l=0;(m=e%81)<
80&&I*l+_*_<6&&20>++u;_=2*l*_+e/81*.09-1,l=I)I=l*l-_*_-2+.035*m;}


From owner-www@net.bio.net Mon Aug 29 23:00:00 1994
Path: biosci!CS.Arizona.EDU!uunet!Germany.EU.net!news.dfn.de!scsing.switch.ch!yogi!bioftp.unibas.ch!moderate
Newsgroups: bionet.software.www
Subject: Medical Genetics management s/ware
Message-ID: 
From: mike@divsun.unige.ch
Date: Tue, 30 Aug 1994 13:00:21 GMT
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Approved: bio-www@comp.bioz.unibas.ch
Lines: 53

Newsgroups: bionet.software.www
Path: divsun!mike
From: mike@divsun.unige.ch (Mike Morris)
Subject: Medical Genetics management s/ware
Message-ID: <1994Aug30.130018.15217@news.unige.ch>
Sender: usenet@news.unige.ch
Organization: University of Geneva, Switzerland
Date: Tue, 30 Aug 1994 13:00:18 GMT



  (This may not be quite the right place to post this message- but the
information is very important to us!)

  We want to install a computer system to manage our Medical Genetics
DNA and Cytogenetics diagnostic laboratories, plus perhaps also the 
clinical consultation service. The package should handle at least sample
reception, labelling, and results; anything else would be a bonus. We 
are not precommitted to any one system, but networking is essential and
a multisystem approach would be ideal. Obviously we could develop our 
own database, but we would rather not reinvent the wheel (having done 
so many times already...).
 
  Does anybody have experience of such packages, positive or negative?
Please answer by email; if I get anwers, I will put a compiled answer 
back on the News. (Even replies from commercial companies would be 
appreciated, for once!)

  Thanks in advance,



*******************************************************************
Michael Morris PhD            
Division of Medical Genetics       tel (Switzerland) (22) 702.56.94
CMU, University of Geneva          fax (Switzerland) (22) 702.57.06
Geneva, Switzerland                email mike@medsun.unige.ch                  

















From owner-www@net.bio.net Wed Aug 31 23:00:00 1994
Newsgroups: bionet.software.www
Path: biosci!CS.Arizona.EDU!uunet!EU.net!dkuug!eunet.no!nuug!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: nager@FMI.CH (Nager Carl David)
Subject: W3 Biology Research Tools
Message-ID: <1994Sep1.114406.5266@comp.bioz.unibas.ch>
Summary: W3 Collection of Biological Programs/Databases/Resources
Keywords: W3, Biology, Tools
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: Friedrich Miescher Institut (FMI), Basle, Switzerland
Date: Wed, 31 Aug 1994 09:41:08 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 34

"Pedro's Research Tools" are now available on the FMI Internet World Wide Web 
(W3) server.

Pedro collects these tools on the Internet, puts them together as a short index
for biologists. The index should make it easier to get quickly your analysis done 
using the fast growing size of biological Internet resources.

Access to W3 Mirrors:
--------------------
in

Switzerland:	http://www.fmi.ch/biology/research_tools.html

US:		http://www.public.iastate.edu/~pedro/research_tools.html

Any comments welcome!

Carl David and Pedro
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bio-Informatics, FRIEDRICH MIESCHER INSTITUTE, P.O.Box 2543, CH 4002 BASEL
C.D. Nager						     (SWITZERLAND)
e-mail: nager@fmi.ch      fax: +41 (61) 697-3976    tel: +41 (61) 697-5678
URL:	http://www.fmi.ch/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
and
--------------------------------- H2N-CH-CO-NH-CH-CO-...-NH-CH-COOH --
Pedro M. Coutinho  - Graduate Student  \        \            \
IOWA STATE UNIVERSITY                   R1       R2           Rn
Department of Chemical Engineering               Phone: 1-515-294-9370          
2114 Sweeney Hall                                Fax:   1-515-294-2689  
Ames, IA 50011-2230                          E-mail: pedro@iastate.edu
U.S.A.                      URL: http://www.public.iastate.edu/~pedro/         
----------------------------------------------------------------------