Web Authoring - BioMoo Session on Section 6 - 6/2/97

ClareS turns the ClareS_recorder on.

ClareS says "OK, firstly, thanks to everyone for turning up (more or less) on time"

Baskin finds his way in.

ClareS says "I would like to introduce today's speaker - John Walshaw (JohnW) who will be going through some of the course material in Section 6 - HTML etc"

ClareS says "Before we begin, does anyone have any particular questions?"

Lulu says "Yes, if it's proper time for it"

ClareS [to lulu] go ahead

Lulu says "From time to time I use Japanese links, which are in Japanese..."

JohnW apologises for being a bit late (some things never change)whisper "my connection is v. slow in fact I had trouble connecting to claresto Jim dddd

Lulu says "However I cannot get Japanese characters. And the text is not readable."

ClareS [to lulu] Japanese characters?

ClareS [to lulu] Can you *read* Japanese? (just out of curiosity ;)

Lulu says "Yes. Kanji, Katakana, and hiragana"

JohnW can't see what he's typing

JohnW . o O ( !!! )

ClareS is impressed

JohnW says "pleased excuse me - back in a mo"

Lulu [to ] C

Ampicilin says "lulu, do you speak mozambikish?"

Lulu says "Sorry, I don't"

Skirgis says "I know some words too hirakiri & kamikadze"

Lulu says "Was it mozambikish?"

Skirgis says "no I've tried to speak in Japanese"

ClareS [to JohnW] OK

ClareS says "I don't have that problem - I don't speak any languages without Roman characters"

ClareS says "but the Israelis switch between Hebrew and Roman characters all the time"

ClareS says "I know they use Macs a lot, and they need extra software"

ClareS . o O ( everyone has better language skills than us English! )

Lulu says "Oh I see. Were you in Japan?"

Gustavo materializes out of thin air.

ClareS says "Hi Gustavo"

Gustavo waves.

ClareS says "this PPS meeting is on the general subject of HTML & associated skills"

Skirgis says "to Lulu no I was'nt"

ClareS says "and we are talking about the support available for non-Roman character sets"

Lulu [to ClareS] That's right.

ClareS says "I have very little experience of this ;)"

Lulu [to ClareS] But there are some compatibility with PC's too

(JohnW has disconnected.)

ClareS says "so I was wondering if you could tell us how the Israelis cope with changing between Hebrew & English"

ClareS [to lulu] Yes, there are now, but only since Windows became common - the Mac interface came first

Lulu [to ClareS] Maybe because they are still very "British"

ClareS says "JohnW is having serious problems with the MOO interface - I'll keep you posted"

Gustavo says "take a look at this: http://www.lib.ox.ac.uk/internet/news/faq/archive/internationalization.iso-8859-1-charset.html"

(JohnW has connected.)

JohnW says "sorry about that"

Gustavo says "There is a standard for non-ASCII charsets."

ClareS [to Gustavo] thanks for that URL

ClareS [to Gustavo] it should prove very useful!

Lulu [to Gustavo] Thank you, I'll try

Gustavo says "There are some fonts that include hebrew charsets in them. To see web pages in hebrew, all that needs to be done is to 1) install the font 2) tell netscape to use that font."

ClareS [to Gustavo] does it then automatically cope with writing from right to left?

Gustavo hmms.

ClareS says "do other character sets work in similar ways?"

Baskin says "Yes"

Gustavo says "I think the web pages with hebrew text are served with the lettering from left to right."

Gustavo says "I mean, the lines are reversed."

Gustavo says "with spacing added to fit."

Gustavo isn't sure.

Gustavo says "There's also ftp://ftp.sunet.se/pub/Internet-documents/rfc/rfc1345.txt, but I think it's a bit outdated."

Gustavo says "You might want to look at http://www.snunit.k12.il/ for an example of a web page with both English and Hebrew."

Gustavo says "The hebrew text is indeed reversed."

ClareS says "I think this could be very helpful - the initial question was abnout Japanese but I expect the techniques are similar for all non-Roman character sets"

ClareS says "unless anyone else has any specific questions on this, I shall hand over to John now"

ClareS [to JohnW] OK??

JohnW says "OK, this section of course material is intended to be an introduction to writing your own HTML documents about proteins"

ClareS [to JohnW] are you ready?

JohnW nods

ClareS apologises for bullying John un-necessarily - slow line (

JohnW says "- because including all the associated 'bells and whis links to interactive protein structures, literature references, movies etc, can be somewhat involved"

JohnW smiles

JohnW says "(not at all)"

JohnW is looking at http//iona.cryst.bbk.ac.uk/course/section6/images.html

JohnW . o O ( I really meant http//iona.cryst.bbk.ac.uk/course/section6/HTML.html )

ClareS is listening carefully - there's a lot she still has to learn...

ClareS has a slow, almost nonexistent netscape connection

ZLeifer finds his way in.

JohnW says "This isnt really the place to talk about HTML as such in much detail, but there are a few tips on this page about making links to specific entries in databases"

ClareS says "it might help if people were to find that URL (net speed willing)"

ClareS says "these tips will be extremely useful for referencing a particular protein structure or sequence in a remote database"

JohnW asks "have most of you spent much time looking at the WWW-interfaces to some of these relevant databases, eg Medline?

Gustavo is very happy with the WWW interface to Entrez

Ampicilin go drink some vodka

ClareS smiles

Skirgis says "I browsed GeneBank, Medline, EMBL some times"

Lulu says "I work with Swiss-prot"

JohnW says "Becauseeach entry in the database has a specific URL, its easy to make hyperlinks to them from your own documents"

JohnW says "This is also true of course for databases besides literature, e.g. Swiss-prot, and GenBank (gene sequences)"

ClareS likes the SwissProt interface, with links to lots of different databases

ClareS says "you will probably have noticed how some interfaces "work" much better than others"

JohnW says "Be warned though that these URLs may be somewhat 'volatile', e.g. if they reference a record by index number, that number could conceivably change if the Database is updated, so your hyperlink might point to the wrong record, or not work at a


ClareS agrees - and they keep moving databases, e.g. the EBI's PDB mirror

JohnW says "However, this does not seem to be a problem with most of the major databases. In fact, some, eg Medline, give you the option of accessing a 'citation format' which is intended to be stable"

JohnW says "Am I making sense?!"

Gustavo nods.

ClareS nods

Kamal [guest] finds its way in.

Skirgis says "I follow you mind"

JohnW says "OK, maybe we'd better move on, unless anyone has any questions"

JohnW says "The next page is aout images."

JohnW says "Its straightforward to produce your own images of structures from molecular graphics packages, including RasMol"

Skirgis says "question"

ClareS says "go ahead"

Skirgis says "Are you working with PC"

Kamal [guest] says "hello all"

JohnW says "But, there is already a wealth of protein images out there on the internet, which you can point to. There are several major libraries and their mirrors"

JohnW . o O ( oops )

ClareS says "Hi, glad you could make it"

JohnW [to skirgal] sorry for ignoring your question there

Skirgis says "Thats connection..."

JohnW says "You mean at the moment, or in general?"

ClareS says "on the subject of databases, http://www.embl-heidelberg.de/srs/wgetz?-np gives a good graphical summary of the major mol. biol. databases & links between them"

Skirgis says "in general"

JohnW says "Yes, I'm working with a PC. At the moment though, I'm using it as a terminal to Unix, from which I'm connecting to the BioMOO"

Skirgis says "Rasmol is very complicated program"

ClareS [to JohnW] could you advise me of some good (preferably free) tools for constructing image maps?

JohnW [to ClareS] yes, thats a very informative link

ClareS says "I am hoping to run a BioMOO on Rasmol soon, and (hopefully) to ask Roger Sayle, its author, along"

JohnW [to Skirgis] do you know how to make an image of the view in your RasMol display window?

Skirgis says "It's same viewers for unix machins "

Skirgis smiles broadly

Skirgis says "je I know"

Skirgis says "but with Setor(for example) its easier"

Baskin says "WebLab produces much better images of proteins than RasMol"

ClareS says "I have used Setor, and I agree it produces some great images"

ClareS says "does anyone know whether it is available for PCs or Macs?"

Skirgis says "and without any efforts"

Kamal [guest] says "Say would you happen to have some pointers to teir locations"

Skirgis says "but I have not seen Setor for PC"

JohnW says "Thats the point, RasMol is a free program which works on all the major platforms. There are of course larger graphics packages, some of which are also free, which do a better job"

Skirgis says "OK let's go further"

JohnW says "But RasMol is nice for using in conjunction with WWW pages, because it fires up quickly and allows fast manipulation of large structures (at the expense of some graphics quality)"

Skirgis says "I agree, but its complicat to see the part of molecule"

ClareS says "That's the point about Rasmol - it's quick, (relatively) simple, very portable between platforms... but there will probably be a better solution for specialist tasks"

Skirgis says "the zoom option is not good enough"

JohnW says "eg I used to have Quanta on an SG, but I wouldnt have wanted to wait for that to start up each time I clicked on a PDB structure.. anyway, this chemical-MIME business is addressed later on in the chapter"

Skirgis smiles broadly

ClareS says "can I ask you all - are you using Chime?"

Baskin says "Yes"

ClareS put "setor" in a Yahoo search and retrieved a lot of sites in Spanish, nothing about protein structure

Skirgis says "je I've the plugin in Netscape"

Ampicilin says "no"

Cockle says "I ve got a plugin for NetScape"

Kamal [guest] says "'No'"

ClareS says "in some ways, when we run a course like this with people using a wide variety of hardware, we have to go with the most easily accessible software - which won't necessarily be the nest"

ClareS . o O ( nest = best  )

Lulu  no

ClareS says "we have made a conscious decision not to rely on students having access to Chime, and I think it was probably the correct one"

JohnW agrees

Kamal [guest] says "Can I just ask what chime is , please"

JohnW says "IMHO using RasMol is better than Chime, because personally I prefer having my active molecule in a separate window."

ClareS says "I have found *a* reference to Setor on the net, and it explicitly mentions that it was written to exploit the graphical abilities of the SG workstations"

ClareS says "so as we don't expect everyone to have access to a SG, we can't expect them all to have Setor"

JohnW says "Chime is a similar application to RasMol, but is a Netscape 'plug-in' which can interpret interactive structures *embedded* in a page of HTML"

JohnW says "see the bottom of http://iona.cryst.bbk.ac.uk/course/section6/multi.html"

ClareS [to kamal] Chime is a Netscape plugin which allows mol graphics on a web page - see http

ClareS . o O ( johnw got there first )

ClareS [to JohnW] sorry

JohnW says "no prob"

Kamal [guest] says "We here within our depart"

ZLeifer says "In the context of this discussion, and for this purpose, is Hyperchem any good?"

Kamal [guest] says "We here within our department used to use the HGMP GCG package before it became necessary to pay for a licence. Can any of you suggest a possible alternative site that would replicate the various functions of that package. We do have

 the geneworks and MacVector packages running on our Macs!"

Lulu says "Oh, about Hyperchem. I have some questions about compatibility between Rasmol and Hyperchem"

ClareS [to ZLeifer] IMHO, Hyperchem is very good for teaching, but its algorithms are really too simple to make it very useful for research

ClareS says "compatibility between graphics files is a real problem"

Lulu [to ClareS] And what about usufulnes of highr versions of Hyperchem eg 5.0?

(Jim Pitts has disconnected.)

ClareS says "every program should really accept coordinates in PDB format. They don't all."

ClareS [to kamal] Local software for bioinformatics is less and less necessary - there's so much free stuff on the WWW?

ClareS [to lulu] I haven't used that version

Ampicilin fell down

(Baskin has disconnected.)

ClareS says "JohnW will have to go shortly - is there anything else related to HTML authoring you'd particularly like to discuss?"

JohnW says "eg. from the index at http://iona.cryst.bbk.ac.uk/course/section6/index.html"

Lulu says "I think I will have many questions but in the future"

Kamal [guest] says "What is your opinion on the usefulness of the application VisualPage, as a HTML editor?"

ClareS says "good question, can I broaden it out - what (if any) HTML editor would you recommend?"

JohnW says "well, this really is a matter of personal preference. In the 'old days' of 18 months or so ago, I personally found that using a bog-standard text editor with programmable function keys was the most painful option."

The housekeeper arrives to cart Jim Pitts off to bed.

JohnW says "but since then, dedicated editors have been improving all the time, of course."

ClareS [to JohnW] do you mean "least painful" by any chance?

JohnW . o O ( (!!!) )

JohnW says "yes, I'll rephrase that... most painless , or least painful !"

ClareS [to JohnW] can you recommend a good, free (or at least shareware) dedicated editor?

Skirgis says "I'm using Frontpage and NetscapeGold"

ClareS was recently warned off FrontPage as mot good value for money ;)

ClareS . o O ( mot=not )

JohnW says "I wasnt too impressed with some of the first 'WYSIWY(D)G' HTML editors, but I think its a different ball-game now. But I'm still happy with a simple ascii-character editor.. maybe force of habit"

ClareS . o O ( typos, typos! )

ClareS is currently using Notepad

JohnW nods

Gustavo is trying AOLpress, the new incarnation of GNNpress - quite good. Free.

Lulu says "think painful options?"

The housekeeper arrives to cart Baskin off to bed.

JohnW says "For example, if you are used to using a particular Word processor, then using a plug-in (or maybe built-in) HTML converter might be for you."

JohnW says "Yes, I was going to mention GNNPress, though I didnt get much chance to use it- looked good though"

ClareS [to Gustavo] I have just acquired GNNpress & I'm quite impressed so far

ClareS . o O ( at least for tables )

Gustavo says "Get AOLpress. GNNpress is the old, buggy version."

ClareS says "I suppose a built-in / plug-in HTML converter for Microsoft Word 7 is too much to hope for??"

ClareS . o O ( www.microsoft.com is down ;) )

JohnW says "Of course, with HTML getting ever more complex, plain-text editing begins to lose out to packages which will format your tables, imagemaps, frames etc for you"

ClareS says "so many people write frames so badly that I'm yet to be persuaded to use them"

(Alg has disconnected.)

Kamal [guest] says "ClareS I will e=[1~say ClareS my e-mail address is k.dulai@ucl.ac.uk, I will forward a email message to you explaining who I am."

JohnW says "yes, maybe I put my foot in it mentioning frames!"

ClareS says "For AOLPress, see http://www.aolpress.com"

(Ampicilin has disconnected.)

ClareS says "I think it would be sensible to wind this up very soon, as JohnW has to go"

JohnW nods

ClareS . o O ( and people are beginning to drift away, anyway )

Skirgis says "I agree.So thanks for all. By..."

Skirgis smiles broadly

ClareS says "but before then I would like to thank John for leading such a valuable discussion, and everyone for participating"

(Skirgis has disconnected.)

(Kamal [guest] has disconnected.)

JohnW apologises for the delays at the beginning... a few hiccups...

Lulu says "Thanks a lot. See you next meeting"

ClareS turns the ClareS_recorder off.