- chemweb - imperial.ac.uk

VEGA ZZ release
by Giulio Vistoli 22 Nov '04

22 Nov '04

Dear all, We are proud to announce that the next generation of the VEGA package for Windows is now available (http://www.ddl.unimi.it) with new powerful features: - Introduction of the HyperDrive technology for an incredible computational speed (the surface calculation, for example, is about 40 times faster). - New graphic interface. - Improved graphic performances (lighting engine and customizable view). - Tube and trace visualization modes. - Fast solid and mesh surface calculation & multiple surface management. - Support for stereo devices and for distributed OpenGL rendering. - MLP/Virtual logP included in the standard version. - Add aminoacid side chain function. - Tools to check protein structures. - Enhanced image rendering capabilities. - LaTex, PDF, PostScript and Encapsulated PostScript export. The VEGA team Alessandro Pedretti & Giulio Vistoli

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http://scholar.google.com/
by Rzepa, Henry 19 Nov '04

19 Nov '04

This new offering from Google has attracted much press attention. "Google Scholar enables you to search specifically for scholarly literature, including peer-reviewed papers, theses, books, preprints, abstracts and technical reports from all broad areas of research. Use Google Scholar to find articles from a wide variety of academic publishers, professional societies, preprint repositories and universities, as well as scholarly articles available across the web." I worry however about one aspect: comprehensiveness. There is an interesting tendency amongst (graduate) students to assume that if a quick search fails to reveal an item, it does not exist. This was particularly prevalent at a time when many electronic journals in say the ISI/WOS database did not go back before 1981. This did actually lead to an outbreak of claims in journals to have discovered a new molecule, when in fact that molecule had been very well recorded in the pre 1981 literature. One wonders how long it would take for eg failure to find a reference in http://scholar.google.com/ to the assumption that the item does not exist. Thus my brief search (taking the form author:name) revealed about 100 articles less than I know I have authored. On the other hand, it is free! And presumably can only get better!! (unless of course publishers start putting a robot exclusion on their ToCs) -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Re: [chemweb] Whatever happened to the Web?
by Rzepa, Henry 06 Nov '04

06 Nov '04

>Elsevier's ScienceDirect.com has this to say about it: > >"You may print or download Content from the Site for your own personal, >non-commercial use, provided that you keep intact all copyright and other >proprietary notices. You may not engage in systematic retrieval of Content >from the Site to create or compile, directly or indirectly, a collection, >compilation, database or directory without prior written permission from >Elsevier." > >Depends a bit on what is a systematic retrievel... would downloading all >interesting articles be systematic? Many issues of journals are "themed". Here the publisher has gone out of their way to create a "collection" of articles, all of which might be interesting scientifically to a particular person or group. But they then prohibit that group treating the collection as a collection and systematically retrieving it. What about database? Well, e.g. EndNote is capable of creating a collection of citations, to each of which the original PDF article can be added. so I presume the use of eg EndNote in this context is prohibited. Further, they do not mention whether any parts of the PDF can be "re-used". Sometimes, clear text can be copied/pasted. It can be parsed using regular expressions. Thus the OSCAR project at Cambridge can extract <<data>> from such clear text. Is this allowed? Would you have to keep intact the copyright notice with this data? > >JCICS: > >"Articles and other information obtained from this service are not to be >systematically downloaded, re-published in any media, print or electronic. >Articles may not be downloaded in aggregate quantities or centrally stored >for later retrieval. " > Centrally stored is a clear negation of Institutional archives. Also included in some publisher restrictions is storage on any sort of Network drive. This means that at our place, where we use a SAN (Storage area network) for all home directories, placing any PDF on this SAN is prohibited >Again vague terminology... I'm sure I've seen it more strict somewhere... will >report when I find it... The issue is that virtually each publisher has slightly different restrictions. Tracking them all by the regular user is almost impossible. I have to say that the publishers are probably trying to promulgate policies that are close to unenforceable, or unsustainable in the medium term. Its tempting to conclude that the very concept of a "publisher" may not itself be sustainable in the long term. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Whatever happened to the Web?
by Rzepa, Henry 01 Nov '04

01 Nov '04

A rant (please excuse). I do so because for the first 8 years or so of the (Chemical) Web, most of my colleagues largely ignored it for teaching. In the last two, most now have some sort of presence on our teaching site. But I cannot remember the last occasion when HTML has been offered. Its all Acrobat now, bloody great big globs of it. Typically between 1 - 5 Mbyte (although the record is 18 Mbytes thus far). The contents are linear, ie depart not all all from the serial fashion of yesteryear, and contain no "interactivity" whatsoever (let alone semantic markup), or simple navigation aids such as a ToC. So I expect most students rail about the cost of printing our lecture notes nowadays! We have of course largely stopped photocopying them for students now that they are "available on the web". None of it streams either (whatever happened to streaming Acrobat?), so the students can forget viewing it unless they use broadband on their computer. In 2nd place is raw Powerpoint. HTML, like eg Apple computers, has possibly 2% of the market! Lets hope Adobe don't go out of business! By the way, talking about libraries, I have heard that Acrobat downloaded from Journals may be subject to surprising restrictions. Thus some journals may require all local copies to be deleted if at any time the institutional subscription is cancelled. Most journals only allow "personal use", which means eg passing a reprint on to a student is disallowed. As for "scraping" say an entire themed issue of a journal, that has resulted in the <<entire institute>> being barred from using the journal (at least for a period; the explanation was that one naughty user called "Web Cache" was responsible, according to the publisher). -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Dear to chemists hearts: Greek characters on the Web
by Rzepa, Henry 01 Nov '04

01 Nov '04

I am posting this because I see "FAQs" on this topic widely, and I dont know many of the answers myself! Its the issue of greek characters, much used in chemistry! Over the last 10 years, it seems many mechanisms have been used to display them in browsers. Many of these mechanisms had short lifetimes! The current recommended way, if using the standard (7-bit) ASCII text character set, is to define an entity. thus β or Β (its case sensitive). Older deprecated methods ( <font face="symbol">b</font> ), along with CSS equivalents, by and large no longer work. The "future way" is to use utf encoding. Here is where confusion can start. Thus http://www.ch.ic.ac.uk/rzepa/greek.html contains (according to my unicode compliant text editor, bbedit 8) a utf-8 encoded beta. One has to tell the browser that the default encoding is indeed Unicode utf-8, but in my hands at least, this does not result in display of a beta. Is there anyone out there who can explain it all to us? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Molecule of the Month - November
by Paul May 01 Nov '04

01 Nov '04

Hi, November's MOTM is the infamous sedative and painkiller, Morphine. It has been written by Enrico Uva, a teacher at LaurenHill Academy, in Montreal, Canada. Direct link: http://www.chm.bris.ac.uk/motm/motm.htm#nov2004 regards, ---------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, BRISTOL BS8 1TS, UK tel: +44 (0)117 9289927 fax: +44 (0)117 9251295 mobile: +44(0)7811371539 Email: Paul.May(a)bristol.ac.uk Web: http://www.chm.bris.ac.uk/staff/pwm.htm MOTM: http://www.chm.bris.ac.uk/motm/motm.htm "If you're not part of the solution, you're part of the precipitate" ----------------------------------------------------------------------------

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Re: [chemweb] Dear to chemists hearts: Greek characters on the Web
by Rzepa, Henry 31 Oct '04

31 Oct '04

>Hi, > >I don't know if that is going to be helpful but... >* By default I see an I with a caret and a square for the first symbol >* If I save your file in local and I open it, I see betas for both characters >* Your file seems to be served as encoded in Latin-1 (ISO-8859-1) according to the page info information in Mozilla > >It looks like that the web server may override your file encoding... >http://www.w3.org/International/tutorials/tutorial-char-enc/#declaring >http://www.w3.org/International/questions/qa-htaccess-charset You correct Jordi. But see http://lists.w3.org/Archives/Public/www-tag/2003Sep/0176.html which says that the server should really NOT do this! At any rate, I have switched a setting off on the server #AddDefaultCharset ISO-8859-1 and now http://www.ch.ic.ac.uk/rzepa/greek.html does indeed show a beta for the utf-encoded version. I strongly suspect however server behaviour will differ wildly. Apache (2.0.49 for above) can be configured, but my experience in asking server administrators to do these things can be very uncertain. I would hazard a guess that dealing with eg greek characters is likely to be a problem for the foreseeable future. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Semantic Web in Life Sciences
by Rzepa, Henry 28 Oct '04

28 Oct '04

Of considerable interest is the conference, occurring as I write this email, in Boston, under the auspices of the World-Wide Web consortium, on the topic of the "semantic Web in Life sciences", with particular emphasis on the so called LSID (Life sciences identifier). With some 4 billion documents and many types of object now described on the Web, uniquely indentifying these is an urgent priority. I offer to this form two "position papers" submitted to the above dealing more specifically with chemistry; http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/ and particularly http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/att-0025/molsem.… and http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/att-0026/inchi.h… The latter in particular deals with the topic of chemical identifiers, namely the INChI project. If you dont know about this project, I urge you to go find out! A futher announcement regarding this conference will be made shortly. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Invitation to submit an abstract: Automation and Remote Access Technology in the Undergraduate Teaching Laboratory
by Bob Hanson 07 Oct '04

07 Oct '04

Call for abstracts: Division of Chemical Education Symposium: Automation and Remote Access Technology in the Undergraduate Teaching Laboratory. ACS 229th National Meeting, San Diego, March 13–17, 2005 http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=meetings\sandie… Deadline for abstract submission: Nov. 15, 2005 http://oasys.acs.org/acs/229nm/ched/papers/index.cgi Title: Automation and Remote Access Technology in the Undergraduate Teaching Laboratory Type: Oral Abstract: One of the interesting aspects of automation is how students and faculty react to it (sometimes quite differently). Does automation "spoil" the experiment, or does it enhance the learning experience? Does remote access unnecessarily isolate the student from "really understanding" what is going on, or does it bring the teaching laboratory into the 21st century? This symposium will focus on the use of laboratory automation and remote access technologies that enable student access to state-of-the-art techniques at any level in the undergraduate or high school curriculum, either at a single institution or via distant "collaboratory" experiences. Presentations related to experimental design, implementation, adaptability, security, safety, and assessment of impact on student learning are welcome. Please forward this announcement to colleagues you think might be interested. If you or someone you know might be interested in presenting at this symposium, please do contact me. Bob Hanson -- Robert M. Hanson, hansonr(a)stolaf.edu, 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:hansonr@stolaf.edu http://www.stolaf.edu/people/hansonr

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Molecule of the Month - October
by Paul May 01 Oct '04

01 Oct '04

Hi, October's MOTM is butane, the fuel in portable cookers. It has been written by Feng Wang from Swinburn University in Melbourne, Australia. http://www.chm.bris.ac.uk/motm/motm.htm#oct2004 Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927 fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> Mobile: 07811371539 Home URL: <http://www.chm.bris.ac.uk/staff/pwm.htm> Molecule of the Month: <http://www.chm.bris.ac.uk/motm/motm.htm> "Ah, a chemist, eh? Do we get to blow something up, then?" League of Extraordinary Gentlemen ------------------------------------------------------------------------------

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