Posts Tagged ‘Macintosh’

Steve Jobs and chemistry: a personal recollection.

Sunday, October 9th, 2011

Steve Jobs death on October 5th 2011 was followed by a remarkable number of tributes and reflections on the impact the company he founded has had on the world. Many of these tributes summarise the effect as a visionary disruption. Here I describe from my own perspective some of the disruptions to chemistry I experienced (for another commentary, see here).

Chemical diagram, circa 1983.

The diagram above originates in 1983 just before the impact of Jobs’ vision burst upon chemistry. It was published in one of the new-generation of camera-ready journal, the objective being to reduce publication times from a typical 12-24 months down to around around three months. Camera-ready meant that the authors had to prepare a photo-ready manuscript; the role of these journals was to photograph, print and publish. The diagram above was prepared using stencils and Rotring technical pens together with Letraset lettering. The snippet above would probably take an hour or two to draft; the diagrams for an entire article were probably about 1 weeks work. Imagine how much time would be needed for a 200 page PhD thesis (some of this time was occupied by rushing out to a purchase more Letraset sheets because one had run out of say the letter r needed to represent the bromine in the above!). The diagram below was publishedin the same camera-ready journal in 1987.

Chemical diagram, circa 1987.

It was produced using Chemdraw on an Apple Macintosh computer introduced in 1984 (and which reached UK chemistry departments in 1985) and printed on an Apple laser printer. It would have taken perhaps 5 minutes to produce. More significantly, by copying and pasting (terms which need little explanation nowadays), one could re-use the diagram repeatedly as a template in a more complex scheme for little extra effort. You might argue that these two diagrams do not actually differ in quality that much (actually, the Apple-derived diagrams are of much higher quality than implied above, and the loss of quality is because the article has subsequently been scanned by the journal). But in fact the impact of Jobs’ Macintosh computer was far greater than just being able to produce nice chemical diagrams. Because it also introduced chemists to disruptive new concepts, the consequences of which are still impacting today.

The first is the idea of the re-use of digital data, as mentioned above. Once one had a diagram drawn, one could use it to almost instantly derive other properties of the molecule. For example, the molecular weight or an atom connection table. This in turn could be used to start an online search. And it was the Macintosh that really bump-started the idea of online activities.

Although chemistry had started going online around 1980 (I remember a single terminal station enabling STN express online access to chemical abstracts being introduced then, and in fact computational chemists were already online around 1974), the idea of an entire department of researchers ALL being online in their lab or office was very much the result of introducing the Macintosh in 1985. It came with a network connector at no extra cost. This in turn allowed all owners of such a computer to connect online to the (then very expensive) laser printer, and as a by-product almost, to the rest of the world! I have described some of the disruption this introduced elsewhere. By around 1987, most of our Mac users were happily going online (it has to be said that owners of IBM PCs were rarely doing so at this time). That is one of the true legacies that Jobs’ disruptive technologies introduced to us chemists.

I am going to quote Samuel Butler now, writing in 1863: “I venture to suggest that … the general development of the human race to be well and effectually completed when all men, in all places, without any loss of time, at a low rate of charge, are cognizant through their senses, of all that they desire to be cognizant of in all other places. … This is the grand annihilation of time and place which we are all striving for, and which in one small part we have been permitted to see actually realised“.

Steve Jobs made a big contribution to that general development of the human race!

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Computers 1967-2011: a personal perspective. Part 3. 1990-1994.

Tuesday, July 12th, 2011

In 1986 or so, molecular modelling came of age. Richard Counts, who ran an organisation called QCPE (here I had already submitted several of the program codes I had worked on) had a few years before contacted me to ask for my help with his Roadshow. He had started these in the USA as a means of promoting QCPE, which was the then main repository of chemistry codes, and as a means of showing people how to use the codes. My task was to organise a speakers list, the venue being in Oxford in a delightful house owned by the university computing services. Access to VAX computers was provided, via VT100 terminals. Amazingly, these terminals could do very primitive molecular graphics (using delightfully named escape codes, which I learnt to manipulate).

An expert on the use of such codes was George Purvis, who hailed from the quantum theory project at the University of Florida at Gainesville. He had developed QUIPU for VAX/VT100 and together we had much fun setting things up for the participants at these QCPE workshops (which ran 1986-1990). During one session, George asked me whether I thought a properly implemented and reasonably cheap graphical user interface might have commercial potential in chemistry. Remember, the VAX/Evans&Sutherland PS390 system we had acquired in 1987 was NOT cheap. I must have encouraged him, since in 1990 George (now part of the CACHE, or computer assisted chemistry, group at the Tektronix corporation in Beaverton) had brought to market a “shrink-wrapped” system which did just that. This was, in many ways, well ahead of its time. It was based on a then state-of-the-art Macintosh computer, with a co-processor that could crunch floating point numbers quite fast (this was then very rare in so called personal computers, being reserved for supercomputers). It had a unique spherical trackball (almost a haptic device) for rotating molecules, and a liquid crystal polarized screen running at 120Hz (60Hz for the left eye, 60Hz for the right eye). Wearing polarized (passive) glasses, the stereo 3D effect via the 19″ screen (big for its day) was awe inspiring. What is more, two people could sit at it and both see molecules in stereo.

We managed to get a grant to purchase such a system, and I well remember taking it to the 1990 Oxford workshop (I had now taken over from Richard for the UK workshops) in the back of my car. This involved driving to my office on a Saturday, and heaving the thing out. A security guard saw me doing this and arrested me. After much ado, I was forced to take the CACHE to my office and told not to try that again. I waited 30 minutes, and took it out the back door (which nowadays has a black security camera watching it, but in those days was not guarded) and on to Oxford (checking for police sirens all the way). I think I made the trip to Oxford with this thing in the back of the car one more time, where I used it to give a poster at a conference, handing out the 3D glasses to anyone who expressed an interest (and reclaiming them rapidly if they posed no interesting question). I still fancy this was almost unique in the history of posters (which tend, even nowadays, to be printed on paper). Reflecting on this, I realise that my total aversion to Powerpoint probably dates from that time.

At this stage, I will tell you about some of the science we did with the remarkable stereographical 3D CACHE system. The first is our realisation that the Pirkle reagent exhibits a π-facial hydrogen bond from the OH group (DOI: 10.1039/C39910000765). Indeed, I notice that four of the posts here relate to this topic! Once you know what you are looking for, its trivial to spot. But I recollect that the crystallographers who did the structure for us had failed to identify this unusual hydrogen bond; it took the CACHE, and its 3D glasses, for us to notice it.

But the really important breakthrough using CACHE was a different molecule, halofantrine (X=Y=Cl, DOI: 10.1039/C39940001135) an antimalarial pharmaceutical molecule.

Halofantrine.

At this stage, pharmaceutical companies were assiduously resolving chiral compounds into their enantiomers and testing each separately for biological activity. It had been noticed that whereas X=H, Y=Cl could NOT be resolved on a chiral column, replacing X=H by X=Cl suddenly made it possible to do so. But why? Well, in order to inspect this with the CACHE system, we asked for the crystal structure to be done. Back it came and Mike Webb and I sat inspecting the coordinates in full stereoscopic glory, as I recollect for about an hour, twiddling the viewpoint here and there. Each of us would take over the haptic trackball for 10-15 minutes, and we would then discuss what we saw. In one of those magical moments (I can assure you that shivers do run down one’s back at moments like this) we spotted that X=H had a strong hydrogen bond to the OH of another molecule, whereas X=Cl did not. Suppressing that C-H…O interaction forces the molecule to π-π stack instead, and this mode now enables it to better interact with the chiral column and hence resolve.

Halofantrine. Click for 3D.

Some of that magic is recreated above. If you click on the image, the coordinates will be loaded. Now that the relevant interaction is highlighted, it is so easy to spot you might wonder how anyone would have ever missed it!. At any rate, shortly after writing this article, I sat down to write another on a new phenomenon called the World-Wide-Web. And to illustrate why the Web might become important, we highlighted halofantrine, and how the Web could carry such immediately visual information to its readers. This blog, in effect, is a direct descendent of that article (which, by the way, is still available in HTML form here). So, 3D graphics led to the (chemical) Web. What a tangled web indeed.

And to end with 3D. I live in hope that shortly, stereoscopic tablets will make an appearance. Given that the CACHE system noted above was heavy (it was a major struggle moving the monitor into the car, as described above), it will be an amazing evolution to see (almost) pocket sized devices being carried around for the same purpose.

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Computers 1967-2011: a personal perspective. Part 2. 1985-1989.

Friday, July 8th, 2011

As a personal retrospective of my use of computers (in chemistry), the Macintosh plays a subtle role.

  1. 1985: In the previous part, I noted how the Corvus Concept computer introduced a network hard drive (these still being too expensive for any one individual to afford one); the same principle applied to the 1985 Macintosh but now relating to the remarkable introduction of the laser printer. Until then, us chemists had used french curves (see previous post for an explanation), stencils or transfer lettering. It could be really tedious preparing a complex manuscript. Indeed, in some published articles of the time, one often saw hand-drawn chemical diagrams! So when the Macs arrived in 1985 (and it has to be said the associated rise of ChemDraw at that time), it became imperative to network them so that everyone could have access to that precious laser printer (I still remember its network name, selected using the aptly named Chooser utility). Fortunately, the Mac came with a network port (unless I am mistaken, this was not an invariable feature of the IBM PC of the period). The network was created using a router (the first time I had come across one of these) from the Webster corporation in Australia, and our local electrician and his colleagues suddenly found themselves putting in Appletalk cables everywhere. The poor chemists in the department not only had to get used to the mouse pointing device and unfloppy floppy disks, but to the idea of selecting network devices.
  2. 1987:We also acquired a Microvax with an Evans and Sutherland PS390 stereographics device at this time (more of which later in another post), and this came with an interesting bonus. Haggling had managed to leave about £25K left over, which I decided to spend on a “grown up proper network”. This took the form of a thickwire ethernet of about 400m length. This stretched from the Microvax to the main college hub and thence the outside world (the “Internet”) and also to the close-by new network distribution cabinet where one end of the Fibre optic cable was terminated (a bonus of all this was a Pirelli calendar, yet another story that must wait to be told).  The fibre was strung to a catenary connecting to our other building (the idea being that it should be immune to lightening strikes. I had earlier explored the idea of a copper cable routed through tunnels connecting the two chemistry buildings, and spent a most interesting day down in those tunnels exploring. Therein lies yet another story for another day). Anyway, we now had a 10 megabit network (1000 times faster than the old PADs, which were still around) and this was connected to the Webster multigate routers (there were two of them now, one for each building). Our Macs all had the Internet!

    Apple, bless their hearts, distributed a control panel called MacTCP, and after I figured out what it all meant (network masks, Class C subnets and the like) I let everyone know that another network device had been added to join the laserprinter. Few IBM PC owners could boast this. At this stage, in truth, there was not that much people could connect to. Using MacTelnet, we could indeed access CAS Online, and print the search to a laserprinter. Using MacFTP, we could get files remotely from other FTP servers, and we started to acquire coordinate files for our molecular modelling. This in turn brought the realisation that the existing formats (Brookhaven protein databank files were the most common at the time) were not ideally suited for the purpose, and this could be seen as another spark for the CML (XML) work that started about nine years later. I also remember discovering that Apple computer ran their own FTP server, where I could download the latest operating system disk images (Systems 5-7 as I recollect were obtained from this site ). Things were free (but not always that easy) in those days. Our Macs ended up have the latest OS on them (in other words, they tended to crash a little less) almost as soon as it was released (and the Mac app store™, with its impending 4.6 Gbyte of OS X Lion about to be downloaded is merely the latest example of this).

  3. 1987: Armed with all this experience, I was also asked to serve a two year stint on the editorial advisory board of the Royal Society of Chemistry. At the time, what is now called supporting information was just starting, and of course it was going to be in print only. I suggested that perhaps the RSC should plan for the day when it could be online instead (the term online was not, I think, in that common use then, and electronic journals were also not yet common). I was still not happy that the only way to access that information would have to be FTP file transfers, but then little did I realise then that Tim Berners-Lee at CERN already had a glimmer in his eye.
  4. 1988: The network on the Macs became a little more useful in this year, when a Macintosh email client called Eudora was released (in truth, I had already sent my first email in 1976, from CMU in Pittsburgh whilst on a visit there, to the person standing next to me!). The Microvax alluded to above provided the mail relay, and a few brave individuals started sending email (not that many people had email addresses in those days mind you). The RSC was still grappling with this. I remember putting my email address at the top of an article submitted to them, and the copy-editor deleted it from the proofs as “unrecognised address form“. I re-instated it, they deleted it again. After some telephone negotiation, it remained (although the RSC assured me it would confuse the journal readers mightily). For the record, if you do manage to find it, it no longer works (being something like rzepa@vaxa.ch.ic.ac.uk. We were still learning how to do things properly then).
  5. 1989: I managed to convince the department that it would be useful to use computers for undergraduate teaching, and we opened a computer room with 12 Macs. I maintained them using a wonderful network utility called  RevRDist for Mac, which cloned a master Mac onto the 12 clients, and made the task of adding new software very easy. There was always lots of good software for Macs in those early days. But to introduce students to how to use them, I did feel impelled to produce a 4 page printed handout explaining it all. And I only did this once a year. Clearly again, the need to manage this better must have been in my mind.

This post focuses on a very short period, because I wanted to get across how (in my mind at least) chemistry became globally networked for the (chemical) masses (or at least those with Apple Macintosh computers!), and the role the laserprinter Pippa played in this development.

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Data-round-tripping: wherein the future?

Tuesday, December 7th, 2010

Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say ChemDraw) and the Word processor used to place them into a context (say Microsoft office), via an intermediate storage area known as the clipboard. The round trip between the Macintosh (OS X) versions of these programs had been broken a little while, but it is now fixed! A small victory. This blog reports what happened when such a Mac-created Word document is sent to someone using Microsoft Windows as an OS (or vice versa).

As you might have guessed, the molecular diagram arrives largely dead, and not re-usable. Opening the .docx archive (it is nothing more than a zip file) reveals only a JPEG file residing inside. Nothing that can be chemically repurposed. If the reverse process is undertaken, of creating a chemdraw diagram, and pasting it into Word on Windows, one finds in the .docx two components; a bit-mapped image linked to an active object containing the data. Only the first of these is recognised if the file makes its way to a Macintosh; i.e. the same story, the data is again lost. So the bottom line is that Mac users and Windows users cannot, after all, exchange repurposable molecular diagrams using Word documents using this combination of programs. This is not good.

But let me remind what happened around 1993. The word processor was joined by a program called the Web browser. In 1996, the underlying content carrier, HTML, became XHTML (an instance of XML). Right from day 1 almost, such XHTML could, and frequently was repurposed. A memorable example is that search engines could use it to index the Web. The XHTML easily survived trips to and from clipboards. In 1996, CML joined HTML as a way of carrying chemical information capable of round-tripping without loss (if need be). There are other chemical XML languages in use nowadays, including CDXML used by the ChemDraw program. Word itself now uses XML (the x in .docx). So, after 14 years, why am I still describing the difficulties above? I am frankly at a loss to explain why there is still a need to write this post.

All is not entirely lost. The CML4Word approach is designed to enable (chemical) data round tripping from the outset. Although I do not yet know if the CML created and stored in the Word document using this mechanism is recognised anywhere outside of Word 2007 on Windows?  If anyone can let me know of examples where such a CML-enabled Word document can be used in other environments, I would be very grateful (but not on  OS X, as I know already).

And as I might have mentioned in the previous post on this topic, things may not however be getting better in that other carrier of information and data, the mobile phone/iPad, as exemplified by operating systems such as iOS or Android. Watch this space, as they say.

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Data-round-tripping: moving chemical data around.

Saturday, November 20th, 2010

For those of us who were around in 1985, an important chemical IT innovation occurred. We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the clipboard, paste it into a word processor (it was called a Macintosh). Perchance even print the result on a laserprinter. Most students of the present age have no idea what we used to do before this innovation! Perhaps not in 1985, but at some stage shortly thereafter, and in effect without most people noticing, the return journey also started working, the so-called round trip. It seemed natural that a chemical structure diagram subjected to this treatment could still be chemically edited, and that it could make the round trip repeatedly. Little did we realise how fragile this round trip might be. Years later, the computer and its clipboard, the chemistry software, and the word processor had all moved on many generations (it is important to flag that three different vendors were involved, all using proprietary formats to weave their magic). And (on a Mac at least) the round-tripping no longer worked. Upon its return to (Chemdraw in this instance), it had been rendered inert, un-editable, and devoid of semantic meaning unless a human intervened. By the way, this process of data-loss is easily demonstrated even on this blog. The chemical diagrams you see here are similarly devoid of data, being merely bit-mapped JPG images. Which is why, on many of these posts, I put in the caption Click for 3D, which gives you access to the chemical data proper (in CML or other formats). And I throw in a digital repository identifier for good measure should you want a full dataset.

It is only now that we (more specifically, this user) understand what had happened under-the-hood to break this round-tripping. In 1984, when Apple produced the Mac, they also produced a most interesting data format called PICT. A human saw the PICT as a PICTure, but the computer saw more. It (could) see additional data embedded in the PICT. The clipboard supported the PICT format, which meant that both picture and data could be transferred between programs. And ChemDraw and Word also understood this. Hence the ability to round-trip noted above (it has to be said between specifically these programs).

Times moved on and the limitations of PICT set in. Apple refocussed on the PDF format. Related, notice, to the Postscript format that Adobe had introduced in order to allow high quality laserprinting. PICT support was abandoned, and the various components no longer carried recognisable data (specifically the clipboard or the ability of Word to recognise the data). Round-tripping broke. Does this matter? Well, one colleague where I work had accumulated more than 1000 chemical diagrams, which he decided to store in Powerpoint (and yes, he threw the original Chemdraw files away). The day came when he wanted to round trip one of them. And of course he could not. He was rather upset I have to say!

PDF was not really a format designed to carry data (see DOI: 10.1021/ci9003688). But, bless their hearts, the three vendors involved in this story all agreed to support data embedded in the PDF hamburger (and Abobe to tolerate it) and now once again, a structure diagram can move into an Office program (on Mac) and out again and retain its chemical integrity. What lessons can be learnt?

  1. Firstly, out of side, out of mind. The clipboard is truly mostly out of sight, and it was not really designed from the outset to preserve data properly. Nowadays I wonder whether clipboards in general recognise XML (and hence CML) and preserve it. I truly do not know. But they should.
  2. Secondly, any system which relies on three or four commercial vendors, who at least in the past, devised proprietary formats which they could change without warning, is bound to be fragile.
  3. We have learnt that data is valuable. More so than the representation of it (i.e. a 2D or 3D structure diagram). But when its lost, the users should care! And tell the vendors.
  4. Peter Murray-Rust and his team have produced CML4Word (or as Microsoft call it, Chemistry add-in for Word). At its heart is data integrity. Fantastic! But I wonder if it survives on Microsoft’s clipboard (I know it does not on Apple’s, since CML4Word is not available on that OS. And is unlikely to ever become so).
  5. And I can see history about to repeat itself. The same seems about to happen on new devices such as the Apple iPad. It too has copy/paste via a clipboard. I bet this will not round trip chemistry (or much other) data! Want to bet that the lessons of this story have not yet been learnt?

Oh, for those who wish to round-trip chemistry on a Mac, you will have to acquire ChemDraw 12.0.2 and Word 2011 (version 14.01), as well as OS X 10.6 for it to work.

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