Posts Tagged ‘GBP’

How-open-is-it?

Thursday, February 12th, 2015

The title of this post refers to the site http://howopenisit.org/  which is in effect a license scraper for journal articles. In the past 2-3 years in the UK, we have been able to make use of grants to our university to pay publishers to convert our publications into Open Access (also called GOLD). I thought I might check out a few of my recent publications to see what http://howopenisit.org/ makes of them.

This was catalysed by an article which revealed that UK universities spent £9M in 2014 on the purchase of such openness. One of the “challenges” identified is the difficulty in converting such payment into an article that actually is open. Apparently, publishers make not a few mistakes in their quality controls in ensuring it is so, relying on irate authors informing them of such mistakes. This can be quite tedious to do, and so a tool that largely automates this checking is most useful. So here we go.

  1. doi: 10.1039/C3SC53416B[1] This is a good start. The output looks like thus. Green is GOLD so to speak. Well done the Royal Society of Chemistry.
    10.1039:C3SC53416B
  2. doi: 10.1021/ci500302p[2] from the ACS this time. Pink, but at least free to read. Quite what that means is less certain. There is an adage, “the right to read means the right to mine” presumably means this article is OK to mine, but then why does it not say so?10.1021:ci500302p
  3. doi: 10.1002/anie.201405238[3]. Pink again, but the colour now simply means no information about the license could be obtained from the publisher (Wiley). 10.1002:anie.201405238

I ran a few more and sadly the third of the above, “no information” was the most common response. And the legal response is invariably that if no information can be obtained, the answer is NO, it is not free to read. In other words, not providing a license is just as bad as saying it’s not free to read.

Article aggregators such as Symplectic do not yet perform the service above (which to be fair is still in beta), and so I cannot yet check how many GOLD articles there are to my name. I think it should be about 8, and I might add that the time I have to spend in arranging for this to happen is not negligible. Hell, I could probably have found a few more reactions mechanism in the time I have spent on achieving GOLD. This is one of those topics which would be interesting to revisit say in five years time to see how the world has changed. So I leave this little time capsule and will update it then!

References

  1. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b
  2. M.J. Harvey, N.J. Mason, and H.S. Rzepa, "Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks", Journal of Chemical Information and Modeling, vol. 54, pp. 2627-2635, 2014. https://doi.org/10.1021/ci500302p
  3. A. Jana, I. Omlor, V. Huch, H.S. Rzepa, and D. Scheschkewitz, "N‐Heterocyclic Carbene Coordinated Neutral and Cationic Heavier Cyclopropylidenes", Angewandte Chemie International Edition, vol. 53, pp. 9953-9956, 2014. https://doi.org/10.1002/anie.201405238

Chemistry in the early 1960s: a reminiscence.

Monday, December 22nd, 2014

I started chemistry with a boxed set in 1962. In those days they contained serious amounts of chemicals, but I very soon ran out of most of them. Two discoveries turned what might have been a typical discarded christmas present into a lifelong career and hobby.

The first was 60 Stoke Newington High Street in north London, the home of Albert N. Beck, Chemist (or his son; my information comes from a historical listing of the shops present on the high street in 1921). I would set out from our home in London SW6 on the #73 bus route (top deck) and it would take about an hour to arrive. On entering the shop, I ventured down a set of stairs into the basement to replenish the chemicals with sensible stocks, and purchase the odd glassware, filter paper, etc. And then venture back across London carrying the proceeds of many weeks, possibly months worth of hoarded pocket-money (apart that is from 1 shilling every two weeks which I reserved for football at Craven Cottage). At some stage, health and safety legislated against 12-year-old boys (and certainly also girls) purchasing chemicals in this manner! However, I can assure you all that I never came to any harm with anything I purchased at A. N. Beck and Sons. Apart that is from giving my parents a good fright.

The second was coming across this book by A. J. Mee. I had thought it was well and truly lost; imagine my delight when I recently found it at home, complete with chemical stains, and dated as from a reprint in 1959.

IFOn the inside cover, I found one shopping list from my expeditions to A. N. Beck and Sons. The price 1/6 is the representation of one shilling and six pence (more than the price of a football match, or perhaps £50 in today’s money? I think football was much cheaper then! Oh, 1/6 is 7.5p in the decimal currency of today, or £0.075). Note that iodine was one of the items purchased. And note the wish list at the bottom! I was clearly starting to do organic chemistry.

shopping-list

The pages of this book list 289 experiments, and I assiduously recorded a tick against all the ones I actually did. This is a typical page (click to expand).

IFThus expt 205 is the preparation of 1,3,5-tribromobenzene from 1,3,5-tribromoaniline (ticked), followed by that of o-cresol from o-toluidine (ticked). You can see how all the aromatic rings are still represented by what now looks like cyclohexane. This book gave me many hours of delightful recreation (I have not counted the ticks, but I think I attempted around half the experiments). Note in particular the huge scale these experiments were done at; 18g of product (I suspect I must have scaled them down a fair bit in order to preserve pocket money). Expt 198 was that of benzidine, of which I do recollect preparing  ~2g. No warnings then about the extremely carcinogenic nature of this substance! Chemistry has certainly changed since then.

Lost unfortunately is the laboratory book where I recorded my results, but one or two samples still exist!

 

 

The price of information: Evaluating big deal journal bundles

Thursday, July 3rd, 2014

Increasingly, our access to scientific information is becoming a research topic in itself. Thus an analysis of big deal journal bundles[1] has attracted much interesting commentary (including one from a large scientific publisher[2]). In the UK, our funding councils have been pro-active in promoting the so-called GOLD publishing model, where the authors (aided by grants from their own institution or others) pay the perpetual up-front publication costs (more precisely the costs demanded by the publishers, which is not necessarily the same thing) so that their article is removed from the normal subscription pay wall erected by the publisher and becomes accessible to anyone. As the proportion of GOLD content increases, it was anticipated (hoped?) that the costs of accessing the remaining non-GOLD articles via a pay-walled subscription would decrease.

But as was shown[1], the publishers have hitherto arranged for the prices of these subscriptions to be covered by non-disclosure clauses. Which makes it quite difficult for us (the readers of these journals, and of course the main sources of their content as well) to find out if this model is (starting) to actually work. Certainly, the entire system does not yet appear to be in any sort of steady state equilibrium; perhaps it never will achieve this in the current model? For example, although extra funds have been made available to promote GOLD publishing, these cover only a small fraction of the total output of a typical research university. One could respond to this in several ways:

  1. Find the missing funds from somewhere else, which probably means less money for the research itself. This of course is the model that maintains or increases a publisher’s incomes.
  2. Decrease the costs of GOLD publishing. Currently a typical article processing charge ranges from £500-5000 depending on the prestige of the journal. Is it beyond the realm of possibility that this range could change to eg £50-500?
  3. Simply persuade everyone to publish less. Perhaps ten times less? Every group might be restricted to one or two block-buster articles a year, and the rest of their output goes into open repositories? Or indeed into blogs! These two options of course are unlikely to increase publishers’ incomes.

Well, after 350 years of scientific publishing, we appear to have arrived at a critical point. A cross-roads if you like. But who should be in charge of deciding what direction is now taken? Should it not be the very people who create and then “consume” scientific information and knowledge!

References

  1. T.C. Bergstrom, P.N. Courant, R.P. McAfee, and M.A. Williams, "Evaluating big deal journal bundles", Proceedings of the National Academy of Sciences, vol. 111, pp. 9425-9430, 2014. https://doi.org/10.1073/pnas.1403006111
  2. C. Woolston, "Secret publishing deals exposed", Nature, vol. 510, pp. 447-447, 2014. https://doi.org/10.1038/510447f

“Text” Books in a (higher) education environment.

Friday, May 18th, 2012

Text books (is this a misnomer, much like “papers” are in journals?) in a higher-educational chemistry environment, I feel, are at a cross-roads. What happens next?

Faced with the ever-increasing costs of course texts, the department where I teach introduced a book-bundle about five years ago. The bundle included all the recommended texts for an appreciable discount over individual purchase. In their first week at Uni, students were encouraged to acquire the bundle. As it happened, I met them for a tutorial shortly after this acquisition. The bundle weighed some 9 kg, and came shrink-wrapped into a strapless plastic sheath, posing a rather slippery and weighty challenge for the student to get back to their residency. A few months later, I asked the students how they were getting on reading their newly acquired texts. You must appreciate that it does take a few months for students to start getting “street-wise” about their uni experience. One savvy student recounted they had learnt that if one did not remove the plastic outer layer from the bundle, it would retain much of its resale value to the next generation of incoming students.

Now, I will not mention the publisher of this particular bundle, but its cost is in the region of £50 per text. And for some students, the 1500 or so pages of each volume remain largely unread. Rarely if ever do I see these texts brought into tutorials, and I expect the margins remain blank, un-annotated with any questions or notes (it affects the resale value if you do that). Which is a stark contrast to how the students nowadays annotate their lecture note hand-outs often (but not invariably) issued to them at the start of a lecture. I also observe that increasingly my tutorials are effectively annotated by the students attending (2-4 pages of notes can be taken during a 50 minute discussion. The unit can be declared as pages, since this is also done on paper).

Despite these trends, pedagogic usage of tablet devices such as Kindles and iPads remains relatively low. It is a chicken-and-egg situation. The aforementioned book bundle is not available for these devices, and if it were, then in the current business model, it would be DRM (digital-rights-management) protected to prevent resale, and would also probably retain (if not exceed) the cost of the printed version. Hardly attractive to a student. The lecture notes we distribute (as printed handouts) do indeed come as PDF versions which can be placed on a mobile tablet, but this advantage alone has not sufficed to promote rapid uptake of tablet here. Few materials are specifically optimised to take advantage of the unique features of a tablet, and so the printed lecture notes are considered acceptable. Perhaps this comes to the core of what such tablets are supposed to be. Are they devices for “content consumption”, or should we also expect them to be capable of “content creation”? Lecture (and tutorial) annotation is of course content creation (or perhaps augmentation). 

I might also take a look at the situation from the point of view of the textbook author. Unless you are a big name, you might expect to redeem about 10% royalties from one of the traditional publishers of academic texts. It might take you a year or so to write it, and you would expect to issue a further edition five years down the line if the book is successful. Two generations ago, every academic might be expected to write at least one book. I suspect that aspect has reduced nowadays; authors can hardly be encouraged to write if they think there is a prospect that the shrink-wrapping might not even be removed! If you are intending to write a text about, lets say stereochemistry, you also have to accept the 2D limitations of a printed book, or the inability to say animate a reaction path.

Where are these thoughts leading? Well, I do have to give an explicit example; Steve Jobs’ vision of the educational text-book, re-invented along the lines of what he famously introduced for music distribution. There, he recognised that the (presumed illegal) sharing of music via download sites that preceded the iTunes store was not a sustainable model. The $.99 download was conspicuously cheaper than the price of a physical music CD (excepting classical music, which did become absurdly cheap in this form), and a compromise on sharing stipulated only on devices owned by you rather than more widely amongst your friends. The same model was introduced for the iBook store. Here, the author of an eBook (I am no longer calling it a textbook) can if they wish retain 70% of whatever income it generates (it can also be free of course). The unit price was a fraction of the traditional paper-based book, low enough that the DRM-imposed inability to resell it was less of an issue.

What are the downsides of moving on from paper?

  1. Well, unlike a paper book which is instantly useable, the reader has to purchase a device. This device can cost more than the book bundle referred to above, although at its cheapest, the device is actually only about half the cost of the book bundle. And one might expect that device to last only 2-4 years before it becomes obsolete.
  2. It can be lost or damaged, although unlike a paper book, the online content can be readily restored at zero cost .
  3. If you purchase an eBook for one (proprietary) device, you cannot transfer it to another such device (say Kindle to iPad or vice versa), although if the content is free, that would not matter.
  4. Authors of such texts will have to retrain themselves to produce ebooks; it is not just a matter of using a standard word processor any more. I suspect writing/imaging/styling/scripting/widgeting (a verb for this collective process is needed; how about to flow?) an ebook takes a lot longer than word processing a text-book.
  5. You might have to consider the ongoing cost of using an ebook. By this I mean the data-plan that you might need in place to download components which are not actually part of the book (see below).

The upsides? Well, rather than my producing a list at this point, you might want to take a look at the first two examples below, both created by Bob Hanson, and think about how such inclusion in an ebook might enhance it:

  1. A device-sensitive page for display (try this out on an iPad or Android tablet; the Kindle might be more of a challenge).
  2. A page for building and minimising a molecular model
  3. This example is included, since it belongs to a chemistry text book, but actually would exist on a mobile device in functional form, if not actually a component of an ebook.

So an ebook becomes an environment where you can download a model from public databases, and annotate it with properties etc. Or you could use your ebook to build a model from scratch, then minimise its (molecular mechanics) energy, to say explore conformational analysis in the context of a chapter on the topic.

Well, at the start I posed the question what happens next? The two above examples give possible answers. An equally interesting question might then be who makes it happen? Will that be the evolutionary role of the traditional publishing houses? Will a new generation of skilful author capable of “flowing” an ebook emerge? Will students instead favour retaining their dependency on paper? Watch this space.

"Text" Books in a (higher) education environment.

Friday, May 18th, 2012

Text books (is this a misnomer, much like “papers” are in journals?) in a higher-educational chemistry environment, I feel, are at a cross-roads. What happens next?

Faced with the ever-increasing costs of course texts, the department where I teach introduced a book-bundle about five years ago. The bundle included all the recommended texts for an appreciable discount over individual purchase. In their first week at Uni, students were encouraged to acquire the bundle. As it happened, I met them for a tutorial shortly after this acquisition. The bundle weighed some 9 kg, and came shrink-wrapped into a strapless plastic sheath, posing a rather slippery and weighty challenge for the student to get back to their residency. A few months later, I asked the students how they were getting on reading their newly acquired texts. You must appreciate that it does take a few months for students to start getting “street-wise” about their uni experience. One savvy student recounted they had learnt that if one did not remove the plastic outer layer from the bundle, it would retain much of its resale value to the next generation of incoming students.

Now, I will not mention the publisher of this particular bundle, but its cost is in the region of £50 per text. And for some students, the 1500 or so pages of each volume remain largely unread. Rarely if ever do I see these texts brought into tutorials, and I expect the margins remain blank, un-annotated with any questions or notes (it affects the resale value if you do that). Which is a stark contrast to how the students nowadays annotate their lecture note hand-outs often (but not invariably) issued to them at the start of a lecture. I also observe that increasingly my tutorials are effectively annotated by the students attending (2-4 pages of notes can be taken during a 50 minute discussion. The unit can be declared as pages, since this is also done on paper).

Despite these trends, pedagogic usage of tablet devices such as Kindles and iPads remains relatively low. It is a chicken-and-egg situation. The aforementioned book bundle is not available for these devices, and if it were, then in the current business model, it would be DRM (digital-rights-management) protected to prevent resale, and would also probably retain (if not exceed) the cost of the printed version. Hardly attractive to a student. The lecture notes we distribute (as printed handouts) do indeed come as PDF versions which can be placed on a mobile tablet, but this advantage alone has not sufficed to promote rapid uptake of tablet here. Few materials are specifically optimised to take advantage of the unique features of a tablet, and so the printed lecture notes are considered acceptable. Perhaps this comes to the core of what such tablets are supposed to be. Are they devices for “content consumption”, or should we also expect them to be capable of “content creation”? Lecture (and tutorial) annotation is of course content creation (or perhaps augmentation). 

I might also take a look at the situation from the point of view of the textbook author. Unless you are a big name, you might expect to redeem about 10% royalties from one of the traditional publishers of academic texts. It might take you a year or so to write it, and you would expect to issue a further edition five years down the line if the book is successful. Two generations ago, every academic might be expected to write at least one book. I suspect that aspect has reduced nowadays; authors can hardly be encouraged to write if they think there is a prospect that the shrink-wrapping might not even be removed! If you are intending to write a text about, lets say stereochemistry, you also have to accept the 2D limitations of a printed book, or the inability to say animate a reaction path.

Where are these thoughts leading? Well, I do have to give an explicit example; Steve Jobs’ vision of the educational text-book, re-invented along the lines of what he famously introduced for music distribution. There, he recognised that the (presumed illegal) sharing of music via download sites that preceded the iTunes store was not a sustainable model. The $.99 download was conspicuously cheaper than the price of a physical music CD (excepting classical music, which did become absurdly cheap in this form), and a compromise on sharing stipulated only on devices owned by you rather than more widely amongst your friends. The same model was introduced for the iBook store. Here, the author of an eBook (I am no longer calling it a textbook) can if they wish retain 70% of whatever income it generates (it can also be free of course). The unit price was a fraction of the traditional paper-based book, low enough that the DRM-imposed inability to resell it was less of an issue.

What are the downsides of moving on from paper?

  1. Well, unlike a paper book which is instantly useable, the reader has to purchase a device. This device can cost more than the book bundle referred to above, although at its cheapest, the device is actually only about half the cost of the book bundle. And one might expect that device to last only 2-4 years before it becomes obsolete.
  2. It can be lost or damaged, although unlike a paper book, the online content can be readily restored at zero cost .
  3. If you purchase an eBook for one (proprietary) device, you cannot transfer it to another such device (say Kindle to iPad or vice versa), although if the content is free, that would not matter.
  4. Authors of such texts will have to retrain themselves to produce ebooks; it is not just a matter of using a standard word processor any more. I suspect writing/imaging/styling/scripting/widgeting (a verb for this collective process is needed; how about to flow?) an ebook takes a lot longer than word processing a text-book.
  5. You might have to consider the ongoing cost of using an ebook. By this I mean the data-plan that you might need in place to download components which are not actually part of the book (see below).

The upsides? Well, rather than my producing a list at this point, you might want to take a look at the first two examples below, both created by Bob Hanson, and think about how such inclusion in an ebook might enhance it:

  1. A device-sensitive page for display (try this out on an iPad or Android tablet; the Kindle might be more of a challenge).
  2. A page for building and minimising a molecular model
  3. This example is included, since it belongs to a chemistry text book, but actually would exist on a mobile device in functional form, if not actually a component of an ebook.

So an ebook becomes an environment where you can download a model from public databases, and annotate it with properties etc. Or you could use your ebook to build a model from scratch, then minimise its (molecular mechanics) energy, to say explore conformational analysis in the context of a chapter on the topic.

Well, at the start I posed the question what happens next? The two above examples give possible answers. An equally interesting question might then be who makes it happen? Will that be the evolutionary role of the traditional publishing houses? Will a new generation of skilful author capable of “flowing” an ebook emerge? Will students instead favour retaining their dependency on paper? Watch this space.

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.

Computers 1967-2011: a personal perspective. Part 1. 1967-1985.

Thursday, July 7th, 2011

Computers and I go back a while (44 years to be precise), and it struck me (with some horror) that I have been around them for ~62% of the modern computing era (Babbage notwithstanding, ~1940 is normally taken as the start of the modern computing era). So indulge me whilst I record this perspective from the viewpoint of the computers I have used over this 62% of the computing era.

  1. 1967: I encountered (but that term has to be qualified) my first computer, suggested to me as an alternative to running quarter marathons on Wimbledon common at school by an obviously enlightened teacher! I wrote a program (in Algol) on paper tape, put the tape in an envelope, and sent it off to Imperial College (by van) to run, on an IBM 7094. A week later, printed output showed you had made a mistake on line 1 of the program. As I recollect, after about eight weeks of this, I got the program to run (and calculated π to 5 decimal places).
  2. 1970: By now I was a student (again at Imperial College), and was introduced to Fortran, then a radical new innovation to a chemistry degree. The delightfully named pufft compiler combined with the 7094 again, but this time with punched Holerith cards as input and line printer output. I cannot remember what we were asked to program. I do remember that the punched cards were produced by a pool of punch card operators, working from code pages written by the programmer. Some students (not me!) thought it great fun to give their Fortran variables naughty names (which the punch card operators then refused to punch, thus causing the student to fail the course!).
  3. 1971: I really liked this programming lark, so when instant-turnaround was introduced that year, I decided to do a proper program. It was called NLADAD (yes, I was no good at names, even then), which stood for non-linear-analysis of donor-acceptor complexes. The idea was to take recorded NMR chemical shifts, and fit them to an equilibrium A+B ⇔ AB+B ⇔ AB2 using non-linear regression analysis. It must have been all of 200 lines of code (OK, I did not write the matrix inversion routine myself)! Instant turnaround was also great, you got to punch your own cards this time, and had the great excitement of feeding them into a card reader yourself. You then walked about 5 yards to the line printer and waited agog. No waiting one week, this was less than a minute. Or it would have been if the line printer did not paper-wreck every two minutes! (I might add that I have a dim recollection of a member of the computer centre staff standing by to recover these paper wrecks. He, by the way, is now the director of the ICT division here!).
  4. 1972: I am now doing a PhD (yes, boringly, yet again at Imperial College). I had found the one and only teletypewriter in the chemistry department. The crystallographers had secreted it away in their empire, but were very dismayed to find me occupying it constantly. Instant was now even more instant. I was now connecting to a time-sharing CDC 6400 computer, at the dazzling speed of 110 baud (or bytes per second). These were small bytes by the way, since the CDC used 6 bits per byte. The result was that one did everything in UPPER CASE, since a 6-bit byte only allows 64 characters! My (still Fortran) programs reached probably 1000 lines of code now, and I was engrossed in deriving non-linear analyses of steady state chemical kinetics (about four different kinds of rate equation as I recollect). Ah, the joys of covariance analysis, and propagation of errors (I was in a kinetics lab, and all the other students plotted graphs on graph paper, and if pressed, plotted gradients of graphs, the so-called Guggenheim plots. I thought this the dark ages, but no-one volunteered to join me in this single teletypewriter room. Not even the attractive girls in the group. I was the geek of my time, no doubt about that. My kinetic analysis did however have one upside. Its how I meet my wife to be a few years later!).
  5. 1974: PhD completed, I was now ready to go to Texas, where everything is bigger (and in terms of computers, slightly better, a CDC 6600 now and a 300 baud teletypewriter!). I had been computing now for seven years, and finally I actually got to SEE the device for the very first time. My mentor, Michael Dewar, had a sort of special relationship with the university. His students (and possibly only his students) were allowed to go into the depths of the machine room, where behind plate glass you could see the CDC 6600. I soon learnt how to get even closer. It was not particularly exciting however. I was more entranced with the CALCOMP flatbed plotter, which was located next to the 6600. Pictures at last (you probably do not want to know that to convert my kinetics in 4 above to pictures, I got quite expert in using a french curve. Look it up before you jump to conclusions). Part of the pact I negotiated was that I was only allowed into the inner sanctum at 03:00 in the morning (sic!). Still a geek then! Oddly, I was one of the few students in Dewar’s group using the CALCOMP, but at least we now had pictures of the molecules I was now calculating (using MINDO/3). To put the computing power into context, in 1975, Paul Weiner, another group member, announced that he had completed a full geometry optimisation of LSD, this having taken about 4 days to do on that over-worked 6600. The entire group went out to celebrate. Many pitchers of beer were drunk that nite.

    Computer graphics from 1976.

  6. 1977: Back to Imperial, where we might have also now had a CDC 6600. And a Tektronix terminal running at the dizzying (hardwired end-to-end) speed of 9600 baud. I learnt to Word process on this device (using a word processor, written in Fortran, although not by me) and I wrote three review articles by this means, using a fancy phototypesetter as the printer. My next program, STEK, probably ran to about 5000 lines of code, and it persuaded the Tektronix to plot all sorts of things, ball&stick diagrams, isometric potential surfaces, molecular orbitals, and the like (and jumping ahead, my experience with this program eventually led to CML, and Peter Murray-Rust, but that is indeed jumping ahead). I think I also managed to gain access to the Imperial machine room, that inner sanctum, yet again. But for reasons I will not go into, it was not as interesting as the Texan machine room.

    Chemistry Computer graphics, circa 1977-85.

  7. 1979: I encountered a Cray 1 computer, and probably also 8-bit bytes (and yes, lower case printer outputs) for the first time at the University of London Computing Centre.
  8. 1980: Remember that teletypewriter, encountered earlier. Well these were now running at 2400 baud and I started to organise the deployment of a chemistry department computer network to sprinkle several such terminals around the department. The controller was a PAD, and in that year, we introduced STN ONLINE using this network. It was the first time we could search CAS online ourselves (previously, it was a service offered by the library). Literature searching has not been the same since.
  9. 1980: I finally again encountered a real computer, which one could happily listen to without creeping into machine rooms in the middle of the night. It was the data system on a Bruker Spectrospin 250 MHz superconducting NMR spectrometer. I had many adventures on this system. It was installed, by the way, on more or less the same day as the birth of my first daughter Joana. It had a hard drive (5 Mbytes as I recollect, and cost an absolute fortune, around £10,000 if I remember correctly).

    Combining Quantum mechanics and NMR.

    Computer graphics 1982, from NMR spectrometer.

  10. 1982: More networks, this time a curious computer known as the Corvus Concept, using a networked hard drive (possibly as big as 20 Mbytes by now), and a large screen.
  11. 1985: Enter the Mac (OK, the IBM PC came a little earlier, but it was not entrancing). Now one really had a tactile computer that made noises (not always nice), produced smoke signals occasionally, and ejected its floppy disk incessantly. Yet another revolution to cope with. As I type this, I look down on that Mac, which is still underneath my desk. Wonder if its worth anything on ebay?

Well, a second consecutive blog, with (almost) no pictures or molecules. And I have only gotten to the half way stage of my story. Better break off then.