Posts Tagged ‘Apple’

What can chemistry learn from photos?

Sunday, June 2nd, 2013

A few years ago, we published an article which drew a formal analogy between chemistry and iTunes (sic)[1]. iTunes was the first really large commercial digital music library, and a feature under-the-skin was the use of meta-data to aid discoverability of any of the 10 million (26M in 2013) or so individual items in the store.‡ The analogy to digital chemistry and discoverability of the 70 or so million known molecules is, we argued, a good one.

Well, the digital photography revolution is very similar; I just checked my personal digital photo library to find it contains almost 14,000 photos dating back ten years now. It is not easy to find a particular photograph! Well, the reason I am posting here is to bring to your attention the first 6 minutes or so of an item in the BBC collection.† It is a very nice accessible explanation of the importance of meta-data for photography, and some of the innovative things that are being done for both acquiring and for manipulating this data. As I listened to this, I felt that for photograph, think molecule! And think of all the innovative things that could be done there as well.

Actually, you might reasonably ask how/whether molecular metadata is deployed here in this blog. It certainly is on Steve Bachrach’s site (see for example this recent post where you will find InChI keys for every molecule displayed; thus InChIKey=GOOHAUXETOMSMM-GSVOUGTGSA-N). I don’t do that on this blog (perhaps I should), but instead I provide URL links to a digital repository where they are displayed: thus follow http://dx.doi.org/10.6084/m9.figshare.706756 and you will find InChIKey=USGIFUSOUDIDJL-UHFFFAOYSA-N where it can be used as a search term to find any other instances of the same molecule at the site.

‡ Historical note: In 1997, we produced a CD-ROM containing the proceedings of the Electronic Conference on Trends in Heterocyclic Chemistry (ECHET96), H. S. Rzepa, J. Snyder and C. Leach, (Eds), ISBN 0-85404-894-4. Because it was entirely digital, we were able to include an “app” which created a visual navigation point derived from analysing the meta-data present (the entire contents had been expressed in HTML and so it was relatively easy to gather this meta-data). The software we used was called Hotsauce and was based on MCF (meta content framework) as developed by Apple engineer Ramanathan V. Guha for an internal experiment (we sometimes forget that in those days Apple was the Google of its day!). Guha left Apple, joined Netscape and MCF became RDF. The rest, as they say, is history. But you can see an early deployment on the CD-ROM I refer to above (these are NOT yet collectors items. Hint!). 

† This being the BBC iPlayer collection, it is quite possible that it is not accessible outside the  UK, or indeed even within the UK it may only be available for 8 days after broadcast.  Which would be a shame.

 

References

  1. O. Casher, and H.S. Rzepa, "SemanticEye:  A Semantic Web Application to Rationalize and Enhance Chemical Electronic Publishing", Journal of Chemical Information and Modeling, vol. 46, pp. 2396-2411, 2006. https://doi.org/10.1021/ci060139e

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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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Embedding molecules in blogs: ChemDoodle, WebGL and SVG

Friday, December 24th, 2010

If you get a small rotatable molecule below, then ChemDoodle/HTML5/WebGL is working. Why might this be important? Well, the future is mobile, in other words, devices that rely on batteries or other sources of built-in power. This means the power guzzling GPU cards of the past (some reach ~400 Watts!) cannot be used. Rather than using e.g. a full power OpenGL library, one will use Web-based graphics libraries, which (to quote Wikipedia) extends the capability of the JavaScript programming language to allow it to generate interactive 3D graphics within any compatible web browser. A typical target device might be for example Apple’s iPad (for which the redoubtable Jmol, which is based on Java, is unlikely to ever work).

To find out if your device and its browser can support this type of graphical display, go to either this test page or this more general one (which at the time of writing actually gets the WebGL test wrong!).

I have deployed an earlier graphical methodology in other posts (SVG), which many browsers now support. This combination of HTML5, SVG and WebGL is the future! For its use on another blog, see here.

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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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