Showing posts with label publications. Show all posts
Showing posts with label publications. Show all posts

Saturday, November 10, 2007

Scientific authoring and publishing in the new age of multimedia: A Better Idea?

I would like you to indulge me for a moment and consider the following item from a recent entry in the Amazon Daily blog and forwarded here via my Google Reader account. Not only is it interesting from a digital photography standpoint, but it has implications on my vocation as an analytical chemist, but more about that after you read the article.

via Google Reader:

via Amazon Daily by Amazon Daily on 11/6/07

I learned about digital photography metadata from the FBI. They didn't give me a course or anything; they sent out a news release years ago that terrorists may be sending messages encoded into pictures on the Internet. As far as I know, your dgital camera isn't serving Al Qaeda's ends, but it did let me to discover that there's a whole world of information in a JPEG beyond the pictures you see.

You probably know what metadata is -- we use it all the time now, whether putting track names on an MP3 or looking up a library book by its Dewey Decimal number. You may even have used it on your photos, tagging a shot of the beach as "vacation." But it can be staggering to learn how much information there actually is.

Example: This is a JPEG:

But this is the information inside. The shutter speed, the aperture, user-added tags, even latitiude and longitude, they're all in there. Don't worry, though -- people can't find out your address from your online photos unless you want them to, or unless you're careless. There are two groups of metadata important to understand -- EXIF and IPTC. Broadly speaking, EXIF is what is captured on the image at the time you shot it, and IPTC are all the user-added comments afterward. Your EXIF knows what the camera was doing -- when the picture was taken, how fast the shutter went, what lens you used, etc., but it doesn't know that you were taking a picture of your aunt. That's for you to add.

What good is metadata? It's hard to even scratch the surface of the possibilities, but two major benefits are organization and improving your craft by figuring out how other people took photos you enjoy. The benefits for organization are obvious to anyone who's ever tried to sort through a basement full of negatives. The different between sorting through a box that says "Mid-80s" and being able to zoom in on photos you took on April 12 is palpable. If you take advantage of programs that can add metadata -- from free programs like Apple's iPhoto to professional software like Adobe Lightroom -- you can be as organized as you want. Maybe you want to note all of the people in the photos you take. Maybe you're into color and want to track which photos were dominantly red, and which were dominantly green. Maybe you want to track all the photos you took in Hawaii -- whatever you want, the notes affix themselves to the photo, so you'll have them wherever you store it.

But there's more. This is the Web 2.0 age, a time of unprecedented sharing. You don't have to ask a photographer "Hey, what camera did you use to take this?" If you can see the EXIF, you'll know, along with what focal length, ISO, shutter speed and aperture he or she used to make the photo look the way it does. Sites like Flickr or Picasa Web Albums have the EXIF available for public viewing on every photo (at the photographer's discretion), and they can be a great course in learning exactly what sorts of images these parameters can create. Sure, you can know intellectually that a long focal length lens plus a wide aperture equals a shallow range of focus, but isn't it easier to see it?

Here's the EXIF for this image.What does it tell us? The shallow focus comes from the combination of focal length (85mm), aperture (f/1.4) and distance (not shown, but about 15-20 feet). The shutter speed had to be 1/100th to freeze motion (and that was pushing it; faster would have been better if possible), and the ISO had to be bumped up to 1600 to allow that shutter speed to happen indoors. You can learn a lot about a photographer's choices from looking through EXIF.

So what can't you learn? In advanced photography, actually snapping the shutter is the least difficult part -- it's getting to the spot where the picture happens that matters. Either that's a physical journey to exotic locales, the sidelines of the big game, waiting for the perfect sunset, setting up studio lights, or simply getting your subject to react to you in an attractive way. EXIF won't help you there.

Take this photo:

This was taken at 102mm at f/13 and ISO 100. We can learn a few things about the photographer's choices from there -- it's attractively proportioned because of a long focal length, the small aperture and low ISO meant standard room light would be totally black, so this was lit by bright flashes, but we can't go out and recreate this photo just knowing those settings. And that's just a studio shot -- EXIF certainly isn't going to get you a gorgeous shot of the Hindu Kush mountains. Because of that, I hope that photographers are more free with letting their EXIF show on Web-based photos so beginners and intermediate students can learn valuable things about the mechanics of a shot. It's a great way to learn Photography 101, especially for the visually-oriented people who become photographers, but it's not going to cost the pros their jobs.


--Ryan Brenizer

Things you can do from here:



Now consider...

In measurement science, analytical chemistry in particular, data are "converted" into pictures in at least two major ways. First, and most obvious, is they are presented as images called photographs and videos. Second, and perhaps less directly obvious are the pictures of data that we scientists would normally call spectra. In both cases, one can imagine the same metadata as described in this article "enhancing" the photographs and videos taken. It could include all instrumental parameters needed to obtain the image. Moreover, standard operating procedures (SOP's), sample preparation, chain of custody, and every datum necessary to establish the pedigree of the sample studied could be directly embedded with the data of the spectra. Indeed, the entire analyst report could be part of the photograph, video, or spectrum.

Today, we consider such data as parts of reports. The emphasis is on the written word and each written report may contain or reference several images, videos, or spectra that enhance an author's point within a specific passage of a report. My questions are... can we do better and is this approach always the best?

Images, whether they are photographs, videos, or spectra make a powerful impact on the viewer. Indeed, the truism that a picture states a thousand words is unrefuted. Why then, as scientists, do we cling to burying such powerful media in written reports. I think there is a better way.

Consider Amazon again for a moment. When you search for a book, you are presented an emphasis on the image of the book, the title and, lately, hovering over images of books bring a list of links leading you to more information, much of it text but, potentially, some of it more imagery. Amazon does not bury the image of the book within the bounds of prose that might describe the book.

So how would such work in science? Imagine that instead of the National Transportation Safety Committee (NTSC) publishing a long report on an accident that includes a few pictures, it chose one image that highlights a particular aspect of the investigation, or the entire investigation, creates links and metadata within those images that reference and cross-reference items in the report. The table of contents could be a series of images followed by one line of text and the reader would quickly connect with the contents through the powerful imagery being presented.

Many other examples can be imagined. Databases emphasizing image based content already exist with the inclusion of chemical structures, spectra thumbnails, etc. Scientific journals are starting to include images as part of their web-based table of contents, but does this go far enough in encouraging authors to emphasize image-based authoring? Show a spectrum and embed the report rather that the other way around. Relative to publishers, research labs in the chemical and petrochemical industry are lagging significantly in this regard with little capability today on content management, knowledge management, and multimedia publishing systems to enable these approaches. As multimedia publication becomes cheaper, ubiquitous, and more flexible, should we consider the traditional scientific publication format passe?

I hope to have time in the future to create some specific examples emphasizing some of the advantages that I envision such a approach to have.

Wednesday, November 01, 2006

My Publications...

Updated 30 November 2007

  1. Morelli, John J., "Scientific authoring and publishing in the new age of multimedia: A Better Idea," http://analytical-science.blogspot.com 10 November 2007, http://analytical-science.blogspot.com/2007/11/scientific-authoring-and-publishing-in.html, accessed: 11 November 2007.
  2. Morelli, John J., "Analytical Science," Worldwide Web 15 November 2006, http://analytical-science.blogspot.com/, accessed: 11 November 2007.
  3. John J. Morelli, "Science Ethics," in: Bridges Program, SUNY - Purchase Summer 2004, State University of New York, Purchase, New York,2004.
  4. Morelli, John J. and Graef, Jean, "Leveraging current awareness information," The Montague Institute Review 21 May 2004, http://www.montague.com/review/awareness.htm, accessed: 28 June 2004.
  5. Morelli, John J., "Automated monitoring of customer access," The Montague Institute Review 21 May 2004, http://www.montague.com/review/monitor.htm, accessed: 28 June 2004.
  6. John J. Morelli, "Ethics In Chemistry," in: SUNY - Purchase, Seminar Series 2004, State University of New York, Purchase, New York,2004.
  7. Rahni, David N. and Morelli, John J., "Persistence, Bioaccumulation and Toxicity," Worldwide Web 2004, http://webpage.pace.edu/dnabirahni/reasearch_proj.htm, accessed: 23 February 2007.
  8. John J. Morelli, "Valuing content by automated monitoring of customer access," in: 2002 Fall Meeting of the IRI-ISDN, published by: Industrial Research Institute, Washington, D.C. October 2002, Annapolis, Maryland, 2002 http://www.iriinc.org/data_infos/Networks/IRI-ISDNoct02p.ppt.
  9. John J. Morelli and Gerald Szajer, "Analysis of Surfactants, Part II," Journal of Surfactants and Detergents 4 (1):75-83, 2001. http://www.springerlink.com/content/656240346075n61r/?p=ef6847b6acf94f19a846e8d5652aab27&pi=1.
  10. John J. Morelli and Gerald Szajer, "Analysis of Surfactants, Part I," Journal of Surfactants and Detergents 3 (4):539-552, 2000. http://www.springerlink.com/content/083614230l7lm18t/.
  11. John J. Morelli and Kristan Frisch, "Facile dehydrochlorination of b-hydroxy-g-chloroprpopyl, dimethyl fatty alkyl quaternary ammonium salts,", published by: American Society for Mass Spectrometry, Santa Fe, New Mexico, Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics 1998, Oralndo, Florida,1998.
  12. John J. Morelli, "The utility of source CID in APCI for characterizing oligomeric aromatic phosphate esters having molecular weight distributions greater than the mass range limit of the mass spectrometer," AAN 97-1, 1997, Akzo-Nobel Analytical Application Note.
  13. Michael A. Grayson, John J. Morelli, and Charles G. Fry, "The kinetic map to determine long-term durability of polymeric materials undergoing weight loss," in: ACS Rubber Division Meeting, published by: The American Chemical Society, Washington, D.C. 08 October 1996-10 October 1996, Louisville, Kentucky,1996.
  14. Gary Moffet, Timothy J. Shelley, and John J. Morelli, "Analyzing gases from decomposing electrical insulation," NASA Tech Briefs (December):47, 1995.
  15. John J. Morelli and Thomas C. Sandreczki, "The vacuum pyrolysis and thermal degradation in air of irradiated poly(ethylene-co-tetrafluoroethylene) films," Journal of Analytical & Applied Pyrolysis 35:121-141, 1995.
  16. J. Kurtz and John J. Morelli, "SSDECON REPORT EXCERPTS -Draft," John J. Morelli, 1994. FAX.
  17. John J. Morelli, "The kinetic map," published by: Akzo Nobel Central Research Laboratory, Dobbs Ferry, New York: AAN 94-3:1, 1994. 1994. Analytical Applications Note.
  18. John J. Morelli, "Ethics in Chemistry," in: The Responsible Chemist (course) - Annual Invited Lecture 1994-1999, University of Massachusetts, Lowell, Massachusetts, 1994-1999.
  19. John J. Morelli, "Mass Spectrometry in the Chemical Industry," in: Westchester Chemical Society Symposium on Mass Spectrometry in Industry 1992, Elmsford, New York, 1992.
  20. John J. Morelli and Richard Shelley, "Test Plan: APU Diaphragm Testing," Raymond Reynaud, David L. Baker, David W. Young, and Tibor Farkas, published by: Lyndon B. Johnson Space Center, White Sands Test Facility, Las Cruces, NM: TP-WSTF-682:i-DIST-1, 1992. Test Plan.
  21. John J. Morelli, "Real-time multi-purpose monitor for assessing the integrity of confined atmospheres," published by: Lyndon B. Johnson Space Center, White Sands Test Facility, Las Cruces, NM: 1991. slide hard copies.
  22. John J. Morelli, Charles G. Fry, Michael A. Grayson, Arthur C. Lind, and Clarence J. Wolf, "The thermal oxidative degradation of an ethylene-tetraflouroethylene-copolymer-based electrical wire insulation," Journal of Applied Polymer Science 43:601-611, 1991.
  23. John J. Morelli, "Validation of NHB 8060.1C, Test 18 Arc Tracking," Rollin C. Christianson, Larry J. Linley, and Frank J. Benz, published by: Lyndon B. Johnson Space Center, White Sands Test Facility, Las Cruces, NM: TP-WSTF-651:i-DIST-1, 1991. Test Plan.
  24. John J. Morelli and J. Kurtz, "Preliminary data from the test project: Evaluating methods for detecting and decontaminating propellant-contaminated surfaces in space - ammonia results phase I," published by: NASA White Sands Test Facility, John Space Center, Houston, Texas: 1991. Final Report.
  25. Ted Steinberg, "Test Report: Validation of NHB 8060.1C, Test 18 arc tracking," John J. Morelli, Larry J. Linley, and Frank J. Benz, published by: Lyndon B. Johnson Space Center, White Sands Test Facility, Las Cruces, NM: TR-651-001:i-DIST-2, 1991. Test Report.
  26. Michael A. Grayson, John J. Morelli, and Clarence J. Wolf, "Effects of tensile stress on the transport of environmnental fluids in thermoplastic composites," in: 33rd IUPAC International Symposium on Macromolecules 1990, 1990.
  27. Paul C. Lyons, John J. Morelli, David M. Hercules, David Lineman, Carolyn L. Thompson-Rizer, and Frank T. Dulong, "The laser microprobe mass analyser for determining partioning of minor and trace elements among intimately associated macerals: an example from the swallow wood coal bed," Fuel 69:771-775, 1990.
  28. John J. Morelli and Michael A. Grayson, "Dielectric Breakdown Mass Spectrometry,", published by: American Society for Mass Spectrometry, Santa Fe, New Mexico, Proceedings of the 38th ASMS Conference on Mass Spectrometry and Allied Topics 03 June 1990-08 June 1990, Tuscon, Arizona, 1990.
  29. John J. Morelli and Michael A. Grayson, "Tandem mass spectrometric investigation of pyrolytic decomposition products from ETFE films,", published by: American Society for Mass Spectrometry, Santa Fe, New Mexico, Proceedings of the 38th ASMS Conference on Mass Spectrometry and Allied Topics Tuscon, Arizona, 1990.
  30. John J. Morelli, "Thermal analysis using mass spectrometry: A review," Journal of Analytical & Applied Pyrolysis 18:1-18, 1990.
  31. John J. Morelli. "Laser micro mass spectrometry for the direct analysis of coal macerals," In: Lasers in Mass Spectrometry, edited by David Lubman, published by: Oxford Press, New York, 1990 http://www.oup.com/us/catalog/general/subject/?view=usa&sf=toc&ci=0195059298.
  32. Paul C. Lyons, John J. Morelli, and David M. Hercules. "Application of the laser microprobe (LAMMA 1000) to the microanalysis of coal constituents," In: New Frontiers in Stable Isotopic Research: Laser Probes, Ion Probes, and Small-Sample Analysis, edited by W. C. Shanks and R. E. Criss, published by: United States Geological Survey, Denver, Colorado, 1989.
  33. John J. Morelli and David M. Hercules, "Laser mass spectra of liquids taken at ambient pressure," Applied Spectroscopy 43 (6):1073-1081, 1989. http://www.ingentaconnect.com/search/expand?pub=infobike://sas/sas/1989/00000043/00000006/art00029&unc=.
  34. John J. Morelli, "Laser micro mass spectrometry (LAMMS) for direct analysis of coal macerals," in: Spring Meeting of the American Chemical Society, published by: American Chemical Soceity, Washington, D.C. 09 April 1989-14 April 1989, Dallas, Texas, 1989.
  35. John J. Morelli, Charles G. Fry, Clarence J. Wolf, Michael A. Grayson, and Arthur C. Lind, "Thermal stability of ETFE copolymer systems,", published by: American Society for Mass Spectrometry, Santa Fe, New Mexico, Proceedings of the 37th ASMS Conference on Mass Spectrometry and Allied Topics :282-283, 1989, Miami Beach, Florida, 1989.
  36. John J. Morelli, Michael A. Grayson, and Clarence J. Wolf, "Thermally labile salts for aiding quantitation of reactive decomposition products," Analytical Chemistry 61 (8):802-805, 1989. http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/1989/61/i08/f-pdf/f_ac00183a004.pdf?sessid=8545.
  37. Clarence J. Wolf, Joan E. Deffeyes, Michael A. Grayson, John J. Morelli, and Ronald S. Soloman, "Stability of irradiated ETFE insulated electrical wires,", 34th International SAMPE Symposium and Exhibition, Reno, Nevada:-10 pages, 1989, 1989.
  38. John J. Morelli, David M. Hercules, Paul C. Lyons, Curtis A. Palmer, and Janet D. Fletcher, "Using laser micro mass spectrometry with the LAMMA-1000 instrument for monitoring relative elemental concentrations in vitrinite," Mikrochimica Acta III:105-118, 1988.
  39. John J. Morelli, Michael A. Grayson, and Clarence J. Wolf, "Quantitative analysis of reactive decomposition products using thermally labile salts,", published by: American Society for Mass Spectrometry, Santa Fe, New Mexico, Proceedings of the 36th ASMS Conference on Mass Spectrometry and Allied Topics :474-475, 1988, San Francisco, California, 1988.
  40. Paul C. Lyons, David M. Hercules, John J. Morelli, George A. Sellers, David Mattern, Carolyn L. Thompson-Rizer, Floyd W. Brown, and Michael A. Millay, "Application of laser microprobe (LAMMA 1000) to 'fingerprinting' of coal constituents in bituminous coal," International Journal of Coal Geology 7:185-194, 1987.
  41. Paul C. Lyons, John J. Morelli, David M. Hercules, David Lineman, Carolyn L. Thompson-Rizer, and Frank T. Dulong, "Laser microprobe (LAMMA 1000) chemical analysis of clay minerals: Potential application to in situ analysis of clay minerals in coal,", Proceedings of the 11th Interantional Congress of Carboniferous Stratigraphy and Gelology 31 August 1987-04 September 1987, Beijing, China, 1987.
  42. John J. Morelli, Zbigniew A. Wilk, David M. Hercules, Paul C. Lyons, Curtis A. Palmer, and Janet D. Fletcher, "Direct analysis of coal macerals using laser micro mass spectrometry,", published by: University of Pittsburgh, School of Engineering, Department of Chemical & Petroleum Engineering, Pittsburgh, Pennsylvania, Proceedings of the Fourth Annual Pittsburgh Coal Conference :166-177, 1987, Pittsburgh, Pennsylvania, 1987.
  43. John J. Morelli, Somayajula K. Viswanadham, Andrew G. Sharkey, Jr., and David M. Hercules, "Laser mass spectrometry of organophosphorus pesticides and related compounds," International Journal of Environmental Analytical Chemistry 31:295-323, 1987.
  44. David M. Hercules, John J. Morelli, Frank P. Novak, and K. Balasanmugam, "Organic laser mass spectrometry - A new microprobe analytical technique,", Proceedings of the 13th Meeting of the Federation of Analytical and Spectroscopy Societies 28 September 1986-03 October 1986, 1986.
  45. Paul C. Lyons, David M. Hercules, John J. Morelli, George A. Sellers, David Mattern, Carolyn L. Thompson-Rizer, Floyd W. Brown, and Michael A. Millay, "Laser microprobe 'fingerprinting' and origin of elements in vitrinite bands from selected coal beds of eastern United States," ,ed: L. M. H. Carter, published by: U.S. Geological Survey, Reston, Virginia, USGS Research on Energy Resources - 1986 Program and Abstracts (Circular 974) 1986.
  46. John J. Morelli, Frank P. Novak, and David M. Hercules, "Comparison of laser mass spectra obtained at ambient conditions vs. sample freezing," ,eds: A. Bennighoven, R. J. Colton, D. S. Simons, and H. W. Werner, published by: Springer-Verlag, Berlin, Secondary Ion Mass Sectrometry, SIMSV, Proceedings of the Fifth International Conference, Washington DC :551-554, 1985, 1986.
  47. John J. Morelli, Kenneth J. Rosnack, Jr., and David M. Hercules, "Laser mass spectra of solutions at ambient pressure,", published by: American Society for Mass Spectrometry, Santa Fe, Proceedings of the 34th Annual Conference on Mass Spectrometry and Allied Topics :509-510, 1986, Cincinnati, Ohio1986.
  48. John J. Morelli and David M. Hercules, "Ambient pressure laser mass spectrometry of organophosphorus pesticides on plant tissues," Analytical Chemistry 58 (7):1294-1298, 1986. http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/1986/58/i07/f-pdf/f_ac00298a006.pdf?sessid=6006l3.
  49. Paul C. Lyons, David M. Hercules, John J. Morelli, George A. Sellers, David Mattern, Carolyn L. Thompson-Rizer, Floyd W. Brown, and Michael A. Millay, "Laser microprobe characterization of vitrinites for the lower Bakerstown coal bed," in: U.S. Geological Survey Symposium on Coal Quality, published by: U.S. Geological Survey, Reston, Virginia Reston, Virginia, 1985.
  50. John J. Morelli and David M. Hercules, "Laser microprobe mass spectrometry of organophosphorous compounds,", Mircrobeam Analysis ,eds: A. D. Romig, Jr. and J. I. Goldstein, published by: San Francisco Press, Inc., San Francisco, CA 94101-6800:15-18, 1984.

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