John Ben DeVette's Blog

Thoughts experiences & learnings about the world of academic publishing …


OpenHelix offers a collection of genomic and bioinformatics learning tools custom designed by scientists for scientists. “Designed by scientists for scientists” may sound vague, but it is the essence of OpenHelix and why they currently offer a collection of tutorials and e-learning tools unprecedented and unrivaled.

Dr. Warren Lathe III, evolutionary biologist, genomicist, is Chief Science Officer at OpenHelix. Dr Lathe first gained notoriety for his breakthrough work in bacteria genomics at European Molecular Biology Laboratory (EMBL). Since 2003, Dr Lathe has been a leader in the area of learning and training in the field of genomics, bioinformatics, and proteomics. The recipient of several NIH grants to study and create e-learning tools, he now spearheads a the team of biologists who have built and maintain a collection of 100+ online tutorials. Introductory and in-depth training tools for researchers, scientists, and students include the well known genome browsers from UCSC, NCBI, Ensembl, Gbrowse, MEME, OMIM, Gramene, Galaxy, XplorMed, KEGG, iHOP, DAVID, TextPresso, GVS, Pfam, and dozens more. A complete list of online OpenHelix tutorials is available here:  Catalog

DeVette Publishing Solutions is the managing agent for OpenHelix LLC in Asia.  We are pleased to be working with Flysheet Information Services (Taiwan), iducation Inc. (Korea), and USACO Corp. (Japan).


23 April 2012 Posted by | E-learning, Uncategorized | , , , , , , , , , , , , , , , , , , , , , | Leave a comment

OpenHelix Wordle

Wordle: openhelix tagcloud 21April 07 blue

13 April 2012 Posted by | Uncategorized | Leave a comment

Building Crowds of Humans into Software – (MIT’s) Technology Review

Building Crowds of Humans into Software – Technology Review.

MobileWorks takes the business of crowdsourcing human work (as opposed to robotic or software-processing) to the next level. Crowdsourcing in its purest form is similar to the Wikipedia not-for-profit publishing model, where anyone (with sufficient knowledge about the topic) anywhere (with a computer and internet access) in the world becomes a contributor.

I applaud MobileWorks for its smart use of mobile phone technology (must be why they put “mobile” in their corporate moniker).  As I have mentioned in previous blogs and tweets: handheld / mobile technology, especially short-messaging-service (SMS) is the primary way the developing world stays connected.  Laptops and PCs are vastly outnumbered by smartphones (phones that can access the web).  SMS from any type of phone is simply faster and often safer (especially in China where email is regularly screened) than computer-based social networking solutions.

MobileWorks pays people (primarily Indian knowledge workers) to do the tasks that robots and software find difficult, like transliterating speech or describing a photo. Their turnaround time is minutes and promises better accuracy than 1st generation for-profit crowdsourcing business sites like Amazon’s Mechanical Turk. Obviously, MobileWorks has teamed up with several data encoding, back office outsourcing, IT companies whose employees now keep their smart phones and iPads turned on 24/7. Win-win. Major corporations get a correct answer faster, and the Indian knowledge workers up their income while sitting in traffic (Bangalore’s favorite pastime)

30 August 2011 Posted by | Crowd Sourcing | , , | Leave a comment

Update on the Southeast Asia Information Market for Western Publishers

International Market Updates: Middle East and Southeast Asia, a webinar was hosted by the Society of Scholarly Publishing and the Association of American University Presses last week.  I had the honor of presenting on Southeast Asia.  Includes details on the market for online and print books and journals, and databases in Southeast Asia.  And detailed information about the institutional information markets in Singapore, Malaysia, Thailand, and Indonesia.
The following is my PowerPoint presentation.


Special thanks to Nick Weir-Williams, Publishing Technology, for organizing the webinar!

20 December 2010 Posted by | Academic Publishing, Patent Copyright Intellectual Property IP, Scholarly Communication | , , , , , | Leave a comment

PERMALINKS, TinyURL, and shortDOI …What’s the Difference? Which One Should I Use?

Permalinks, TinyURL and Mini-URL are all condensed, space-saving versions of an original full-length URL address.  As a link they are all permanent, as long as the original content is still hosted at the original URL address then a mini-URL “pointer” will take you the website just as effectively as a permalink.  However, all publishers eventually move their old content to a digital archive somewhere.  The better publishers of the world plan ahead and the URL that appears when an article is first published will stay with it for “eternity”, regardless of which server the fulltext is hiding in today.  But not all publishers are as technically savvy, and chose instead to offer us a permalink, which the publisher guarantees will always find the content even after being moved into a digital archive somewhere.  And, yes, permalinks are considered permanent.

Permalinks are 2-3 times longer than a mini-URL.  And they are obviously longer than the technology requires, but they also serve as a form of visual bookmark.  So if you want your blog readers to know exactly where the shortened URL is taking them before they click, permalinks do this.   This is especially helpful when pasting several URL links close to each other, using a permalinks instead of a TinyURL will certainly reduce confusion about which link is going to what website.  A TinyURL is usually shorter than a permalink.

The New York Times uses permalinks.  Here’s what one looks like: (80 characters)

As an example, I subsequently created a TinyURL link to the NYT’s permalink: (26 characters)

As you can see, if you want to go through the hassle, it is not difficult to make a (very short) mini-URL that points directly to the content VIA a (not as short) permalink.  Ergo. clicking on the TinyURL takes you directly and immediately to the article, AND it will continue taking you directly to the article five years from now because the TinyURL is piggy-backing onto the permalink which will always know where the content has been archived.

In conclusion, if you want the shortest URL possible:  Use TinyURL.  If you want the most durable:  Use a permalink.  If you want BOTH a short & durable link, then create a mini-URL that links to a permalink (or a DOI) that links to the content.

If you are still reading this post, you must be really interested in this stuff!

So, you will certainly want to know about a NEW SERVICE that shortens lengthy DOI URI addresses called shortDOI™ Service.  The shortDOI Service functions exactly like TinyURL, but is operated by the International DOI Foundation, whom the whole world trusts implicitly.

This is an excellent 149 word introduction to DOI:

DOI is the acronym for a Digital Object Identifier.  On the surface, a DOI functions the same as a mini-URL or a permalink.  But DOI’s are really only used for journal articles, academic books (book chapters), and soon datasets.  They are used primarily by the academic and scientific communities, and are created and managed by a small group of not-for-profit organizations ( ).  A DOI is really not an URL or an URI, but acts like one and it will always link to the same article or book.   Within the publishing industry DOI’s are considered 99.99% permanent (more reliable than TinyURL).  The main advantage of a DOI is when citation of the original content is required (footnotes, bibliographies, etc.).  The DOI is now an integral part of the global bibliometrics system whereby authors (professors, scientists, students, etc.) receive recognition and funding (money) based on how much they publish.  Short DOI


Have you seen my earlier post?  TINY URL – Now Everyone Can Make Permanent Mini-URL Addresses on the Fly (Just like Twitter)




14 October 2010 Posted by | Archival, Self Publishing, Uncategorized | , , , , , , , , , , , , , | Leave a comment

XML: A SIMPLE & SHORT INTRODUCTION for people who want to understand WHY IS XML SO IMPORTANT?

Attached is a brief, 7-slide PowerPoint presentation explaining in very simple English why XML is important to publishers, authors, universities, and almost anyone who is creating content to be loaded onto websites, published as an e-book, stored in a digital archive / institutional repository, or needs to be findable via Google or other search engines.

[This PowerPoint presentation is a excerpt of a longer presentation I gave to the Japan Science and Technology Agency (JST) on 2010 September 17, entitled:  FUTURE TRENDS OF ACADEMIC PUBLISHING:  Creating an Efficient Access & Distribution System for Japan’s Research Output.  A copy of the JST presentation has been translated into Japanese and is available either from JST or by contacting me directly.]

4 October 2010 Posted by | Archival, Digital Publishing, Self Publishing, University Publishing | , , , , , , , | Leave a comment

China Must Create a New Academic Publishing Business Model

China’s top libraries issued a warning to the world’s major (for profit) academic publishers:  “develop a reasonable, realistic price policy…” or else!

The fallacy behind the 1 September 2010 “Joint Open Letter to International Publishers” [ ]  is that the group is all librarians, albeit, prominent librarians from prominent institutions. But in the information world of today, the librarian is no longer the customer.  If the declaration had come direct from the Ministry of Education, Ministry of Science & Tech or other member of the State Council, or even from an organized group of Chinese scientists, that would bear more weight.   Elsevier pushed through a huge price increase 2-3 years ago in China in spite of cancellations from basically the same group of libraries that issued the 1 Sept declaration.  Elsevier took its case direct to the university administrators who ordered the librarians to renew ScienceDirect and pay the increase.

The only way for China to reduce its dependance on “a few international STM publishers” is to sever the umbilical cord that measures PhD achievement in China with publishing in high impact factor journals (that are primarily owned by “a few international STM publishers”).  Simply building a larger consortia by adding the Chinese Academy of Sciences, the National Library, and NSTL to CALIS will not solve the fundamental problem.

China is seeing huge growth in paper submissions to the world’s top peer-reviewed journals.  The number of papers accepted has been gradually increasing, too, as the quality of research reporting in English improves.

China must proactively promote the open access green model to Chinese authors, and China must build top quality academic publishing houses inside China.  China should be an early adopter of the new publishing paradigms that are being experimented with globally today.  China has the potential to build a new academic publishing business model that will be an example for the rest of the world to follow.

Librarians around the globe have been writing letters to “a few international STM publishers” and complaining about price increases for more than 30 years!  Another letter will not make any difference, its time for a more fundamental change in the way knowledge management is done.


Link to the original English letter on the Chinese Academy of Sciences website:

Joint Open Letter to International Publishers – 中国科学院国家科学 …

13 September 2010 Posted by | Scholarly Communication, University Publishing | , , , , , , , , | Leave a comment

Do You Want to Publish In Japanese?

Do You Want to Publish In Japanese?  Are you boggled by the differences between English typesetting and Japanese text layouts?

Here are the links to two excellent resources explaining the challenges English language authors and publishers must face when preparing to have print or online works translated and published in the Japanese language.

The first link is to an excellent 6-page article by Tony Graham:  Layout of Japanese documents posted on in July 2009.  Tony uses 11 charts and about 20 paragraphs to summarize the entire problem facing Western publishers who want to publish Japanese language books, journals or high-quality websites in Japanese.

I particularly appreciate Tony’s comment:  “In the Western tradition, pages are designed from the outside in: the page size is decided first, followed by the size and placement of the main text block … [where as] In the Japanese tradition, it is the opposite: the size of the main text block (kihon-hanmen) is determined first … and the size of the page (trim size) is determined based on the proportions of the kihon-hanmen.

The second link is to a 4 June 2009 detailed English language document created by a working group of the World Wide Web Consortium, with the accurate but boring title: Requirements for Japanese Text Layout .  This 163-page tome is an excellent primer for software developers and page designers who have already decided to publish something in Japanese, and want a detailed outline of the differences between Western and Japanese typesetting and page construction.  You are still going to need to hire or outsource the work to a fluent Japanese crew, but at least you will now understand why it is taking so long, and why they are charging you so much!

The W3C document will also be beneficial to western marketing professionals who want to adopt their corporate theme to the Japanese market and wonder if the corporate brochures and Annual Report can be easily translated into Japanese.

Tony Graham’s summary on how the Japanese format published pages:  Layout of Japanese documents

The W3C’s Note (and soon to become a standard) on Requirements for Japanese Text Layout

6 September 2010 Posted by | Digital Publishing, Self Publishing | , , , , | Leave a comment

The Future Library Should Focus on Collecting and Formatting In-house, Locally Created Content

My vision for the future library is to have it focus on collecting and formating all local content into a single knowledge base. When all content: data sets, science notebook, papers, books, reports, manuals, blogs are part of the same knowledge base, then the archive, search, and distribution interfaces are easily managed and updated as technology evolves. In concept, this is similar to what Adam Bly refers to as a “digital core,” but Adam’s vision is global. The focus here is making the local institution’s in-house content future friendly.

27 April 2010 Posted by | Archival, Digital Publishing, University Publishing | , , , , , | Leave a comment

Yale Launches Course for the Book and Magazine Publishing Industry

The famous Stanford University publishing course SPPC  (Stanford Professional Publishing Course) was discontinued in 2009.  But New York based helmsman Robert Baensch stays involved with the new Yale start-up.   Yale’s new program, called simply “The Yale Publishing Course,”  intends to replace and supersede Stanford’s previous 5-day summer program by placing more emphasis on new technologies and digital publishing.

The new Yale course was just announced last week, and as yet no curriculum or syllabus is available online, but the focus remains helping commercial publishers adapt to a changing world.  The intended customer for the annual course will be publishing industry executives.

Open Access models will be covered, but I am curious to see if Yale will include a session on the new campus-based publishing movement which many academics and university administrators view as a direct, albeit fledgling competitor to the traditional publishing industry.

Link to the press release:

Yale Launches Course for the Book and Magazine Publishing Industry.

7 April 2010 Posted by | Digital Publishing | , , | Leave a comment

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