John Ben DeVette's Blog

Thoughts experiences & learnings about the world of academic publishing …

GENOMIC and BIOINFORMATICs LEARNING TOOLS “DESIGNED BY SCIENTISTS FOR SCIENTISTS” OpenHelix

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).

openhelix

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

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:

http://bits.blogs.nytimes.com/2010/10/12/amazon-introduces-a-new-type-of-e-book/ (80 characters)

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

http://tinyurl.com/252u49l (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 (http://www.doi.org ).  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

RESOURCES:

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

PERMALINKS: http://codex.wordpress.org/Using_Permalinks

TinyURL:            http://tinyurl.com/

shortDOI:           http://shortdoi.org/

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

Contract Law Takes Precedence Over Copyright Law: PINK FLOYD WINS IN COURT

“Pink Floyd Wins Court Battle With EMI Over Downloads” was announced last week in London. [ http://www.nytimes.com/2010/03/12/business/media/12pink.html ] A good reminder to authors and creators of intellectual property. Whenever you enter into a contract with a publisher (or in this case a recording company or record label) the wording of the contract supersedes and overrides copyright law.

In the case of Pink Floyd versus EMI, the contract in question was favorable to the artists’ interests, and limited the way EMI was allowed to sell (online or in any format) Pink Floyd’s recordings. In effect, EMI must sell only entire the entire album or CD, and is not allowed to sell individual songs online or in any format.

In essence this is the same battle that academic publishers are having with authors. Increasingly, authors want to control how their intellectual property (IP) is being used. Any contracts signed between author and publisher will supersede common copyright law. So when submitting articles for publication, please pay close attention to the fine print before signing away your future rights.

This has implications for university institutional repositories and open access publishing endeavors, obviously.  Choosing a Creative Commons License in effect will also supercede common copyright law, but once again, any contracts signed between author and publisher will supersede a Creative Commons license in the same way it overrides common copyright law.

LINK TO ORIGINAL NYT ARTICLE:   http://www.nytimes.com/2010/03/12/business/media/12pink.html

Creative Commons:  http://creativecommons.org/

15 March 2010 Posted by | Digital Publishing, Patent Copyright Intellectual Property IP, Self Publishing, Uncategorized | , , , , , | Leave a comment

NEW PARADIGMS IN SCHOLARLY COMMUNICATION / A Series of Lectures on the Future of Academic Publishing

NEW PARADIGMS IN SCHOLARLY COMMUNICATION
A Series of Lectures on the Future of Academic Publishing

John Ben DeVette
DeVette Publishing Solutions
johndevette@devettepublishing.com
https://devette.wordpress.com

Assuming libraries are unsustainable, universities are re-engineering scholarly communication models, and forcing publishers to re-engineer business models. Legacy publishing systems must evolve or become redundant. A host of new publishing, social networking, and online communication tools now exist and are pushing academics toward a significant new way of interacting with peers and the publishers.
The series begins with a review of the goals of scholarly communication. A session will focus on why ScienceDirect and PLOS in their unique and seemingly contradicting ways have become huge successes. The group will learn about a variety of new publishing and online communication tools, and methods for measuring academic achievement. Twittering will be strongly recommended and real time examples given of its effectiveness in learning and communication.
[9 LECTURE SERIES. 17 HOURS]
1. What is Scholarly Communication. Why scholars communicate. [1 hour]
a. Finding the truth & making it known
b. Humans are a social organism: Teamswork
c. Importance of interdisciplinary communication

2. Overview of publishing models: present and future [3 hours]
a. Science publishing.
i. Case study: the evolution of Elsevier’s ScienceDirect.
ii. Case study: PLOS, publishing articles, not journals.
b. User-generated science. Online collaboration. Crowdsourcing.
c. Blogs and other social networking tools are building global societies of scholars.
d. How to use Twitter.

3. Bottlenecks to communication & learning [2 hours]
a. Copyright. Protecting the author’s idea or the publisher’s profits?
b. Applying Cournot’s Model of Oligopoly to the publishing market.
c. Publish or perish. The difficulties of measuring academic success.
d. Information overload. Finding the needle of truth in a haystack of hubris
e. Journals are better for storage than communication.
f. Language barriers to learning

4. The role of e-books in scholarly communication [2 hours]
a. E-books, e-readers, e-platforms, and why the iPad will change everything.
b. 30 million e-books. How will these impact the future of libraries and online use of information?
c. The Google Books Library Project
d. Digital text books are different
e. Print on Demand

5. Copyright [2 hours]
a. History of copyright law. Why we protect intellectual property.
b. Enforced scarcity in a market of overproduction?
c. Public Knowledge Project.
d. SPARC. Open Access Movement.
e. Creative Commons.
f. How Google is changing the rules.

6. The Self-publishing Movement. [3 hours]
a. Role of universities in the information chain.
i. Campus-based publishing. Merging the library and the university press. Case study: Univ of Michigan.
b. Leveraging the university institutional repository.
c. Role of learned societies.
d. Micro-publishing in a mega-publisher world.
e. New (and often open source) tools for publishing.
f. The blog as a record of scholarly achievement.

7. How to create scholarly communities for people who cannot speak the same language. [1 hour]
a. OAI-MPH compatibility
b. Translation strategies
c. Symbol-based evaluation and feedback models
d. Visual learning. Use of videos and charts in publishing.
e. Aural communication solutions

8. Findability. Improving the way online content is accessed. [1 hour]
a. Digital formats
b. Indexes. Human or Machine
c. How to get hit by Google
d. Metadata & XML. CrossRef & DOIs.

9. Evaluating scholarly performance / Bibliometrics. How we spotlight quality and evaluate scholarly performance. Are we rewarding excellence or limiting innovation? [2 hours]
a. Impact Factors, including their role in academic advancement.
b. Focusing on the quality of an article or an author. New metrics. Article Level Metrics. ResearcherID.
c. Using the Hirsch Index to measure an author, a faculty, a university, and even a nation.
d. How to measure tagging activity.
e. Self-mediated peer review.

ONLINE LINK TO GOOGLE DOCS AT:
http://docs.google.com/View?id=dcbj2pbh_6ktz93cdn

Copyright info at Creative Commons:

Creative Commons License
NEW PARADIGMS IN SCHOLARLY COMMUNICATION A Series of Lectures on the Future of Academic Publishing by John Ben DeVette is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License.

24 February 2010 Posted by | Crowd Sourcing, Digital Publishing, Self Publishing, Uncategorized, University Publishing | , , , , , , , , , , , , , | 1 Comment

Heavy Consumers of Romance Novels Love E-Readers

In a conversation last June (2009) with Paul Keith, Electronic Resources Librarian at Chicago Public Library, he said that circulation of e-books provided by his library was up noticeably. An interesting note about the kind of library patrons who are early adopters of e-books, Paul said: “Heavy readers of romance novels love e-readers.” My ‘nutshell’ interpretation of that is affluent commuters & urbanites who read lots of thick novels, with sensual cover-art prefer e-readers for their privacy and convenience.

More specifically, e-books and e-book readers are attractive to people who are:
1. Heavy readers of thick books. Ie. romance, science fiction & fantasy, best sellers.
2. Students. Again, because text books are heavy.
3. Commuters & urbanites, who don’t want to advertise what they are reading.
4. Business travelers.
5. Early adopters.

22 February 2010 Posted by | Digital Publishing, Uncategorized | , , , , | Leave a comment

What is CAMPUS-BASED PUBLISHING? An Excerpt from My Upcoming Article…

Campus-based publishing is a new phenomenon taking place at some of the world’s leading universities. Campus-based publishing is where the university press and the library form a partnership, often one combined organization with singular leadership and a mandate from the university chancellor to be the general manager of the entire flow of information from consumption to creation to storage to dissemination. These new entities are self-serving and proud of it!

For decades, universities have had established university presses. Also, for decades these in-house publishing units have acted mostly independent of their faculties’ traditional activities of research and reporting, and their libraries’ information management responsibilities. It has become obvious that universities have been sitting in a vast pool of learning (a knowledge base) that has been growing and maturing in their own back yard, but has been grossly miss-managed and underutilized.

It is crucial for the long term viability of universities to retain control of the knowledge they create. University presses know how to publish. Libraries are experts at acquiring and archiving information.

The world wide web changed the way scholars communicate, creating new opportunities for information management. Academia is making fundamental changes to the way the universities package and distribute scholarly communications and published results.

25 December 2009 Posted by | Uncategorized | , , , | Leave a comment

CAMPUS-BASED PUBLISHING: Building a New E-book Publishing Platform for a University Press

Discussion of the challenges and opportunities facing campus-based publishers, specifically in regard to academic e-books.
The Andrew W. Mellon Foundation has awarded a grant to a consortium of NYU U Penn, Temple, and Rutgers Presses, to brainstorm and recommend how university presses might collaborate and build new publishing models for e-books.

HIGHLIGHTS from Monica’s Talk:

The aim is to jointly build ONE PLATFORM that can eventually be used by any academic press anywhere in the world.

The strategy reminds me of the Public Knowledge Project’s vision when they began developing OJS open source software 10 years ago.

Academic E-BOOKS ARE SIGNIFICANTLY DIFFERENT from e-journals, largely because 75-80% of e-books buyers are INDIVIDUALS (therefore buying single books). As opposed to e-journals for whom 99% of their purchase are libraries. Ergo: e-books sales are mostly BtoC, but e-journals are BtoB.

The intended business model is not open access. They intend to sell the content online.

They plan to develop a REVENUE SHARE MODEL where a percentage of revenues is paid to the author.

Two friends of mine: Judy Luther and October Ivins are consulting on the project ;-D

Monica McCormik, of NYU Press, had a webinar on November 20, which was taped and posted on SPARC’s website. Watch the complete talk with Q&A (1 hour) here= http://blip.tv/file/2916345

16 December 2009 Posted by | Uncategorized | , , , , | Leave a comment

Spain and Finland Say: It Is My Legal Right To Have Internet Access

On October 14, Finland announced a new law that makes access to the Internet a legal right. By July 2010, a 1Mb Internet connection must be available to every Finlander, and it jumps to a 100 Mb broadband connection in 2015.

Then on Nov 17, Spain declared Internet access a legal right, too.

I expect to see most of the European Union follow suit over the next couple years.

While most people in Finland and Spain already have online access, guaranteeing that everyone has access at a controlled fair price will have a deep impact on the development of infrastructure, public services, and a socioeconomic watershed effect into daily life. The long term side effects are barely imaginable.

If developing, impoverished countries are given the same “rights of online access” the improvements to quality of life and learning will be colossal!

References:
Finland: http://www.techcrunch.com/2009/10/14/applause-for-finland-first-country-to-make-broadband-access-a-legal-right/

Spain: http://www.pcmag.com/article2/0,2817,2356014,00.asp

1 December 2009 Posted by | Uncategorized | , , , | Leave a comment

Selling E-book Readers in China. Using Patent Laws to restrict competition. A Lesson from the DVD player.

I expect China will plan to use its own local technology for e-book readers. This is what they did for DVD players several years ago. The government created a new and unique standard for the type of laser that must be used in Chinese DVD machines. The standard is different from the rest of the world. The result is all locally sold DVD players, even if manufactured by a foreign-owned factory located in China, have to use Chinese technology in order to be Chinese compliant, and therefore everyone has to pay a royalty to the Chinese patent owner of the “new” DVD standard. The problem is the standard was not decided by open market forces, but rather has been artificially created and legislated into existence by the Chinese government.
The future demand for e-book readers in China will be huge. China Mobile, the world’s largest cellular company, has already announced it intends to dominate the e-reader market and plans to use Chinese technology.

19 November 2009 Posted by | Uncategorized | , , , | Leave a comment

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