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“Sure, you’d rather focus on science than think about open access.  But the decisions made today about publishing models are relevant not only to your work, but also to the future of biomedical research.   So pay attention.” 

Here’s your opportunity to catch up with the debate, read well-thought-out essays, and figure out where you want to stand.   

The November issue of Genome Technology focuses its cover story on Open Access (and has been made openly available under a Creative Commons license).   The quote above is from the opening editorial.  

Check it out at http://www.genome-technology.com/Nov08.html

RefWorks has announced its webinar training schedule for December 2008.  All Jeffersonians are welcome to register for any of the workshops below.  They’re FREE! However, attendance is limited and registration is required. All times on the schedule are Eastern Standard Time.

RefWorks Fundamentals

This 75 minute session covers all the basics – creating a RefWorks account, importing data, organizing your database and generating a bibliography; great for new users or even existing users who would like a refresher.

Tuesday, December 2, 2008 10:00 a.m.
Enroll Now!

Tuesday, December 16, 2008 6:00 p.m.
Enroll Now!

RefWorks Advanced Features
This 75-minute session covers topics such as advanced searching, using RefGrab-It to import data, working offline, editing multiple references, viewing, printing and sorting references and more. Attendees should have a working knowledge of RefWorks’ basic features.

Wednesday, December 3, 2008 2:00 p.m.

Thursday, December 4, 2008 10:00 a.m.
Enroll Now!

Write-N-Cite III for Windows
This 30-minute session introduces the latest update (version 3) to the Write-N-Cite utility in RefWorks. In this brief session we will discuss what’s new in Write-N-Cite III, how to install it, and how to use it to insert citations and create bibliographies in your documents – including while working offline.  Attendees should have a basic knowledge of RefWorks functionality.

Tuesday, December 9, 2008 2:00 p.m.
Enroll Now!

RefAware
RefAware is a web-based current awareness service designed to provide researchers with immediate access to new research and publications in their field. During this Webinar, we’ll cover the basic features of RefAware:

Wednesday, December 3, 2008 10:00 a.m.
Enroll Now!

RefWorks in 15 Minutes
While the ideal way to teach users the basic features of RefWorks is to conduct a full training session, we realize that in some situations you may have only a few minutes to demonstrate the power of RefWorks. During this session, you’ll rapidly learn: how to create an account;  direct export citations from two databases; create a folder;  create a bibliography from a list of citations; and create a bibliography using Write N’ Cite.

Wednesday, December 10, 2008 2:00 p.m.
Enroll Now!

Tuesday, December 16, 2008 10:00 am, Eastern Standard Time
Enroll Now!

Thursday, December 18, 2008 11:00 a.m.
Enroll Now!

Globally Editing Multiple References in RefWorks
In the August 2008 update for RefWorks, the flexibility to edit multiple citations at once was enhanced. This session will teach you how to efficiently apply changes to a group of citations on a page, in a folder or even an entire RefWorks database.

Thursday, December 11, 2008 2:00 p.m.
Enroll Now!

Creating Non-English and Multi-Language Bibliographies in RefWorks
In the August 2008 release we added a new field to RefWorks citations: Output Language. Selecting one of several Romance languages (or German) as an output language for a citation will display ordinal numbers and sort articles properly for the language. The Output Language field can also be used in conjunction with the Bibliographic Output Style Editor to apply distinctions to specific languages in multiple-language bibliographies.

Wednesday, December 17, 2008 12:00 p.m. (noon)
Enroll Now!

The latest issue of Neuroinformatics describes the new Neuroscience Information Framework (NIF), an inventory of web-based neurosciences data, resources and tools for scientists and students:  http://nif.nih.gov.

An initiative of the National Institutes of Health Blueprint for Neuroscience Research, the NIF seeks to advance neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. It enables users to discover global neuroscience web resources that cut across traditional boundaries – from experimental, clinical and translational neuroscience databases to knowledge bases, atlases, and genetic and genomic resources.

The NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally ‘hidden’ from web search engines.  All components of the NIF are available Open Source to encourage multiple community, institution and publisher development of NIF-compatible portals and web resources.

The entire special issue of the journal is freely available at http://www.springerlink.com/content/120559.  An introductory White Paper summarizes the project and its development in the context of the present and future of neuroinformatics, as well as the challenges of serving the entire neuroscience community.

Mashup your data with Google Maps or Microsoft Virtual Earth; build process models; create maps layered with your data.    Sound exciting?  Then you’ll want to try out the new ArcView software now available from AISR Learning Resources. 

ArcView geographic information system (GIS) software is now available on all stations in the Scott LRC 30-seat computer classroom as well as on instructors’ stations in the Edison LRC. 

ArcView is valuable for visualizing, managing, creating, and analyzing geographic data.  Using ArcView, you can understand the geographic context of your data, allowing you to see relationships and identify patterns in new ways.

Learn more about ArcView at  http://www.esri.com/software/arcgis/arcview/.

In early 2005, Thomas Jefferson University created a strategic plan to affirm Jefferson’s place as a leader in academic healthcare.

On November 21, TJU President Robert Barchi will provide an in-depth update on this plan, our progress in the areas of education, research and clinical practice, and the challenges that lie ahead.

Please join Dr. Barchi for this presentation on:

Friday, November 21, 2008
12:00 noon - 1:00 p.m.
Connelly Auditorium
Dorrance H. Hamilton Building

No matter what your role, you will find this to be a highly informative session that offers insights into strategic initiatives at Jefferson that are driving results in education, research and clinical care.

A question and answer session with Dr. Barchi will follow the presentation.

The campus identity management system has recently experienced some difficulties, leading some Jeffersonians to be refused access when they tried to use JEFFLINE’s journals, databases, and other Campus Key-protected materials.   

If you are unable to log into a JEFFLINE resource, please notify the Reference Desk at 215-503-8150 or AskaLibrarian@jefferson.edu.  It will help Jeff-IT to diagnose the problem.

Some users have been able to log into Pulse and then follow links in the JEFFLINE Resources box (one of the optional modules available when you modify the content of your My Pulse presentation page).

This problem appears to be isolated to just a few Jeffersonians, but if you are one of them, of course it is highly frustrating.  Jeff-IT is working on finding a solution to this problem.  

In the meantime, if your Campus Key is blocked, the Library staff can find alternative ways to provide the resources you need.

Thank you for your patience.

Scientific organizations representing over 130 countries have agreed to overhaul existing world data centers and services to create a World Data System, the International Council for Science (ICSU) has announced. The existing networks for collecting, storing and distributing data in many areas of science are seen to be inadequate and not designed to enable the inter-disciplinary research that is necessary to meet major global challenges. These networks must be transformed into a new inter-operable data system and extended around the world and across all areas of science. The General Assembly of ICSU has agreed to take the first strategic steps to establish such a system.

More scientific data and information is now available than at any other time in history and the volume is increasing daily, particularly via the web. Yet the quality, long-term stewardship and availability of this data is largely uncertain and a large amount of valuable scientific data remains inaccessible. Over 50 years ago, ICSU established networks of data centres and services to provide full and open access to scientific data and products for the global community. With advances in technology, it is now time for the existing structures to be integrated into a new expanded system such as the ICSU World Data System.

The expert report recommending the new system and presented to the ICSU General Assembly asserts that there is a need for global federations of professional state of the art data management institutions, working together and exchanging practices. Such federations can provide quality assurance and promote data publishing, providing the backbone for a global virtual library for scientific data. The report concludes that ICSU itself can play a leading role by restructuring its own data bodies.

ICSU will be implementing the recommendations in the report over the next three years. The report and more information on the General Assembly are available online at www.icsu.org/3_mediacentre/GA_29.html.

A message from Dean Cooter:

As you may know, a three-year classroom renovation project was approved last spring and the first phase of the project, which includes the “07″ (207, 307, 407) rooms in Jefferson Alumni Hall, began this summer. The first few months involved development of the floor plans and AV upgrades as well as finalization of the related schedule. Construction is due to start soon and to that end, JAH 207 was taken out of service as of October 1, and will remain out of service through mid-January. Rooms 307 and 407 will be taken out of service starting in late December and will remain unavailable throughout the spring semester.

We know removing classrooms for this extended length of time is a hardship for the campus community and want to thank you for your patience and cooperation during this renovation period.  A work schedule is available (PDF document).

From the press release:

The Journal of Biomedical Science is transitioning to open access format, published by BioMed Central. The journal is indexed in MEDLINE and Web of Science and has an Impact Factor of 2.02. It is now accepting submissions via its new BioMed Central website and will publish its first open access articles in January 2009.

The Journal of Biomedical Science, launched in 1994, is supported by the National Science Council (NSC) of Taiwan. Thanks to support from the NSC, authors will not be required to pay any article processing charges to publish in the journal.

Led by Editor-in-Chief Michael M. C. Lai, the journal aims to be an important forum for communication among experts from different biomedical fields and between the scientific community in Asia and the rest of the world.

Matthew Cockerill, BioMed Central’s Publisher, said he was very pleased that the journal’s Editors and the National Science Council of Taiwan had chosen BioMed Central as their partner for the transition to open access. “We are seeing increasing interest from traditional journals in the benefits of a switch to open access.  Journal of BioMedical Science is the latest journal to make the move, and we very much look forward to working with the journal and its Editors to maximize its potential under the open access model”.

Several other established journals affiliated with scientific societies/organisations have recently transferred to BioMed Central’s open access platform, including Journal of Experimental & Clinical Cancer Research (Italian National Cancer Institute), Asia Pacific Family Medicine (Asia Pacific Region of WONCA), and Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine (affiliated with 9 Scandinavian societies).

For further details about Journal of Biomedical Science please visit the journal information page or see the instructions for authors before submitting your next research article to the journal.

The Pennsylvania Health Care Cost Containment Council (PHC4) has released its latest Hospital Performance Report, covering October 2006 - September 2007.

The report includes information about risk-adjusted mortality, readmissions, lengths of hospitalization (stay), and hospital charges for patients admitted to 162 Pennsylvania hospitals. The print version evaluates hospital performance across 31 common medical procedures and treatments, but data for 20 additional treatment categories is available online.  

View and/or download the Hospital Performance Report

Access to the online version is FREE.

October 14 was the first international Open Access Day.   In recognition of the day, several announcements were made:

1) BMJ celebrates 10 years of offering open access content online by formally declaring themselves as Open Access (OA) publishers.

In 1998, the British Medical Journal (BMJ), published by medical publisher BMJ Group, UK,  became the first major general medical journal to provide free full text online access to its research articles; to deposit the full text in PubMed Central; and to allow authors to retain the copyright of their articles.  While BMJ used to require authors to pay an author fee in order to make their work OA, they have evolved their business model so that now authors do not need to pay.

2) OA publishers form an Association.

The Open Access Scholarly Publishers Association, OASPA, seeks to support and represent the interests of Open Access (OA) journals publishers globally in all scientific, technical, and scholarly disciplines. This mission will be carried out through exchanging information, setting standards, advancing business and publishing models, advocating for gold OA journals publishing, education and the promotion of innovation.

Membership in OASPA is open to both scholar publishers and professional publishing organisations, including university presses and for profit and non-profit organisations. Members are expected to demonstrate a genuine interest in OA journals publishing by having signed either the Berlin or Budapest Declarations and must publish at least one full OA journal. Other individuals and organisations who support OA journals publishing or who are interested in exploring opportunities are also welcome. Membership criteria and an application form can be found on the OASPA website at www.oaspa.org.

The founding members of OASPA represent a broad spectrum of OA publishers and include BioMed Central, Co-Action Publishing, Copernicus, Hindawi Publishing Corporation, Journal of Medical Internet Research (Gunther Eysenbach), Medical Education Online (David Solomon), the Public Library of Science (PLoS), SAGE, SPARC Europe and Utrecht University Library (Igitur). Representatives from each of these publishers will form an interim board until a first General Meeting is held during 2009.

Read the full press release.

3) Effects of self-archiving to be examined in Europe.

Now that several European funders mandate manuscript deposit in OA repositories, it is timely to examine the impact this has on information access and publishing.  PEER, the Publishing and the Ecology of European Research (supported by the European Union), has announced that it will investigate the effects of the large-scale, systematic depositing of authors’ final peer reviewed manuscripts (so called Green Open Access or stage-two research output) on reader access, author visibility and journal viability, as well as on the broader ecology of European research. The project is a collaboration between publishers, repositories and researchers lasting from 2008 to 2011.

Peer reviewed journals are seen to play a key role in scholarly communication and as essential for scientific progress and European competitiveness. The publishing and research communities share the view that increased access to the results of EU-funded research is necessary to maximise their use and impact. However, they hold different views on whether mandated deposit in open access repositories will achieve greater use and impact, and as to the most appropriate embargo periods. No consensus has been reached on a way forward so far.

Read the full press release.

And, of course, no event is complete these days without its own blog.  If you are interested in learning more about Open Access Day, please visit the OA Day Blog, or listen to the Voices of Open Access video blog.

In its most recent update, RefWorks has added 58 new output styles and a number of style corrections or enhancements.  This set emphasizes health literature heavily — all the new styles are now automatically included in your RefWorks account.  There’s no need to download anything or otherwise update your account.  You’ll find them now on your regular output style list.  

Of most interest to Jeffersonians are:

• American Journal of Pharmaceutical Education
• Annals of Oncology
• Annals of Pharmacotherapy
• ASQ - Administrative Science Quarterly
• Biology of Blood and Marrow Transplantation
• Canadian Journal of Plant Pathology
• Developmental and Comparative Immunology
• Ecosystems
• Electrophoresis
• Epidemiology and Infection
• European Journal of Nuclear Medicine and Molecular Imaging
• Globalization and Health
• Gut Pathogens
• Harm Reduction Journal
• Head & Face Medicine
• Health and Quality of Life Outcomes
• Health Research Policy and Systems
• International Journal of Nursing Studies
• Journal of Behavioral Health Services & Research
• Journal of Biogeography
• Journal of Biological Engineering
• Journal of Cardiovascular Magnetic Resonance
• Journal of Cerebral Blood Flow and Metabolism
• Journal of Clinical Nursing
• Journal of Conflict Resolution
• Journal of Ethnobiology and Ethnomedicine
• Journal of Materials Science
• Journal of Microscopy
• Journal of Neuro-Oncology
• Journal of Orthopaedic & Sports Physical Therapy -Journal of Pain, The
• Journal of Paleontology
• Journal of Pharmaceutical and Biomedical Analysis
• Journal of Psychiatric Research
• Molecular Nutrition & Food Research
• Neuropsychopharmacology
• Physical Therapy
• Placenta
• Plant and Cell Physiology
• Scandinavian Journal of Infectious Diseases
• Thorax
• Transfusion
• Transplantation
• Veterinary Parasitology
• World Journal of Surgery

Open access journal PLoS Medicine has published a paper that analyzes the current system of publishing medical and scientific research, and concludes that the system distorts the reality of scientific data that are generated in the laboratory and clinic.

The team of authors  - Neal Young of the National Institutes of Health; John Ioannidis of Tufts University School of Medicine and University of Ioannina School of Medicine, Greece; and Omar Al-Ubaydli of George Mason University - apply principles from the field of economics to present evidence consistent with a distortion.  Their essay “makes the underlying assumption that scientific information is an economic commodity, and that scientific journals are a medium for its dissemination and exchange.”

According to these researchers, there is an extreme imbalance between the abundance of supply and increasingly limited venues for publication. The result is that only a small proportion of all research results are eventually chosen for publication, and these results are “unrepresentative of scientists’ repeated samplings of the real world.” The authors argue that there is a “moral imperative  to reconsider how scientific data are judged and disseminated.”  They address impact factors, rejection rates, and digital vs. print publishing.

The analytical essay also offers a series of options and solutions for consideration in addressing the problem and improving the exchange of scientific ideas.

Read the complete paper, “Why Current Publication Practices May Distort Science,” freely available online.

PLoS Medicine is a peer-reviewed, international, open-access journal published by the Public Library of Science (PLoS), a nonprofit organisation. The journal provides an open-access venue for publishing important original research and analysis relevant to human health.

The JeffALERT emergency communications system, launching shortly, will provide an added means of rapid communication, in conjunction with other vehicles already in place at the University. Its effectiveness will depend on the availability of up-to-date personal contact information from students.

This summer the University engaged an organization called MIR3, a leader in emergency communications, to install an alert system that can send notifications if there is ever a threat to campus safety. The system— JeffALERT —will enable Jefferson to quickly disseminate critical information via text messaging, voicemail and email using a variety of devices such as cell phones, landline phones, and desktop/laptop computers.

To implement JeffALERT effectively and efficiently, the University will be phasing in this notification system during the next several months–beginning with students. Faculty and staff will follow.

All students are asked to update their contact information as soon as possible in Banner Web so they will receive these important alerts. It is especially important to have student cell phone numbers—which will allow the University to send text message alerts—the quickest and most efficient way to disseminate information to large groups in the event of an emergency.

To enter your cell phone information:

• Logon to Banner Web
• Select “Personal Information”
• Click on “Update Jeff ALERT Emergency Communications System”
• Next to “Cell Phone” select “Click here to Update”
• Scroll to the bottom of the page and use the drop down menu to select Phone Type “Cell” and enter your information.

The effectiveness of JeffALERT depends on the availability of up-to-date personal contact information from students. This information will remain confidential and will only be used in cases of serious public safety emergencies on campus and for system testing.

While Jefferson hopes it will never have to activate JeffALERT, the system provides an added means of rapid communication, in conjunction with other communication vehicles already in place at the University.

Within the next two months students will receive additional information on how the system works and what to do when a message is received. The University will also conduct several emergency alert “tests” to ensure that the system works.

Students—please revise your contact information today.