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Saturday, July 28, 2012

First articles now live on F1000 Research

Faculty of 1000 (F1000) announces the publication of initial articles on F1000 Research, the innovative open access publishing program in biology and medicine. These articles also feature a novel inline data viewer, and a new method of article citation.

F1000 Research's revolutionary vision has been inspiring debate across the scientific community since the beginning of the year. Its informed contribution to the wider discussion about open access publishing has advanced to a new level this week with the publication of its first few articles (please see http://f1000research.com/articles). A call for papers has been issued and further articles will be published on the current consultation site while the publishing model and editorial systems are fine-tuned in preparation for a complete launch later this year.

F1000 Research challenges traditional models by defining new standards for speed, peer review, and the sharing of data. Features include:

* immediate publication
* rapid, formal, and completely open peer review process post-publication
* acceptance of null/negative and replication/refutation findings
* publication and refereeing of datasets as separate data articles

All submissions to F1000 Research will go through a fast initial review by the in-house editorial team who will check to ensure that articles are sensible, intelligible, and written in good English. Each article will then be published with the status 'awaiting peer review'.

On publication, the article will be sent to 3-5 expert referees who will be asked to state, firstly, whether the work seems scientifically sound. These responses will be displayed immediately alongside the article and its citation, and will be updated as new referee responses arrive. Subsequently, referees will be asked to provide more detailed comments and feedback, which will also be displayed with the article. Authors will be encouraged to revise their articles in response to referee comments and each article version will be citable with its own DOI. A novel article citation mechanism, developed with the assistance of the F1000 Research Advisory Panel and the leading indexers, will capture the article version number and referee status.

Once an article receives two positive referee responses, it will be indexed. Scopus, Embase and Google Scholar have agreed to index F1000 Research content immediately, and discussions aimed at putting in place similar arrangements with other major indexers are ongoing. Should an article receive no positive reviews it will not be indexed and will be removed from the default search on the site.

These first articles showcase a novel inline data viewer that has been developed in conjunction with figshare (http://figshare.com). It enables readers to preview data files without having to download them, and allows all readers, even those without suitable viewers for these files, to view the datasets in a 'friendly' format.

All publishing charges are waived for 2012. Moderate author processing charges will be introduced in 2013. More information can be found at: http://f1000research.com.

Commenting on this significant development, Dr Rebecca Lawrence, Publisher for F1000 Research, said: "We are very excited to announce the publication of our first articles on F1000 Research. We would like to thank everyone who has helped us get this far, not least our Advisory Panel and Editorial Board. The discussion continues on Twitter at @F1000Research, and we invite the research community to join us as the project takes shape."

More than 200 of the most eminent names in biology and medicine have joined the international Advisory Panel (see all members at: http://f1000research.com/advisory-panel), and more than 1000 global experts sit on the newly formed Editorial Board (see http://f1000research.com/editorial-board). The project has received great support from the wider scientific community, sparking extensive discussions about the future of scholarly publishing.

To find out more about F1000 Research, please contact Rebecca Lawrence at rebecca.lawrence@f1000.com. For more information, visit http://f1000research.com.

To find out more about Faculty of 1000, please contact Eleanor Howell on +44 (0)20 7631 9129 or email press@f1000.com. For more information, visit http://f1000.com.


About F1000
Faculty of 1000 is a unique online service that selects, rates, and evaluates important articles based on the opinions of global leaders in biology and medicine. The distinguished international Faculty identify articles that impact their research, providing a rapidly updated, authoritative guide to the life science literature. Find out more at http://f1000.com.

About F1000 Research
F1000 Research is a new fully Open Access publishing program across biology and medicine. It is addressing the major issues afflicting scientific publishing today: timely dissemination of research, peer review, and sharing of data. Diverging from traditional journal publishing, F1000 Research offers immediate publication; open, post-publication peer review; open revisioning of work including ongoing updates; and encourage raw data deposition and publication. In addition, F1000 Research is accepting a broad range of article formats and content types.

URL: http://f1000.com/resources/Announcing_the_start_of_publishing_on_F1000Research_WEB_FINAL.pdf

Contact Person: Eleanor Howell  (press@f1000.com)

Announcing BioGene - a Mobile Web Browser Application

This is to announce BioGene, a free application for mobile web browsers to quickly look up gene function.

The Computational Biology Center at MSKCC (cBio) has recently released BioGene, an application for mobile web browsers, with primary content from NCBI's (US National Center for Biotechnology Information) Entrez search engines.  BioGene allows you to quickly and easily access gene information from Entrez.  For example, should you see a reference to "NCOA3" in a lecture presentation, within moments you can have basic and reasonably up-to-date information about the function of this gene at your fingertips on your smartphone; including a list of references with abstracts (from GeneRIFs).

We are making BioGene available to the public free of charge to promote its use in scientific research and lecture rooms.

You can access BioGene from your iPhone, Android, or Blackberry OS device by visiting the following link: http://cbio.mskcc.org/biogene/
You can also continue to use BioGene for iOS which is available for download via the App Store:

More information at: http://cbio.mskcc.org/tools/biogene/mobile.html

We would appreciate feedback including ideas for additional features to be incorporated in future versions.  To do so, please send email to biogene@cbio.mskcc.org.

BioGene has been fun to develop and has already had a positive impact on our research.

We invite you to explore the function of genes of interest instantly and from anywhere.


Benjamin Gross, Nathan Marks, and Chris Sander

Computational Biology Center
Memorial Sloan Kettering Cancer Center, New York City

Contact Person: Benjamin Gross (grossb@cbio.mskcc.org)

Thursday, July 12, 2012

Hop on the Ion Bus @ ISMB- NGS on wheels!

Join Ion Torrent aboard our mobile sequencing laboratory to see Ion NGS sequencers & Software in action!

See a 1976 Tour bus converted to a molecular biology laboratory- the Ion Bus will be parked atop the Grand Staircase by the Solar Flora at the Long Beach Convention Center.

Check out semiconductor sequencing data on iPads while learning about Torrent Browser plugins. Register for a spot between 12-3pm Sun & Mon http://ow.ly/ccYPI

URL: http://ow.ly/ccYPI

Contact Person: Eric Vennemeyer (eric.vennemeyer@lifetech.com)

Wednesday, July 11, 2012

Prize4Life Launches Prize Competition to Unlock Mysteries of Disease Progression in Amyotrophic Lateral Sclerosis (ALS) Patients

Prize4Life is proud to announce the launch of a computational challenge to predict the future progression of disease in Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig's disease. The DREAM-Phil Bowen ALS Prediction Prize4Life (or ALS Prediction Prize) is being run by Prize4Life in collaboration with The DREAM Project and carries a $25,000 prize for the winning prediction.

The new Prize4Life Challenge is based on the PRO-ACT database, which upon completion will contain clinical data for more than 7,500 ALS patients from completed clinical trials. The entire PRO-ACT database will be available for research purposes by year's end and the ALS Prediction Prize will use a subset of this data. Ultimately, it is expected that the solution resulting from this Challenge will improve disease prediction and lead to more accurate methods of forecasting progression earlier on in the course of the disease.

The ALS Prediction Prize challenge will be run on the InnoCentive prize platform (https://www.innocentive.com/ar/challenge/9933047). Use your computational expertise to win a Prize4Life, register now.

If you are interested in receiving more information as the challenge launches, please send us your name and e-mail at: Prediction@Prize4Life.org. To read more about the prize criteria, visit http://www.prize4life.org/page/prizes/predictionprize.

URL: http://www.prize4life.org/page/prizes/predictionprize

Contact Person: Neta Zach, Ph.D. (Prediction@Prize4Life.org)

Tuesday, July 10, 2012

Casual pizza'n'beer workshop introducing CLC bio'€™s SDK

Join us for a casual workshop introducing how to use our SDK to create plugins - and stay for pizza, beer, and a fun quiz with cool prizes!

Hope to see you this Sunday in Long Beach!
Don’t miss this workshop on Sunday the 15th of July, from 6 to 10 PM. You’ll find the workshop in rooms E-F on the 3rd level at the Hyatt Regency Long Beach. You don’t have to register, but there’s only 50 seats…

The program is centered around four external speakers from Convey (US), Bioformatix (US), NICTA (AUS), and Ablynx (BE), who all have used our API for different kinds of integrations, including examples of commercial plugin development. You can also learn how to distribute your own algorithms and workflows to our customer community through plugins for our platform.
URL: http://www.clcngs.com/2012/07/clc-bio-presents/

Contact Person: Lasse Goerlitz - CLC bio (lgoerlitz@clcbio.com)