EMBnet.journal 16.1.18-19

2010 Annual General Meeting – Publicity & Public Relations Project Committee Report

(November 2009 – June 2010)

Chair: Pedro Fernandes

Secretary: Lubos Klucar

Member: Domenica D’Elia

Member: Martin Norling

The main mission of the P&PR PC is to nurture and promote EMBnet’s visibility and to establish cooperation with other (even dissimilar) major groups, networks and societies.

Starting from November 2009 up to June 2010 the organization of the PC’s activities was discussed and agreed during three committee’s meetings (March 4th, May 31st and June 18th 2010) and four meetings of the EMBnet.news Editorial Board (February 22th, March 8th, May 26th and June 17th, 2010).

The main issues on which the Committee has worked are the following:

  1. supporting the organization of the second edition of the EMBnet-EMBRACE joint workshop on Next Generation Sequencing, held in Ruvo di Puglia (IT) on June 2010 [1];
  2. preparation of a P&PR PC’s position paper as a basis for structuring themed discussions at the 2010 AGM in Ruvo di Puglia (IT);
  3. transition of the EMBnet.news magazine to an Open Access Peer Reviewed journal.

Committee’s initiatives proposed to the EMBnet EB and VGM have been:

  1. establishment of a Special Interest Group (SIG) to study the input of EMBnet’s PCs and generate clear scenarios on the future activities of EMBnet and its societary role (March 2010);
  2. re-designing of the EMbnet’s web site with a new easy-to-use structure and with more informative content. This work will be lead by the P&PR PC in collaboration with the EB and with the technical support of the TM PC. In addition to TM PC also the P&PR PC will have administrative access to the web portal;
  3. “EMBnet Members 2009” geographical distribution published on Google Earth is being updated and a new version will be linked from the new embnet.org pages and regularly updated;
  4. managing, updating and publishing Quick Guides will be handed over to the ET-PC at EMBnet AGM 2010.

From EMBnet.news to
“EMBnet.journal – Bioinformatics in Action”

The EMBnet.news magazine, edited by the P&PR PC and EB Chair since its first edition (1994) has gone under a strong transformation which has taken much of PC’s members efforts and delayed the release of new issues (2010 editions).

One EMBnet.news issue has been published on March 2010 (vol. 15, issue 4). This issue represents the last one of the EMBnet.news edition. Starting from the next one the EMBnet.news magazine is replaced by the “EMBnet.journal – Bioinformatics in Action”, an Open Access peer-reviewed journal published by EMBnet. EMBnet-RIBio 2009 Conference Proceedings are published as the first Supplement issue of the EMBnet.journal (Vol. 16 Suppl. A) [2].

The OJS (Open Journal System), implemented by Lubos Klucar in 2008 for the management of the publishing process, becomes the official web-based journal management system of the EMBnet.journal. In 2009 a new version (OJS freely distributed by the Public Knowledge Project [3] has been implemented. This new version includes additional facilities that better support the OJS editorial and publishing process. Users have different access privileges depending on their own category: Editor, Section Editors, Copyeditors, Proofreaders, Layout Editor, Authors and Reviewers. The system provides users’ alert and notification facilities and allows full text search and commenting for all articles published. This new implementation has been tested by the Editorial Board under the guidance of Lubos who held two virtual tutorials workshops on the organization of the OJS editorial process, the procedures to be used and roles for each one of the Editorial Board member.

According to the complexity of the publishing process, the Editorial Board of the journal has agreed on a formal detachment from the P&PR PC, being effective starting from the EMBnet AGM 2010, and on the enlargement of the board to an “Executive Editorial Board” and a “Full Editorial Board”. The Executive EdB will consist of 5-10 people, mostly current members of EdB while the Full EdB will be composed of all EMBnet node managers. Professionals outside the EMBnet will be invited to join the Full EdB depending on specific needs. Inside the Executive EdB each member has been designed for a specific role, such as Section Editor, Copyeditor and so on, and Erik Bongcam-Rudloff has been officially designed as Editor in Chief. The board has also been working on the Journal’s Copyright, Privacy statement, Focus and Scope and on the Editorial policy.

The journal contains two main sections, one that caters for peer-reviewed primary research articles, reviews and technical notes, and one for non-peer-reviewed commentary, reportage, user-guides, training information and news. In addition the journal will also publish Special Issues focusing on ‘hot’ topics that fall within the scope of the journal and Supplements publishing peer reviewed conference proceedings and meeting abstracts.

EMBnet.news past issues have been moved from the embnet.org site to the new system [4] where all the old issues are collected in a retrievable archive. This work has been carried out by Lubos with the support of a student hired by Nazim Rahman and is now complete, while the transformation of all back issues into OJS is still ongoing. This requires the creation of abstract, HTML and PDF versions for each past published article.

Google Analytics statistics are collected since February 2010. Author’s fees for peer-reviewed articles will be charged starting from 2011, and a policy for the article processing charge has also been agreed. The P&PR PC will collaborate with the Executive EdB in promoting EMBnet.journal as a new peer reviewed journal across bioinformatics related web sites and at main Bioinformatics and related conferences. The committee has also been working for retrieving information on how to get indexing in PubMed. DOI is under investigation. The journal is currently indexed in Google Scholar.


  1. http://www.embnet.org/NGS-AGM2010
  2. http://journal.embnet.org/index.php/embnetjournal/
  3. http://pkp.sfu.ca/
  4. http://journal.embnet.org/index.php/embnetnews/


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