July 20, 2017

The tutorial program meeting was held in Toronto Sept 28, 2-4 pm.

The following people were present:

  • Juan Pablo Albar, representing EuPA education committee
  • Wehbeh Bargachie, HUPO headquarters
  • Ralph Bradshaw, editor in chief of Molecular and Cellular Proteomics
  • William Hancock, editor in chief of Journal of Proteome Research
  • Peter James, University of Lund, and proposed Tutorial programme coordinator
  • Adriaan Klinkenberg, Publisher of Journal of Proteomics
  • Hans-Joachim Kraus, managing editor of Proteomics and Proteomics Clinical Applications
  • Pierre Legrain, HUPO secretary general
  • Thierry Rabilloud, chair of HUPO education and training committee (starting 1/2010), and in charge of this topic by mandate of HUPO executive committee
  • Jennifer Van Eyk, representing associate editor Proteomics and Proteomics Clinical Applications

The purpose of the meeting was to set an agreement between all the interested parties to launch effectively the tutorial program. The points discussed and agreed were the following

A) Definition of the program

The tutorial program is intended to make basic information about proteomics available to anyone in the community, aiming more precisely at newcomers in the field or in a particular subfield of proteomics. It is cooperation between selected journal publishers in the field of proteomics on the one hand, and HUPO and its affiliated regional and national organizations on the other hand. It is clearly a service made available to the proteomics community at large.

  • What shall comprise a tutorial paper?
  • A tutorial paper is made of two parts. A detailed tutorial article AND a supporting information consisting of a slideshow.  A tutorial paper will be published by a scientific journal in the field of proteomics. It shall be accessible to anyone without paying any fee of any kind. From a technical point of view, the slideshow is considered as a supplementary material of the article and therefore available with the article from the journals websites
  • Which journals are associated with this tutorial program?
  • Four journals have been selected to publish tutorial papers. They are (in alphabetical order) Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, Proteomics

B) Scope and coordination of the program

  • How shall the program be coordinated?
  • Peter James (University of Lund, Sweden) has been approved by all parties to become the program coordinator. He will work in close relation with both the journal editors and the international proteomics organizations involved in the program. Kazuyuki Nakamura has agreed to be a deputy coordinator for backup purposes.
  • What is the list of tutorial topics?
  • Peter James has prepared a detailed list of tutorial topics, with putative authors. It comprises an initial first list of 48 topics (with authors) and a secondary list of more than 50 additional topics. For the initial phase of the tutorial program, there has been agreement on the first initial list of 48 papers

C) Technical aspects

  • How are tutorial papers assigned to journals?
  • After an initial draw for assigning a to determine the receiving order, the manuscripts are will be assigned in their order of reception to each journal in turn. With four journals enrolled in the program, this means that journal  #1 will receive papers #1, #5, #9 etc.; journal #2 will receive papers #2, #6, #10 etc. To ensure transparency in this process, Peter James has reserved the domain name www.proteomictutorials.org. In this website, which will serve as a central index (see below) there will be an area accessible only to persons involved in the management of the program. This area will be used for management of the manuscripts, e.g. date stamping, journal assignment, status in the reviewing process etc.
  • How will the reviewing process take place?
  • The journals will retain complete control of their individual editorial policies and review the tutorial paper freely according to their policy, taking into account the specificities of tutorial papers. Only the manuscript is reviewed by the journals. The accompanying slideshow is reviewed by an international proteomic organization mandated by the journal, but is also made available to the journal reviewers mandated by the journals, as all supplementary material is.
  • For the moment, two international proteomic organizations have manifested declared their interest in the program, HUPO and EuPA. With the reshaping of the HUPO E&T committee, where the education committees of the regional organizations will have a larger role, the process shall integrate all the interested education committees.
  • Instructions.
  • As the tutorial papers represent a new class of articles, Peter James will prepare guidelines for authors, detailing how the article and the slideshow should be prepared. At the stage of their invitation, authors will be informed that they will not choose the journal to which their work will be submitted, and submitting a tutorial paper will mean acceptance of this rule. In addition, instructions for reviewers will also be prepared, to ensure the consistency of the reviewing process between the four journals. In order to further increase the consistency of the program, some journals have proposed to invite Peter James as guest editor for the handling of the tutorial papers, while other journals will prefer a tandem work between Peter James and one of their current editors.
  • What to do when a tutorial article is rejected?
  • As the tutorial papers are solicited, this should not happen too often. Several cases shall be distinguished.
  • First case, only the slideshow is weak. In this case, the reviewing entity (educational committee and journals) will go back to the authors to obtain an acceptable slideshow. The manuscript will be held back from publication until an acceptable slideshow is obtained.
  • Second case, the paper and/or both the paper and the slideshow are weak. This case is more difficult to handle, as this may easily result in either gaps in the range of the tutorial papers or in breaking the equality of article distribution between the partner journals. The solution in this case is to try to find new authors for to covering the topic, and by reassigning the new article to the same journal to which the initial paper was assigned. In this case, the managing area of the central website will also keep all the participating journals informed of such decisions, in order to prevent any misconduct from the authors.
  • Third case, normally more frequent, revision will be required. In this case, the journals will handle it in their usual way.
  • How to make access to the tutorials easy
  • As mentioned above, the tutorials are will be made freely accessible to anyone. However, as the information will be distributed among four journals, a centralized index will be built constructed by the coordinator, with any help that he may find necessary. This centralized index will be fully hyperlinked to the proteomics organizations’ websites as well as to the journal websites. The articles and slideshows will be available and downloadable from the journals websites, but the hyperlinks will ensure easy access from any entry point.
  • Technical publication points
  • Both the article and slideshow will be made available as pdf files. In addition, the slides will be marked with the logo of the program. In cases where animations will be part of the slideshow, it will be possible to make such complex slideshows available from the central website with restricted rights, so that the intellectual property of the authors and copyright of the journals will be respected.
  • Technically speaking, the copyright will be transferred to the journals, as for any scientific paper. However, the journals agree to grant free access to the material, and also to grant copyright exemption for classical educational purposes.
  • In order to avoid piling an excess of logos and names, and to be as inclusive as possible, it was decided that the program will be named “International Tutorial Program in Proteomics” and logoed accordingly.
  • Time scope scale for the tutorial program
  • It has been agreed to launch an initial phase with the agreed terms for a period of two years.  The 48 invitations shall be issued shortly, so that the first manuscripts can be expected in around 4-6 months.
  • The four journals have agreed to hold the first accepted manuscripts until each journal has accepted one of them, to make a coordinated public release. Each journal will make an editorial accompanying this first tutorial paper.
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