About Slide Shows

The slide show are intended to be used as teaching aids in the classroom.  The slides should be low in text and as far as possible, diagrams, pictures and photographs should be used. Clear illustrative diagrams are of greatest importance for the student’s comprehension of concepts.

The whole Tutorial should provide approximately one hours lecture time.  The slides will be extensively explained in the notes section of the presentation and include references at the appropriate points and more extensive reading references (preferably recent books and monographs).  The basic format should follow that of the flow in the article since both should be complimentary to each other and expand concepts. 

Slide Show Format

The PowerPoint Tutorial should be in English and should be between 20-50 slides long (excluding references).  The slides should be low in text and as far as possible, diagrams, pictures and photographs should be used to illustrate concepts.  The whole PowerPoint Tutorial should provide an hours lecture time.  The slides should be extensively explained in the notes section of the presentation (please see the PowerPoint example slides) and include references at the appropriate points and more extensive reading references (preferably recent books, reviews and monographs).  The PowerPoint Tutorial should be aimed at Masters/PhD level students with good basic training in biology, biochemistry and mathematics/statistics.

The PowerPoint Tutorials will be made freely available (as will the Tutorial Articles) here and on the websites of the European Proteomics Association (EuPA), the Human Proteome Organisation (HUPO) and the collaborating journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics and Proteomics.

The PowerPoint Tutorial should be constructed in the manner described in the PowerPoint example supplied, though clearly there will be certain subjects that will have requirements that differ.  This will be dealt with on an individual basis. The basic format should follow that of the flow in the article since both should be complimentary to each other and expand concepts.

The PowerPoint slides should be made with no background Master slide and no logos should be displayed. Text should be Times or Courier/Helvetica.  Figures should be clear and large and in a compressed format such as JPEG. Please avoid large data formats such as TIFF.

Authors are responsible for assigning copyright to all illustrations used in both the articles and PowerPoint tutorials.

The Tutorial Articles

Tutorial articles will be grouped into two categories:

  • Core methods and concepts
  • Applied proteomic techniques

The tutorials should provide a historical background to enable students to understand how the techniques evolved to meet research demands.  The basic concepts that underlie the subject will be clearly introduced and explained before state-of-the-art developments are described.  The aim is to provide a novice with enough information to be able to critically read and understand articles in the current literature.  Worked examples from recent papers will serve as a guide.

The articles should provide extensive references to allow students to grasp the key concepts involved and how they evolved from a historical perspective. The references are extremely important and should guide students to major up-to-date reviews, key historical/breakthrough articles and indicate the main reference and entry-level books into the subject.  However it is expected that the tutorials are also balanced and that the limitations and pitfalls involved should be highlighted. 

 

The Article Format

The Tutorial article should be in English and should be between 5-10,000 words long (excluding references) and include around 100 references. These should be labelled with a symbol: * key major reviews, ** key historical/breakthrough article, # reference book and especially ##entry-level guides into the subject.

The Tutorial Articles will be assigned, as described in the submission guide, to one of the four following journals:  Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics and Proteomics.

The article should be constructed in the manner described below, though clearly there will be certain subjects that will have requirements that differ.  This will be dealt with on an individual basis.  Clear illustrative diagrams are of greatest importance for the student’s comprehension of concepts.

Title page:    Authors, affiliations, contact addresses etc

Abstract:      No more than 200 words.

Outline:        Table of Contents

1.  Historical Background

2.  Basic concepts

      a.  Concept 1

      b.  Concept 2

3.  How is the approach used today in research

4.  Worked example

5.  Current limitations and useful working limits

6.  Future developments

Manuscripts together with the PowerPoint tutorial should be sent to

The manuscripts will be forwarded to the randomly allocated Journal where they will undergo normal Peer-Review by the Journal. Even though the articles are solicited, there is no guarantee of acceptance by a Journal. The slide show will be subject to review by the HUPO and EuPA education committees. Only if both the Tutorial article and PowerPoint presentation pass review, will the contributions be accepted.

Submission Guidelines

Submission Procedure

Tutorial Articles will initially be by invitation, however suggestions for new and timely articles and obvious gaps will be gratefully accepted. Once you have finished the manuscript and the accompanying powerpoint presentation, send the the powerpoint presentation by email to Peter James. The arrival time will be date stamped and the manuscript will be assigned to a journal in the order that they arrive.  The authors cannot chose which Journal they wish to submit the article to. 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... and so on. 

  • Once the manuscript and powerpoint outline are finished. Send the powerpoint to Peter James
  • The author will then be informed which Journal he/she should submit the manuscript to so that the manuscript can be formatted according to the specific instructions for that journal.
  • The Author submits the article to that specific journal, clearly mentioning the Tutorial Programme.
  • You must submit both the Tutorial manuscript and the Powerpoint show
  • The guest/associate editor is assigned the manuscript for further editorial review.
  • The  manuscript is sent to two reviewers for peer evaluation.
  • The slide show is sent to the education committees for review.

PLEASE. BE VERY CLEAR AND INDICATE ON THE FRONT PAGE OF THE MANUSCRIPT THAT THE MANUSCRIPT IS INTENDED FOR THE TUTORIAL PROGRAMME

Even though the articles are solicited, there is no guarantee of acceptance by a Journal.  The tutorials will be subject to normal peer review by the Journal and the slide show will be evaluated by the HUPO and EuPA education committees. Only if both the Tutorial article and PowerPoint presentation pass review, will the contributions be accepted.  N.B.  Authors are responsible for assigning copyright to all illustrations used in both the articles and PowerPoint tutorials. The Journals have specific instructions as to how to submit the tutorial manuscripts.

Journal of Proteome Research

  • Authors MUST submit text and graphics of tutorial as a “Tutorial” manuscript-type at the journal manuscript submission site:

Journal of Proteome Research

  • When prompted to answer the question ” If accepted for publication, this work may be published on the ACS Web site as a 'Just Accepted' manuscript before it is technically edited and composed.” authors must choose the “NO” option.
  • The accompanying slide presentation should be uploaded as Supplementary Information.
  • Authors MUST also include a letter indicating that the tutorial has been approved by HUPO as a cover letter.

Journal of Proteomics

  • The authors should submit the manuscript to the website: Journal of Proteomics
  • Authors submitting a tutorial should define the type of submission (select article type Tutorial) and in a further step also select a preferred Editor (select Peter James). For a general Guide to Authors, please consult the journal homepage.

Molecular and Cellular Proteomics

  • The manuscript should be submitted to the usual MCP submission website Molecular and Cellular Proteomics (by the author) and the the author should select category "13 Other" and indicate in the cover letter that it is part of the tutorial series.

Proteomics

  • Manuscripts should be submitted online to the PROTEOMICS MS-Central site at: Proteomics
  • In the manuscript submission forms the authors should then answer the question “Is this submission for a special issue ?” with “Yes” (see page 1 of the forms).
  • At the bottom of page 5 of these forms the authors should then specify the special issue they are submitting to by typing in “Tutorial Program (James)”.
  • They should then complete the submission process and submit the paper.

The Official Mandate for the Project

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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