Guidelines regulating service, collaborations, fees and scientific publications

These guidelines have been written based on those provided by the Protein Analysis Facility of the Unil.

Services and fees

The mission of the PMF of the University of Lausanne is to support the local research community in the analysis and use of macromolecules structures using molecular modeling tools. To help support its activity and equipment purchases, the facility operates with fees, which apply to a well defined list of activities.
The PMF does not have dedicated funding for carrying out collaborative projects. Therefore, in principle all PMF users have to arrange payment of the requested activities according to the fees and categories mentioned above.

We strongly encourage investigators to request specific funding for molecular modeling at the time of grant application. The facility coordinator can provide support and suggestions for the writing of research proposals and can of course prepare letters of support and confirmation.


For manuscript writing, the PMF will provide the users upon request i) descriptions of materials and methods relevant to the computer-aided experiments performed ii) comprehensive supplementary tables in a format accepted by the journal (.txt, .pdf or .xls), iii) high quality figures in the format accepted by the journal (e.g. jpeg or tiff, at 300 dpi) and iv) all the raw data if required. Unless agreed differently (see below) the PMF will not prepare publication-style tables and figures to be included in the main article body nor write portions of article text.


As a minimum, the work carried out by the PMF should be acknowledged in all publications which either present data directly produced by the facility or results for the generation of which the work of the PMF played an important role. The name and affiliation of the facility should be fully and correctly mentioned as follows :

Protein Modeling Facility, University of Lausanne, Switzerland”.



In general we apply the guidelines established by the International Committee of Medical Journal Editors and similar organizations as discussed by Huth (Huth, E. J. [1986] Guidelines on Authorship of Medical Papers, Annals Int. Med. 104 : 269-274) and Bailey (Bailey, B. J. [2001] What Is an Author? Otolaryngol. Head Neck Surg. 124 :2-3 ).

These guidelines suggest that if scientists from the PMF have significantly helped to design or conceive the study, have done non-standard computer-aided analysis and interpretation of data, or both, they should be coauthors of papers that use data generated by the facility. In this case facility scientists should participate in drafting the paper or revising it for critically important content, and give final approval of the version to be published. If these conditions are not met, the PMF should appear only in the acknowledgements (see above). In case of uncertainty about authorship, the investigator should clarify these issues with the facility coordinator, preferably before start of the experiments.


We define two types of collaborations :

1) User-initiated collaborations are those in which the proponent is a PMF user. The PMF coordinator, in agreement with his Steering Committee, can accept to carry out such collaborative projects in which the PMF will make its molecular modeling tools available so as to perform the best data production (including images and videos) or analysis  as possible. Such projects are in principle subject to the same fees as routine work. The proponent should provide a written statement in advance on the availability of sufficient funding. In such projects, the personnel of the PMF engages in a closer collaboration with the user group to provide optimized support and improve aspects such as experimental design and data analysis. Also, the PMF team can decide to use the data from the project to implement and test new technologies which are not yet part of the regular catalog of services. In such case, these analyses can (but must not be) be free of charge. For this type of collaborations, the PMF members involved will be co-authors of resulting publications. The details of co-authorship (position, etc) should be discussed at the beginning of the project.

2) PMF-initiated collaborations : the PMF can contact biologists and biomedical investigators to propose collaborations. One of the primary purposes is to acquire experimental feedback for the implementation, test or development of new techniques which are not yet in the regular catalog of PMF services. Such analyses are generally free of charge for the user. The PMF coordinator has to ensure, in planning such experiments, that i) the workload is compatible with the capacity of the platform, ii) that it does not interfere with the normal operation of the PMF service and iii) that it does not lead to a significant increase in the waiting times for other regular users. For this type of collaborations the PMF members involved will be co-authoring the resulting publications together with the lab providing the samples. The details of co-authorship should be discussed at the beginning of the project.