Welcome to the BioInformatics Ɔompetence Center

Examples of how our skills can be applied

To give you an idea of what we can achieve to help you, here are some selected publications where we contributed in method development and/or analysis.

• Genomics
• Flow Cytometry
• Signal processing
• Image analysis
• Protein structure analysis
• Web-tool data visualisation

ChipSeq analysis: Transcription factor

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ChipSeq analysis: Epigenetic marks

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WGS, Exome, RNAseq analysis

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Vibrio Cholera genome analysis

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Genome assembly and variant detection

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Detect Chromosome Aneuploidies (Prenatal screening)

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Metagenomics

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HiC

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Guidelines for collaborations and scientific publications

Publications

For manuscript writing, the BIƆC will provide their users upon request with i) descriptions of materials and methods relevant to the analyses performed ii) comprehensive supplementary tables in a format accepted by most journals (.txt, .pdf or .xls) and iii) all the raw data if required. Unless agreed differently (see below) the Bioinformatics Competence Center will not prepare publication-style tables and figures to be included in the main article body nor write portions of article text.

Acknowledgements

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

“BioInformatics Competence Center, University of Lausanne, Switzerland”

No specific person names need to be listed, unless desired by the authors.

Authorship

In general we apply the directive 4.2 established by the direction of the University about Scientific Integrity, which is based on directives of the Swiss Academy of Sciences (ASSM). This directive states in article 2.10 al. 2 that the author of a scientific publication is a person that, through his or her work has provided an essential scientific contribution to the research work during its planning, realization, interpretation, or control. This is in line with 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 BIƆC have significantly contributed to the design or conception of the experiments, have performed non-standard analyses and/or interpretation of data, or both, they should be lsited as coauthors. In this case these 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 BIƆC should appear only in the acknowledgements (see above). In case of uncertainty about authorship, the investigator should clarify these issues with the center coordinator, preferably before starting the experiments.

Collaborations

We define two types of collaborations:

1. User-initiated collaborations are those in which the proponent is a BIƆC user (usually a biomedical researcher). The BIƆC coordinator can accept to carry out such collaborative projects in which the BIƆC makes its competences available to push the limits of analyses on a set of relevant and challenging datasets. Such projects are in principle subject to the same fees as routine work, and we recommend to discuss these collaborations with the BIƆC coordinator at the time of grant writing so as to include a “Bioinfomratics Support” budget line to the grant. The proponent should provide a written statement in advance on the availability of sufficient funding. In such projects, the personnel of the BIƆC 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 BIƆC team can decide to use the data from the project to implement and test new analysis methods 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 BIƆC 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. BioInformatics Competence Center-initiated collaborations: the BIƆC can contact biomedical investigators to propose collaborations. One of the primary purposes is to acquire challenging datasets for the implementation, test or development of new analysis methods which are not yet in the regular catalog of BIƆC services. Such analyses are generally free of charge for the user. The BIƆC coordinator will 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 Bioinformatics Competence Center 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 BIƆC members involved will be co-authoring the resulting publications together with the lab providing the samples and data. The details of co-authorship should be discussed at the beginning of the project.

These guidelines have been written based on similar guidelines applied by other core facilities.