Lipidomics Informatics for Life Sciences Partner Project

as part of the Service Center “Bioinformatics for Proteomics – BioInfra.Prot” within the
“German Network for Bioinformatics Infrastructure – de.NBI”

Date Created: Dec. 15th, 2020
Last Updated: Dec. 21st, 2020

Preamble

As part of de.NBI (https://www.denbi.de/) and ELIXIR (https://elixir-europe.org/) we, the Lipidomics Informatics for Life Sciences (LIFS) partner project, provide comprehensive bioinformatics and biostatistics services to users that perform lipidomics in life science research including medicine. de.NBI is a third party project funded by the ”German Federal Ministry of Education and Research” (BMBF), which aims at the provision of frequently required high quality bioinformatics services including software, consulting and training.

Service Conditions

Are the services of LIFS free of charge?
Yes, we provide our services to all users at no cost if they are manageable regarding our resources. However, to be able to provide services free-of-charge we have to document satisfied users and service usage. Thus, our co-authorships in scientific articles based partly or completely on our data analyses, citation of our services and their related papers as well as acknowledging our project including our grant number in all scientific articles are mandatory (see “Publication of results”).

Does LIFS guarantee that services will be available 24/7?
We try to keep our services available 24/7 on a best-effort basis. Planned downtimes are announced on the LIFS website (https://lifs.isas.de) and on the LIFS Webapplication Portal (https://apps.lifs.isas.de). We do not guarantee that long running tasks for our ad-hoc computational services can run for more than a few hours. If you require more processing time or resources on our systems, please consult with us directly.

Does LIFS guarantee to complete the agreed services at the appointed time?
We always strive to adhere to agreed dates and deadlines, but this cannot be guaranteed. In case of delays, we will inform the service user as soon as possible to rearrange the further course of action.

Is LIFS responsible for the correctness of the provided information and the results?
We assume no responsibility or liability for errors, the resulting disadvantages or resulting damages or losses.

Data transfer

What has to be considered when transferring data to LIFS?
For person-related data the data privacy regulations of the requesting institution (data provider) must be fulfilled. To fulfill our (data receiver) data privacy regulations, data must be pseudonymized and an informed consent of the patient/experimentee about data privacy must exist (if relevant). It is the sole responsibility of the service user to ensure the that current data protection laws for data processing (e.g. upload) of person-related data with our service (e.g. informed consent, pseudonymization, anonymization, commissioned data processing) are respected. This may require that the service user signs a data processing agreement with ISAS e.V. and the data handlers of the LIFS project beforehand. For such cases, please use our Service & Support form to request further assistance.

Does the data need to have a certain format?
Please provide mass spectrometry-based metabolomics and lipidomics data in PSI standard formats. For quantitative or clinical data, please agree upon a suitable data format and presentation (e.g. coding of categorical variables, representation of missing values) with our responsible scientist. Our tools generally state, which input formats they except and provide examples.

Publication of results

What has to be considered for publication of results acquired in collaboration with LIFS?
It is mandatory that users of our services publish results along with an appropriate reference to LIFS according to the extent of our support as co-authorships and/or citations of our services.

All tools that we provide contain instructions on how to cite them properly. Please consult the individual tool pages on our LIFS portal for details.

If results from the data analysis have been achieved with assistance of LIFS staff and are to be published, our responsible researcher(s) and the PI have to be included as co-authors. Acknowledging our project is always mandatory.

For LipidCreator, Goslin, mzTab-m:

This work was supported by the German Network for Bioinformatics Infrastructure – de.NBI, funded by the German Federal Ministry of Education and Research (BMBF) – Grant FKZ 031L0108A.

For LUX Score, lxPostman and SpeCS:

This work was supported by the German Network for Bioinformatics Infrastructure – de.NBI, funded by the German Federal Ministry of Education and Research (BMBF) – Grant FKZ 031L0108B.

For LipidXplorer:

This work was supported by the German Network for Bioinformatics Infrastructure – de.NBI, funded by the German Federal Ministry of Education and Research (BMBF) – Grant FKZ 031L0108C.

We need these references to document service usage and satisfied users to acquire further funding. Please contact us in rational time before paper submission (about two weeks) to exercise our scientific responsibility and check the manuscript.

Exploitation / Intellectual Property

Is there a claim of LIFS regarding patents?

If users plan inventions, patents or applications for industrial/intellectual property rights, the participation of the Leibniz-Insitut für Analytische Wissenschaften ISAS-e.V. as LIFS primary hosting institution, and / or, depending of the origin of the tool used, the Leibniz Lung Center Borstel or the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden  must be arranged in advance.