Omics Discovery

[Yasset Perez-Riverol @ypriverol]

what do you use for proteomics downstream analysis:

[Yasset Perez-Riverol @ypriverol]

Moving forward with the idea of proteomics pipelines in the cloud, collaboration with @OpenMSTeam. Label-free pipelines in development using @nextflowio @nf_core @BioContainers @OpenMSTeam #MSstats #SDRFproteomics

[Yasset Perez-Riverol @ypriverol]

Thanks to @JohnRYatesIII and @JProteomeRes for the invitation to publish a perspective on sample metadata in public repositories https://t.co/ObfE4b8iUd , Thanks to all @EuBIC_ms contributors. Since the publication, we have opened 10 new PRs in the repo https://t.co/LOtlgIKyj8

[biomodels @biomodels]

About half of #systemsbiology models fail to directly reproduce #simulation results! Over the past 3 years we investigated >450 models published in 152 journals & identified the root cause for the lack of #reproducibility. Read our #biorxiv_sysbio article https://t.co/7sjuBOnSYF

[Yasset Perez-Riverol @ypriverol]

Sample metadata in Proteomics repositories https://t.co/pRQh0uX19P https://t.co/UNznftCUah a project from @EuBIC_ms

[Yasset Perez-Riverol @ypriverol]

While in genomics + transciptomics everyone is in conda + containers. In proteomics, we can't distribute the software without clicking a license page. New tool MutCombinator following the same style... I don't know how the field will move to large-scale data analysis.

[BioContainers @BioContainers]

The @BioContainers Registry is a light-metadata interface to quickly find the tool and the corresponding container (https://t.co/F0Vu7yu7uW). You can get info about NAME, Number of downloads, short description, License. What other information you would like to see?

[Yasset Perez-Riverol @ypriverol]

For those that would like to know more about SDRF here the link to the @EuBIC_ms Hackathon https://t.co/WWnwGYiPxN
RT !!!! #ASMS2020 #proteomics @ProteomeXchange

[Yasset Perez-Riverol @ypriverol]

You can register for the Hackathon next week on Sample metadata annotations hosted by @EuBIC_ms.

[Yasset Perez-Riverol @ypriverol]

If you are wondering how to sample annotations will look like in Proteomics. Here an example of the first annotated submission in @pride_ebi with Sample annotations from @GygiLab https://t.co/KUT45fp1pP . All the annotations have been done based on SDRF (https://t.co/UNznftCUah)

[Yasset Perez-Riverol @ypriverol]

Online Hackathon and Workshop about the sample to data file format (SDRF) in proteomics. @EuBIC_ms #HUPOPSI @pride_ebi @ExpressionAtlas https://t.co/WWnwGYiPxN.

[Yasset Perez-Riverol @ypriverol]

Thanks to @ExpressionAtlas Team for their support. Anja Fullgrabe @pabloOmics and @irenepapatheodo.

[Yasset Perez-Riverol @ypriverol]

Thanks to @EuBIC_ms the new SDRF file format for proteomics is really getting adopted. Multiple contributions from @EuBIC_ms members such as @mvaudel @OpenMSTeam @lgatt0 and Lev Levitsky, Johannes Griss https://t.co/EU5S0Ugywr . We hope more people get involved.

[Yasset Perez-Riverol @ypriverol]

Should we make the experimental design based on the SDRF (sample to a data file format - https://t.co/UNznftCUah) on each PRIDE submission:

[Yasset Perez-Riverol @ypriverol]

Beta version of an Annotator of the SDRF is now deployed https://t.co/ccaowTBXRG semantic auto-complete of ontology terms.

[Yasset Perez-Riverol @ypriverol]

The specification is here (https://t.co/hrYQ0X7bDX). If you have submitted a dataset to @pride_ebi help us to re-annotate them.

[Yasset Perez-Riverol @ypriverol]

61 projects annotated using the SDRF specification (https://t.co/NUnEEpt82g). TMT, SILAC, Label-Free, phospho-proteomics, protein-protein interactions experiments. A validator is now in place, every time a collaborator add a new experiment, the PR will be validate before merge.

[Yasset Perez-Riverol @ypriverol]

Finally out: OmicsDI REST interface https://t.co/pzJiUaWnEp

[Yasset Perez-Riverol @ypriverol]

What do you think is the next step for proteomics archives?

[Yasset Perez-Riverol @ypriverol]

Great effort from @OpenMSTeam, @MuenchLab, and myself to annotated the SARS-Cov-2 submission Experimental design in SDRF https://t.co/Nrcj6bjUkV